1
|
de los Angeles Becerra Rodriguez M, Gonzalez Muñoz E, Moore T. Oligodendrocyte-specific expression of PSG8- AS1 suggests a role in myelination with prognostic value in oligodendroglioma. Noncoding RNA Res 2024; 9:1061-1068. [PMID: 39022681 PMCID: PMC11254506 DOI: 10.1016/j.ncrna.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/03/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
The segmentally duplicated Pregnancy-specific glycoprotein (PSG) locus on chromosome 19q13 may be one of the most rapidly evolving in the human genome. It comprises ten coding genes (PSG1-9, 11) and one predominantly non-coding gene (PSG10) that are expressed in the placenta and gut, in addition to several poorly characterized long non-coding RNAs. We report that long non-coding RNA PSG8-AS1 has an oligodendrocyte-specific expression pattern and is co-expressed with genes encoding key myelin constituents. PSG8-AS1 exhibits two peaks of expression during human brain development coinciding with the most active periods of oligodendrogenesis and myelination. PSG8-AS1 orthologs were found in the genomes of several primates but significant expression was found only in the human, suggesting a recent evolutionary origin of its proposed role in myelination. Additionally, because co-deletion of chromosomes 1p/19q is a genomic marker of oligodendroglioma, expression of PSG8-AS1 was examined in these tumors. PSG8-AS1 may be a promising diagnostic biomarker for glioma, with prognostic value in oligodendroglioma.
Collapse
Affiliation(s)
- Maria de los Angeles Becerra Rodriguez
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland
| | - Elena Gonzalez Muñoz
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590, Málaga, Spain
- Universidad de Malaga, Dpto. Biología Celular, Genética y Fisiología, 29071, Málaga, Spain
| | - Tom Moore
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| |
Collapse
|
2
|
Semik-Gurgul E, Pawlina-Tyszko K, Gurgul A, Szmatoła T, Rybińska J, Ząbek T. In search of epigenetic hallmarks of different tissues: an integrative omics study of horse liver, lung, and heart. Mamm Genome 2024:10.1007/s00335-024-10057-0. [PMID: 39143382 DOI: 10.1007/s00335-024-10057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024]
Abstract
DNA methylation and microRNA (miRNA) expression are epigenetic mechanisms essential for regulating tissue-specific gene expression and metabolic processes. However, high-resolution transcriptome, methylome, or miRNAome data is only available for a few model organisms and selected tissues. Up to date, only a few studies have reported on gene expression, DNA methylation, or miRNA expression in adult equine tissues at the genome-wide level. In the present study, we used RNA-Seq, miRNA-seq, and reduced representation bisulfite sequencing (RRBS) data from the heart, lung, and liver tissues of healthy cold-blooded horses to identify differentially expressed genes (DEGs), differentially expressed miRNA (DE miRNA) and differentially methylated sites (DMSs) between three types of horse tissues. Additionally, based on integrative omics analysis, we described the observed interactions of epigenetic mechanisms with tissue-specific gene expression alterations. The obtained data allowed identification from 4067 to 6143 DMSs, 9733 to 11,263 mRNAs, and 155 to 185 microRNAs, differentially expressed between various tissues. We pointed out specific genes whose expression level displayed a negative correlation with the level of CpG methylation and miRNA expression and revealed biological processes that they enrich. Furthermore, we confirmed and validated the accuracy of the Next-Generation Sequencing (NGS) results with bisulfite sequencing PCR (BSP) and quantitative PCR (qPCR). This comprehensive analysis forms a strong foundation for exploring the epigenetic mechanisms involved in tissue differentiation, especially the growth and development of the equine heart, lungs, and liver.
Collapse
Affiliation(s)
- Ewelina Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland.
| | - Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland
| | - Justyna Rybińska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
| | - Tomasz Ząbek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
| |
Collapse
|
3
|
Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
Collapse
Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
| |
Collapse
|
4
|
Montfort J, Hervas-Sotomayor F, Le Cam A, Murat F. FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes. Nucleic Acids Res 2024; 52:W65-W69. [PMID: 38587202 PMCID: PMC11223851 DOI: 10.1093/nar/gkae264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/09/2024] Open
Abstract
Teleost fish represent one of the largest and most diverse clades of vertebrates, which makes them great models in various research areas such as ecology and evolution. Recent sequencing endeavors provided high-quality genomes for species covering the main fish evolutionary lineages, opening up large-scale comparative genomics studies. However, transcriptomic data across fish species and organs are heterogenous and have not been integrated with newly sequenced genomes making gene expression quantification and comparative analyses particularly challenging. Thus, resources integrating genomic and transcriptomic data across fish species and organs are still lacking. Here, we present FEVER, a web-based resource allowing evolutionary transcriptomics across species and tissues. First, based on query genes FEVER reconstructs gene trees providing orthologous and paralogous relationships as well as their evolutionary dynamics across 13 species covering the major fish lineages, and 4 model species as evolutionary outgroups. Second, it provides unbiased gene expression across 11 tissues using up-to-date fish genomes. Finally, genomic and transcriptomic data are combined together allowing the exploration of gene expression evolution following speciation and duplication events. FEVER is freely accessible at https://fever.sk8.inrae.fr/.
Collapse
|
5
|
Yazarlou F, Lipovich L, Loeb JA. Emerging roles of long non-coding RNAs in human epilepsy. Epilepsia 2024; 65:1491-1511. [PMID: 38687769 PMCID: PMC11166529 DOI: 10.1111/epi.17937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 05/02/2024]
Abstract
Genome-scale biological studies conducted in the post-genomic era have revealed that two-thirds of human genes do not encode proteins. Most functional non-coding RNA transcripts in humans are products of long non-coding RNA (lncRNA) genes, an abundant but still poorly understood class of human genes. As a result of their fundamental and multitasking regulatory roles, lncRNAs are associated with a wide range of human diseases, including neurological disorders. Approximately 40% of lncRNAs are specifically expressed in the brain, and many of them exhibit distinct spatiotemporal patterns of expression. Comparative genomics approaches have determined that 65%-75% of human lncRNA genes are primate-specific and hence can be posited as a contributing potential cause of the higher-order complexity of primates, including human, brains relative to those of other mammals. Although lncRNAs present important mechanistic examples of epileptogenic functions, the human/primate specificity of lncRNAs questions their relevance in rodent models. Here, we present an in-depth review that supports the contention that human lncRNAs are direct contributors to the etiology and pathogenesis of human epilepsy, as a means to accelerate the integration of lncRNAs into clinical practice as potential diagnostic biomarkers and therapeutic targets. Meta-analytically, the major finding of our review is the commonality of lncRNAs in epilepsy and cancer pathogenesis through mitogen-activated protein kinase (MAPK)-related pathways. In addition, neuroinflammation may be a relevant part of the common pathophysiology of cancer and epilepsy. LncRNAs affect neuroinflammation-related signaling pathways such as nuclear factor kappa- light- chain- enhancer of activated B cells (NF-κB), Notch, and phosphatidylinositol 3- kinase/ protein kinase B (Akt) (PI3K/AKT), with the NF-κB pathway being the most common. Besides the controversy over lncRNA research in non-primate models, whether neuroinflammation is triggered by injury and/or central nervous system (CNS) toxicity during epilepsy modeling in animals or is a direct consequence of epilepsy pathophysiology needs to be considered meticulously in future studies.
Collapse
Affiliation(s)
- Fatemeh Yazarlou
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH, U.S.A
| | - Leonard Lipovich
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co. Ltd., 601 Building C1, Guangming Science Park, Fenghuang Street, 518000, Shenzhen, Guangdong, People’s Republic of China
- College of Science, Mathematics, and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai District, 325060, Wenzhou, Zhejiang, People’s Republic of China
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, 3222 Scott Hall, 540 E. Canfield St., Detroit, Michigan 48201, U.S.A
| | - Jeffrey A. Loeb
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, Illinois 60612, U.S.A
- University of Illinois NeuroRepository, University of Illinois at Chicago, Chicago, Illinois 60612, U.S.A
| |
Collapse
|
6
|
Costa VA, Ronco F, Mifsud JCO, Harvey E, Salzburger W, Holmes EC. Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes. Curr Biol 2024; 34:1247-1257.e3. [PMID: 38428417 DOI: 10.1016/j.cub.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/18/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of cross-species transmission and hence disease emergence. We examined how the rapid adaptive radiation of the cichlid fishes of African Lake Tanganyika over the last 10 million years has shaped the diversity and evolution of the viruses they carry. Through metatranscriptomic analysis of 2,242 RNA sequencing libraries, we identified 121 vertebrate-associated viruses among various tissue types that fell into 13 RNA and 4 DNA virus groups. Host-switching was commonplace, particularly within the Astroviridae, Metahepadnavirus, Nackednavirus, Picornaviridae, and Hepacivirus groups, occurring more frequently than in other fish communities. A time-calibrated phylogeny revealed that hepacivirus diversification was not constant throughout the cichlid radiation but accelerated 2-3 million years ago, coinciding with a period of rapid cichlid diversification and niche packing in Lake Tanganyika, thereby providing more closely related hosts for viral infection. These data depict a dynamic virus ecosystem within the cichlids of Lake Tanganyika, characterized by rapid virus diversification and frequent host jumping, and likely reflecting their close phylogenetic relationships that lower the barriers to cross-species virus transmission.
Collapse
Affiliation(s)
- Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Fabrizia Ronco
- Natural History Museum, University of Oslo, 0562 Oslo, Norway
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| |
Collapse
|
7
|
Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Marques Bonet T, Farh KKH. Identification of constrained sequence elements across 239 primate genomes. Nature 2024; 625:735-742. [PMID: 38030727 PMCID: PMC10808062 DOI: 10.1038/s41586-023-06798-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
Collapse
Affiliation(s)
- Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Jacob C Ulirsch
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Sabrina Rashid
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Mohamed Ameen
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Anthony J Cox
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Arvind Kumar
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Mareike C Janiak
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Martin Kuhlwilm
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Joseph D Orkin
- Département d'Anthropologie, Université de Montréal, Montréal, Quebec, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Lidia Agueda
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Julie Blanc
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Rede de Pesquisa em Diversidade, Conservação e Uso da Fauna da Amazônia - RedeFauna, Manaus, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna, Iquitos, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | | | - Sree Kanthaswamy
- School of Interdisciplinary Forensics, Arizona State University, Phoenix, AZ, USA
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Professorship for International Animal Health/One Health, Faculty of Veterinary Medicine, Justus Liebig University, Giessen, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- School of Geosciences, Edinburgh, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, Germany
| | - Ivo Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA.
| |
Collapse
|
8
|
Kornienko AE, Nizhynska V, Molla Morales A, Pisupati R, Nordborg M. Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing. THE PLANT CELL 2023; 36:85-111. [PMID: 37683092 PMCID: PMC10734619 DOI: 10.1093/plcell/koad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/07/2023] [Accepted: 07/30/2023] [Indexed: 09/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) are understudied and underannotated in plants. In mammals, lncRNA loci are nearly as ubiquitous as protein-coding genes, and their expression is highly variable between individuals of the same species. Using Arabidopsis thaliana as a model, we aimed to elucidate the true scope of lncRNA transcription across plants from different regions and study its natural variation. We used transcriptome deep sequencing data sets spanning hundreds of natural accessions and several developmental stages to create a population-wide annotation of lncRNAs, revealing thousands of previously unannotated lncRNA loci. While lncRNA transcription is ubiquitous in the genome, most loci appear to be actively silenced and their expression is extremely variable between natural accessions. This high expression variability is largely caused by the high variability of repressive chromatin levels at lncRNA loci. High variability was particularly common for intergenic lncRNAs (lincRNAs), where pieces of transposable elements (TEs) present in 50% of these lincRNA loci are associated with increased silencing and variation, and such lncRNAs tend to be targeted by the TE silencing machinery. We created a population-wide lncRNA annotation in Arabidopsis and improve our understanding of plant lncRNA genome biology, raising fundamental questions about what causes transcription and silencing across the genome.
Collapse
Affiliation(s)
- Aleksandra E Kornienko
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
| | - Almudena Molla Morales
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
| | - Rahul Pisupati
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
| |
Collapse
|
9
|
Xu Y, Bush SJ, Yang X, Xu L, Wang B, Ye K. Evolutionary analysis of conserved non-coding elements subsequent to whole-genome duplication in opium poppy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1804-1824. [PMID: 37706612 DOI: 10.1111/tpj.16466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
Whole-genome duplication (WGD) leads to the duplication of both coding and non-coding sequences within an organism's genome, providing an abundant supply of genetic material that can drive evolution, ultimately contributing to plant adaptation and speciation. Although non-coding sequences contain numerous regulatory elements, they have been understudied compared to coding sequences. In order to address this gap, we explored the evolutionary patterns of regulatory sequences, coding sequences and transcriptomes using conserved non-coding elements (CNEs) as regulatory element proxies following the recent WGD event in opium poppy (Papaver somniferum). Our results showed similar evolutionary patterns in subgenomes of regulatory and coding sequences. Specifically, the biased or unbiased retention of coding sequences reflected the same pattern as retention levels in regulatory sequences. Further, the divergence of gene expression patterns mediated by regulatory element variations occurred at a more rapid pace than that of gene coding sequences. However, gene losses were purportedly dependent on relaxed selection pressure in coding sequences. Specifically, the rapid evolution of tissue-specific benzylisoquinoline alkaloid production in P. somniferum was associated with regulatory element changes. The origin of a novel stem-specific ACR, which utilized ancestral cis-elements as templates, is likely to be linked to the evolutionary trajectory behind the transition of the PSMT1-CYP719A21 cluster from high levels of expression solely in P. rhoeas root tissue to its elevated expression in P. somniferum stem tissue. Our findings demonstrate that rapid regulatory element evolution can contribute to the emergence of new phenotypes and provide valuable insights into the high evolvability of regulatory elements.
Collapse
Affiliation(s)
- Yu Xu
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Stephen J Bush
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xinyi Yang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Linfeng Xu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Kai Ye
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| |
Collapse
|
10
|
Puccio G, Ingraffia R, Giambalvo D, Frenda AS, Harkess A, Sunseri F, Mercati F. Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families. FRONTIERS IN PLANT SCIENCE 2023; 14:1302337. [PMID: 38023895 PMCID: PMC10665861 DOI: 10.3389/fpls.2023.1302337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture.
Collapse
Affiliation(s)
- Guglielmo Puccio
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
| | - Rosolino Ingraffia
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Dario Giambalvo
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alfonso S. Frenda
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Francesco Sunseri
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
- Department Agraria , University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Francesco Mercati
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
| |
Collapse
|
11
|
Khayati S, Dehnavi S, Sadeghi M, Tavakol Afshari J, Esmaeili SA, Mohammadi M. The potential role of miRNA in regulating macrophage polarization. Heliyon 2023; 9:e21615. [PMID: 38027572 PMCID: PMC10665754 DOI: 10.1016/j.heliyon.2023.e21615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Macrophage polarization is a dynamic process determining the outcome of various physiological and pathological situations through inducing pro-inflammatory responses or resolving inflammation via exerting anti-inflammatory effects. The miRNAs are epigenetic regulators of different biologic pathways that target transcription factors and signaling molecules to promote macrophage phenotype transition and regulate immune responses. Modulating the macrophage activation, differentiation, and polarization by miRNAs is crucial for immune responses in response to microenvironmental signals and under various physiological and pathological conditions. In term of clinical significance, regulating macrophage polarization via miRNAs could be utilized for inflammation control. Also, understanding the role of miRNAs in macrophage polarization can provide insights into diagnostic strategies associated with dysregulated miRNAs and for developing macrophage-centered therapeutic methods. In this case, targeting miRNAs to further regulate of macrophage polarization may become an efficient strategy for treating immune-associated disorders. The current review investigated and categorized various miRNAs directly or indirectly involved in macrophage polarization by targeting different transcription factors and signaling pathways. In addition, prospects for regulating macrophage polarization via miRNA as a therapeutic choice that could be implicated in various pathological conditions, including cancer or inflammation-mediated injuries, were discussed.
Collapse
Affiliation(s)
- Shaho Khayati
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sajad Dehnavi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahvash Sadeghi
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Seyed-Alireza Esmaeili
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojgan Mohammadi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
12
|
Bhaskara GB, Haque T, Bonnette JE, Napier JD, Bauer D, Schmutz J, Juenger TE. Evolutionary Analyses of Gene Expression Divergence in Panicum hallii: Exploring Constitutive and Plastic Responses Using Reciprocal Transplants. Mol Biol Evol 2023; 40:msad210. [PMID: 37738160 PMCID: PMC10556983 DOI: 10.1093/molbev/msad210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/27/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified FST-QST outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis-environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.
Collapse
Affiliation(s)
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Jason E Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Diane Bauer
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
13
|
Liu A, Wang N, Xie G, Li Y, Yan X, Li X, Zhu Z, Li Z, Yang J, Meng F, Dou M, Chen W, Ma N, Jiang Y, Gao Y, Wang Y. GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes. Genome Res 2023; 33:1673-1689. [PMID: 37884342 PMCID: PMC10691551 DOI: 10.1101/gr.277784.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/23/2023] [Indexed: 10/28/2023]
Abstract
Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.
Collapse
Affiliation(s)
- Anguo Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Faculty of Mathematics and Natural Sciences, University of Cologne, and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, Cologne 50931, Germany
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xixi Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenliang Zhu
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuohui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yang
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fanxin Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weihuang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nange Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanpeng Gao
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
14
|
Smith SK, Frazel PW, Khodadadi-Jamayran A, Zappile P, Marier C, Okhovat M, Brown S, Long MA, Heguy A, Phelps SM. De novo assembly and annotation of the singing mouse genome. BMC Genomics 2023; 24:569. [PMID: 37749493 PMCID: PMC10521431 DOI: 10.1186/s12864-023-09678-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston's singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions. RESULTS Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types. CONCLUSIONS These resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.
Collapse
Affiliation(s)
- Samantha K Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Paul W Frazel
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratory, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Paul Zappile
- Genome Technology Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Christian Marier
- Genome Technology Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Mariam Okhovat
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Present Address: Oregon Health & Science University, Portland, OR, USA
| | - Stuart Brown
- NYU Center for Health Informatics and Bioinformatics, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Present Address: Exxon Mobil Corporate, Houston, TX, USA
| | - Michael A Long
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Adriana Heguy
- Genome Technology Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Steven M Phelps
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| |
Collapse
|
15
|
Ricci V, Ronco F, Boileau N, Salzburger W. Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika. SCIENCE ADVANCES 2023; 9:eadg6568. [PMID: 37672578 PMCID: PMC10482347 DOI: 10.1126/sciadv.adg6568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Tuning the visual sensory system to the ambient light is essential for survival in many animal species. This is often achieved through duplication, functional diversification, and/or differential expression of visual opsin genes. Here, we examined 753 new retinal transcriptomes from 112 species of cichlid fishes from Lake Tanganyika to unravel adaptive changes in gene expression at the macro-evolutionary and ecosystem level of one of the largest vertebrate adaptive radiations. We found that, across the radiation, all seven cone opsins-but not the rhodopsin-rank among the most differentially expressed genes in the retina, together with other vision-, circadian rhythm-, and hemoglobin-related genes. We propose two visual palettes characteristic of very shallow- and deep-water living species, respectively, and show that visual system adaptations along two major ecological axes, macro-habitat and diet, occur primarily via gene expression variation in a subset of cone opsin genes.
Collapse
Affiliation(s)
- Virginie Ricci
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Fabrizia Ronco
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Nicolas Boileau
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| |
Collapse
|
16
|
Trost N, Mbengue N, Kaessmann H. The molecular evolution of mammalian spermatogenesis. Cells Dev 2023; 175:203865. [PMID: 37336426 PMCID: PMC10363733 DOI: 10.1016/j.cdev.2023.203865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
The testis is a key male reproductive organ that produces gametes through the process of spermatogenesis. Testis morphologies, sperm phenotypes, and the process of spermatogenesis evolve rapidly in mammals, presumably due to the evolutionary pressure on males to give rise to their own offspring. Here, we review studies illuminating the molecular evolution of the testis, in particular large-scale transcriptomic studies, which were based on bulk tissue samples and, more recently, individual cells. Together with various genomic and epigenomic data, these studies have unveiled the cellular source, molecular mechanisms, and evolutionary forces that underlie the rapid phenotypic evolution of the testis. They also revealed shared (ancestral) and species-specific spermatogenic gene expression programs. The insights and available data that have accumulated also provide a valuable resource for the investigation and treatment of male fertility disorders - a dramatically increasing problem in modern industrial societies.
Collapse
Affiliation(s)
- Nils Trost
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Noe Mbengue
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
17
|
Li Y, Zhai H, Tong L, Wang C, Xie Z, Zheng K. LncRNA Functional Screening in Organismal Development. Noncoding RNA 2023; 9:36. [PMID: 37489456 PMCID: PMC10366883 DOI: 10.3390/ncrna9040036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023] Open
Abstract
Controversy continues over the functional prevalence of long non-coding RNAs (lncRNAs) despite their being widely investigated in all kinds of cells and organisms. In animals, lncRNAs have aroused general interest from exponentially increasing transcriptomic repertoires reporting their highly tissue-specific and developmentally dynamic expression, and more importantly, from growing experimental evidence supporting their functionality in facilitating organogenesis and individual fitness. In mammalian testes, while a great multitude of lncRNA species are identified, only a minority of them have been shown to be useful, and even fewer have been demonstrated as true requirements for male fertility using knockout models to date. This noticeable gap is attributed to the virtual existence of a large number of junk lncRNAs, the lack of an ideal germline culture system, difficulty in loss-of-function interrogation, and limited screening strategies. Facing these challenges, in this review, we discuss lncRNA functionality in organismal development and especially in mouse testis, with a focus on lncRNAs with functional screening.
Collapse
Affiliation(s)
- Yang Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Huicong Zhai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Lingxiu Tong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Cuicui Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhiming Xie
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| |
Collapse
|
18
|
Srinivas T, Mathias C, Oliveira-Mateos C, Guil S. Roles of lncRNAs in brain development and pathogenesis: Emerging therapeutic opportunities. Mol Ther 2023; 31:1550-1561. [PMID: 36793211 PMCID: PMC10277896 DOI: 10.1016/j.ymthe.2023.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The human genome is pervasively transcribed, producing a majority of short and long noncoding RNAs (lncRNAs) that can influence cellular programs through a variety of transcriptional and post-transcriptional regulatory mechanisms. The brain houses the richest repertoire of long noncoding transcripts, which function at every stage during central nervous system development and homeostasis. An example of functionally relevant lncRNAs is species involved in spatiotemporal organization of gene expression in different brain regions, which play roles at the nuclear level and in transport, translation, and decay of other transcripts in specific neuronal sites. Research in the field has enabled identification of the contributions of specific lncRNAs to certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders, resulting in notions of potential therapeutic strategies that target these RNAs to recover the normal phenotype. Here, we summarize the latest mechanistic findings associated with lncRNAs in the brain, focusing on their dysregulation in neurodevelopmental or neurodegenerative disorders, their use as biomarkers for central nervous system (CNS) diseases in vitro and in vivo, and their potential utility for therapeutic strategies.
Collapse
Affiliation(s)
- Tara Srinivas
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Catalonia, Spain
| | - Carolina Mathias
- Department of Genetics, Federal University of Parana, Post-graduation Program in Genetics, Curitiba, PR, Brazil; Laboratory of Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, PR, Brazil
| | | | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Catalonia, Spain; Germans Trias i Pujol Health Science Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain.
| |
Collapse
|
19
|
Noel B, Denoeud F, Rouan A, Buitrago-López C, Capasso L, Poulain J, Boissin E, Pousse M, Da Silva C, Couloux A, Armstrong E, Carradec Q, Cruaud C, Labadie K, Lê-Hoang J, Tambutté S, Barbe V, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Allemand D, Planes S, Gilson E, Zoccola D, Wincker P, Voolstra CR, Aury JM. Pervasive tandem duplications and convergent evolution shape coral genomes. Genome Biol 2023; 24:123. [PMID: 37264421 DOI: 10.1186/s13059-023-02960-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. RESULTS In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. CONCLUSIONS At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.
Collapse
Affiliation(s)
- Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Alice Rouan
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | | | - Laura Capasso
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
- Sorbonne Université, Collège Doctoral, 75005, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Emilie Boissin
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Mélanie Pousse
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Eric Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Sylvie Tambutté
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | | | - Guillaume Iwankow
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Sarah Romac
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire Des Sciences du Climat Et de L'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-Sur-Yvette, 91191, France
| | - J Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Pierre E Galand
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls Sur Mer, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de La Mer de Villefranche Sur Mer, Sorbonne Université, Laboratoire d'Océanographie de Villefranche, Villefranche-Sur-Mer, 06230, France
- Institut Universitaire de France, Paris, 75231, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, OR, 97331, USA
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Department of Human Genetics, CHU Nice, Nice, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France.
| |
Collapse
|
20
|
Monroy-Eklund A, Taylor C, Weidmann CA, Burch C, Laederach A. Structural analysis of MALAT1 long noncoding RNA in cells and in evolution. RNA (NEW YORK, N.Y.) 2023; 29:691-704. [PMID: 36792358 PMCID: PMC10159000 DOI: 10.1261/rna.079388.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/02/2023] [Indexed: 05/06/2023]
Abstract
Although not canonically polyadenylated, the long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) is stabilized by a highly conserved 76-nt triple helix structure on its 3' end. The entire MALAT1 transcript is over 8000 nt long in humans. The strongest structural conservation signal in MALAT1 (as measured by covariation of base pairs) is in the triple helix structure. Primary sequence analysis of covariation alone does not reveal the degree of structural conservation of the entire full-length transcript, however. Furthermore, RNA structure is often context dependent; RNA binding proteins that are differentially expressed in different cell types may alter structure. We investigate here the in-cell and cell-free structures of the full-length human and green monkey (Chlorocebus sabaeus) MALAT1 transcripts in multiple tissue-derived cell lines using SHAPE chemical probing. Our data reveal levels of uniform structural conservation in different cell lines, in cells and cell-free, and even between species, despite significant differences in primary sequence. The uniformity of the structural conservation across the entire transcript suggests that, despite seeing covariation signals only in the triple helix junction of the lncRNA, the rest of the transcript's structure is remarkably conserved, at least in primates and across multiple cell types and conditions.
Collapse
Affiliation(s)
- Anais Monroy-Eklund
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Colin Taylor
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Chase A Weidmann
- Department of Biological Chemistry, University of Michigan Medical School, Center for RNA Biomedicine, Rogel Cancer Center, Ann Arbor, Michigan 48109, USA
| | - Christina Burch
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| |
Collapse
|
21
|
Shabna A, Bindhya S, Sidhanth C, Garg M, Ganesan TS. Long non-coding RNAs: Fundamental regulators and emerging targets of cancer stem cells. Biochim Biophys Acta Rev Cancer 2023; 1878:188899. [PMID: 37105414 DOI: 10.1016/j.bbcan.2023.188899] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
Cancer is one of the leading causes of death worldwide, primarily due to the dearth of efficient therapies that result in long-lasting remission. This is especially true in cases of metastatic cancer where drug resistance causes the disease to recur after treatment. One of the factors contributing to drug resistance, metastasis, and aggressiveness of the cancer is cancer stem cells (CSCs) or tumor-initiating cells. As a result, CSCs have emerged as a potential target for drug development. In the present review, we have examined and highlighted the lncRNAs with their regulatory functions specific to CSCs. Moreover, we have discussed the difficulties and various methods involved in identifying lncRNAs that can play a particular role in regulating and maintaining CSCs. Interestingly, this review only focuses on those lncRNAs with strong functional evidence for CSC specificity and the mechanistic role that allows them to be CSC regulators and be the focus of CSC-specific drug development.
Collapse
Affiliation(s)
- Aboo Shabna
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India; Laboratory for Cancer Biology, Department of Medical Oncology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai 610016, India; Department of Endocrinology, Indian Council of Medical Research - National Institute of Nutrtion, Tarnaka, Hyderabad 50007, India
| | - Sadanadhan Bindhya
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India
| | - Chirukandath Sidhanth
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Sector-125, Noida 201301, India
| | - Trivadi S Ganesan
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India; Laboratory for Cancer Biology, Department of Medical Oncology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai 610016, India.
| |
Collapse
|
22
|
Zhao F, Yan Y, Wang Y, Liu Y, Yang R. Splicing complexity as a pivotal feature of alternative exons in mammalian species. BMC Genomics 2023; 24:198. [PMID: 37046221 PMCID: PMC10099729 DOI: 10.1186/s12864-023-09247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND As a significant process of post-transcriptional gene expression regulation in eukaryotic cells, alternative splicing (AS) of exons greatly contributes to the complexity of the transcriptome and indirectly enriches the protein repertoires. A large number of studies have focused on the splicing inclusion of alternative exons and have revealed the roles of AS in organ development and maturation. Notably, AS takes place through a change in the relative abundance of the transcript isoforms produced by a single gene, meaning that exons can have complex splicing patterns. However, the commonly used percent spliced-in (Ψ) values only define the usage rate of exons, but lose information about the complexity of exons' linkage pattern. To date, the extent and functional consequence of splicing complexity of alternative exons in development and evolution is poorly understood. RESULTS By comparing splicing complexity of exons in six tissues (brain, cerebellum, heart, liver, kidney, and testis) from six mammalian species (human, chimpanzee, gorilla, macaque, mouse, opossum) and an outgroup species (chicken), we revealed that exons with high splicing complexity are prevalent in mammals and are closely related to features of genes. Using traditional machine learning and deep learning methods, we found that the splicing complexity of exons can be moderately predicted with features derived from exons, among which length of flanking exons and splicing strength of downstream/upstream splice sites are top predictors. Comparative analysis among human, chimpanzee, gorilla, macaque, and mouse revealed that, alternative exons tend to evolve to an increased level of splicing complexity and higher tissue specificity in splicing complexity. During organ development, not only developmentally regulated exons, but also 10-15% of non-developmentally regulated exons show dynamic splicing complexity. CONCLUSIONS Our analysis revealed that splicing complexity is an important metric to characterize the splicing dynamics of alternative exons during the development and evolution of mammals.
Collapse
Affiliation(s)
- Feiyang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yubin Yan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaxi Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuan Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| |
Collapse
|
23
|
Aydın E, Saus E, Chorostecki U, Gabaldón T. A hybrid approach to assess the structural impact of long noncoding RNA mutations uncovers key
NEAT1
interactions in colorectal cancer. IUBMB Life 2023. [PMID: 36971476 DOI: 10.1002/iub.2710] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/25/2023] [Indexed: 03/29/2023]
Abstract
Long noncoding RNAs (lncRNAs) are emerging players in cancer and they entail potential as prognostic biomarkers or therapeutic targets. Earlier studies have identified somatic mutations in lncRNAs that are associated with tumor relapse after therapy, but the underlying mechanisms behind these associations remain unknown. Given the relevance of secondary structure for the function of some lncRNAs, some of these mutations may have a functional impact through structural disturbance. Here, we examined the potential structural and functional impact of a novel A > G point mutation in NEAT1 that has been recurrently observed in tumors of colorectal cancer patients experiencing relapse after treatment. Here, we used the nextPARS structural probing approach to provide first empirical evidence that this mutation alters NEAT1 structure. We further evaluated the potential effects of this structural alteration using computational tools and found that this mutation likely alters the binding propensities of several NEAT1-interacting miRNAs. Differential expression analysis on these miRNA networks shows upregulation of Vimentin, consistent with previous findings. We propose a hybrid pipeline that can be used to explore the potential functional effects of lncRNA somatic mutations.
Collapse
Affiliation(s)
- Efe Aydın
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Ester Saus
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, Barcelona, Spain
| | - Uciel Chorostecki
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, Barcelona, Spain
| | - Toni Gabaldón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| |
Collapse
|
24
|
Zhu N, Zhang F, Zhou H, Ma W, Mao H, Wang M, Ke Z, Wang J, Qi L. Mechanisms of Immune-Related Long Non-Coding RNAs in Spleens of Mice Vaccinated with 23-Valent Pneumococcal Polysaccharide Vaccine (PPV23). Vaccines (Basel) 2023; 11:vaccines11030529. [PMID: 36992112 DOI: 10.3390/vaccines11030529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/05/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
The 23-valent pneumococcal vaccine (PPV23) is a classical common vaccine used to prevent pneumococcal disease. In past decades, it was thought that vaccination with this vaccine induces humoral immunity, thereby reducing the disease associated with infection with 23 common serotypes of Streptococcus pneumoniae (Sp). However, for this polysaccharide vaccine, the mechanism of immune response at the transcriptional level has not been fully studied. To identify the lncRNAs (long noncoding RNAs) and mRNAs in spleens related to immunity after PPV23 vaccination in mice, high-throughput RNA sequencing of spleens between a PPV23 treatment group and a control group were performed and evaluated in this study. The RNA-seq results identified a total of 41,321 mRNAs and 34,375 lncRNAs, including 55 significantly differentially expressed (DE) mRNAs and 389 DE lncRNAs (p < 0.05) between the two groups. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to T-cell costimulation, positive regulation of alpha–beta T-cell differentiation, the CD86 biosynthetic process, and the PI3K-Akt signaling pathway, indicating that the polysaccharide component antigens of PPV23 might activate a cellular immune response during the PPV23 immunization process. Moreover, we found that Trim35 (tripartite motif containing 35), a target gene of lncRNA MSTRG.9127, was involved in regulating immunity. Our study provides a catalog of lncRNAs and mRNAs associated with immune cells’ proliferation and differentiation, and they deserve further study to deepen the understanding of the biological processes in the regulation of PPV23 during humoral immunity and cellular immunity.
Collapse
Affiliation(s)
- Nan Zhu
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Fan Zhang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Huan Zhou
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Wei Ma
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Haiguang Mao
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Mengting Wang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Zhijian Ke
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Jinbo Wang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Lili Qi
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| |
Collapse
|
25
|
Amy Lyu MJ, Tang Q, Wang Y, Essemine J, Chen F, Ni X, Chen G, Zhu XG. Evolution of gene regulatory network of C 4 photosynthesis in the genus Flaveria reveals the evolutionary status of C 3-C 4 intermediate species. PLANT COMMUNICATIONS 2023; 4:100426. [PMID: 35986514 PMCID: PMC9860191 DOI: 10.1016/j.xplc.2022.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/16/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
C4 photosynthesis evolved from ancestral C3 photosynthesis by recruiting pre-existing genes to fulfill new functions. The enzymes and transporters required for the C4 metabolic pathway have been intensively studied and well documented; however, the transcription factors (TFs) that regulate these C4 metabolic genes are not yet well understood. In particular, how the TF regulatory network of C4 metabolic genes was rewired during the evolutionary process is unclear. Here, we constructed gene regulatory networks (GRNs) for four closely evolutionarily related species from the genus Flaveria, which represent four different evolutionary stages of C4 photosynthesis: C3 (F. robusta), type I C3-C4 (F. sonorensis), type II C3-C4 (F. ramosissima), and C4 (F. trinervia). Our results show that more than half of the co-regulatory relationships between TFs and core C4 metabolic genes are species specific. The counterparts of the C4 genes in C3 species were already co-regulated with photosynthesis-related genes, whereas the required TFs for C4 photosynthesis were recruited later. The TFs involved in C4 photosynthesis were widely recruited in the type I C3-C4 species; nevertheless, type II C3-C4 species showed a divergent GRN from C4 species. In line with these findings, a 13CO2 pulse-labeling experiment showed that the CO2 initially fixed into C4 acid was not directly released to the Calvin-Benson-Bassham cycle in the type II C3-C4 species. Therefore, our study uncovered dynamic changes in C4 genes and TF co-regulation during the evolutionary process; furthermore, we showed that the metabolic pathway of the type II C3-C4 species F. ramosissima represents an alternative evolutionary solution to the ammonia imbalance in C3-C4 intermediate species.
Collapse
Affiliation(s)
- Ming-Ju Amy Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiming Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Yanjie Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Jemaa Essemine
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Faming Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxiang Ni
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Genyun Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
26
|
Activity-Dependent Non-Coding RNA MAPK Interactome of the Human Epileptic Brain. Noncoding RNA 2023; 9:ncrna9010003. [PMID: 36649033 PMCID: PMC9844323 DOI: 10.3390/ncrna9010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
The human brain has evolved to have extraordinary capabilities, enabling complex behaviors. The uniqueness of the human brain is increasingly posited to be due in part to the functions of primate-specific, including human-specific, long non-coding RNA (lncRNA) genes, systemically less conserved than protein-coding genes in evolution. Patients who have surgery for drug-resistant epilepsy are subjected to extensive electrical recordings of the brain tissue that is subsequently removed in order to treat their epilepsy. Precise localization of brain tissues with distinct electrical properties offers a rare opportunity to explore the effects of brain activity on gene expression. Here, we identified 231 co-regulated, activity-dependent lncRNAs within the human MAPK signaling cascade. Six lncRNAs, four of which were antisense to known protein-coding genes, were further examined because of their high expression and potential impact on the disease phenotype. Using a model of repeated depolarizations in human neuronal-like cells (Sh-SY5Y), we show that five out of six lncRNAs were electrical activity-dependent, with three of four antisense lncRNAs having reciprocal expression patterns relative to their protein-coding gene partners. Some were directly regulated by MAPK signaling, while others effectively downregulated the expression of the protein-coding genes encoded on the opposite strands of their genomic loci. These lncRNAs, therefore, likely contribute to highly evolved and primate-specific human brain regulatory functions that could be therapeutically modulated to treat epilepsy.
Collapse
|
27
|
Murat F, Mbengue N, Winge SB, Trefzer T, Leushkin E, Sepp M, Cardoso-Moreira M, Schmidt J, Schneider C, Mößinger K, Brüning T, Lamanna F, Belles MR, Conrad C, Kondova I, Bontrop R, Behr R, Khaitovich P, Pääbo S, Marques-Bonet T, Grützner F, Almstrup K, Schierup MH, Kaessmann H. The molecular evolution of spermatogenesis across mammals. Nature 2023; 613:308-316. [PMID: 36544022 PMCID: PMC9834047 DOI: 10.1038/s41586-022-05547-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Abstract
The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1-6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and include seven primates. We find that the rapid evolution of the testis was driven by accelerated fixation rates of gene expression changes, amino acid substitutions and new genes in late spermatogenic stages, probably facilitated by reduced pleiotropic constraints, haploid selection and transcriptionally permissive chromatin. We identify temporal expression changes of individual genes across species and conserved expression programs controlling ancestral spermatogenic processes. Genes predominantly expressed in spermatogonia (germ cells fuelling spermatogenesis) and Sertoli (somatic support) cells accumulated on X chromosomes during evolution, presumably owing to male-beneficial selective forces. Further work identified transcriptomal differences between X- and Y-bearing spermatids and uncovered that meiotic sex-chromosome inactivation (MSCI) also occurs in monotremes and hence is common to mammalian sex-chromosome systems. Thus, the mechanism of meiotic silencing of unsynapsed chromatin, which underlies MSCI, is an ancestral mammalian feature. Our study illuminates the molecular evolution of spermatogenesis and associated selective forces, and provides a resource for investigating the biology of the testis across mammals.
Collapse
Affiliation(s)
- Florent Murat
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany. .,INRAE, LPGP, Rennes, France.
| | - Noe Mbengue
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
| | - Sofia Boeg Winge
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Timo Trefzer
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Julia Schmidt
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Thoomke Brüning
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Francesco Lamanna
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Christian Conrad
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Rüdiger Behr
- German Primate Center (DPZ), Platform Degenerative Diseases, Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Miquel Crusafont Catalan Institute of Paleontology, Autonomous University of Barcelona, Barcelona, Spain
| | - Frank Grützner
- The Robinson Research Institute, School of Biological Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Kaessmann
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
28
|
Singh D, Roy J. A large-scale benchmark study of tools for the classification of protein-coding and non-coding RNAs. Nucleic Acids Res 2022; 50:12094-12111. [PMID: 36420898 PMCID: PMC9757047 DOI: 10.1093/nar/gkac1092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 10/22/2022] [Accepted: 10/28/2022] [Indexed: 11/27/2022] Open
Abstract
Identification of protein-coding and non-coding transcripts is paramount for understanding their biological roles. Computational approaches have been addressing this task for over a decade; however, generalized and high-performance models are still unreliable. This benchmark study assessed the performance of 24 tools producing >55 models on the datasets covering a wide range of species. We have collected 135 small and large transcriptomic datasets from existing studies for comparison and identified the potential bottlenecks hampering the performance of current tools. The key insights of this study include lack of standardized training sets, reliance on homogeneous training data, gradual changes in annotated data, lack of augmentation with homology searches, the presence of false positives and negatives in datasets and the lower performance of end-to-end deep learning models. We also derived a new dataset, RNAChallenge, from the benchmark considering hard instances that may include potential false alarms. The best and least well performing models under- and overfit the dataset, respectively, thereby serving a dual purpose. For computational approaches, it will be valuable to develop accurate and unbiased models. The identification of false alarms will be of interest for genome annotators, and experimental study of hard RNAs will help to untangle the complexity of the RNA world.
Collapse
Affiliation(s)
- Dalwinder Singh
- To whom correspondence should be addressed. Tel: +91 172 5221206;
| | - Joy Roy
- Correspondence may also be addressed to Joy Roy.
| |
Collapse
|
29
|
Qian SH, Chen L, Xiong YL, Chen ZX. Evolution and function of developmentally dynamic pseudogenes in mammals. Genome Biol 2022; 23:235. [PMID: 36348461 PMCID: PMC9641868 DOI: 10.1186/s13059-022-02802-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Pseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and disease, especially cancer. However, systematic functional characterization and evolution of pseudogenes remain largely unexplored. RESULTS To systematically characterize pseudogenes, we date the origin of human and mouse pseudogenes across vertebrates and observe a burst of pseudogene gain in these two lineages. Based on a hybrid sequencing dataset combining full-length PacBio sequencing, sample-matched Illumina sequencing, and public time-course transcriptome data, we observe that abundant mammalian pseudogenes could be transcribed, which contribute to the establishment of organ identity. Our analyses reveal that developmentally dynamic pseudogenes are evolutionarily conserved and show an increasing weight during development. Besides, they are involved in complex transcriptional and post-transcriptional modulation, exhibiting the signatures of functional enrichment. Coding potential evaluation suggests that 19% of human pseudogenes could be translated, thus serving as a new way for protein innovation. Moreover, pseudogenes carry disease-associated SNPs and conduce to cancer transcriptome perturbation. CONCLUSIONS Our discovery reveals an unexpectedly high abundance of mammalian pseudogenes that can be transcribed and translated, and these pseudogenes represent a novel regulatory layer. Our study also prioritizes developmentally dynamic pseudogenes with signatures of functional enrichment and provides a hybrid sequencing dataset for further unraveling their biological mechanisms in organ development and carcinogenesis in the future.
Collapse
Affiliation(s)
- Sheng Hu Qian
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
| | - Lu Chen
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
| | - Yu-Li Xiong
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
| | - Zhen-Xia Chen
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
- Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, 430070 PR China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518124 PR China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124 PR China
| |
Collapse
|
30
|
McQuillan MA, Ranciaro A, Hansen MEB, Fan S, Beggs W, Belay G, Woldemeskel D, Tishkoff SA. Signatures of Convergent Evolution and Natural Selection at the Alcohol Dehydrogenase Gene Region are Correlated with Agriculture in Ethnically Diverse Africans. Mol Biol Evol 2022; 39:msac183. [PMID: 36026493 PMCID: PMC9547508 DOI: 10.1093/molbev/msac183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The alcohol dehydrogenase (ADH) family of genes encodes enzymes that catalyze the metabolism of ethanol into acetaldehyde. Nucleotide variation in ADH genes can affect the catalytic properties of these enzymes and is associated with a variety of traits, including alcoholism and cancer. Some ADH variants, including the ADH1B*48His (rs1229984) mutation in the ADH1B gene, reduce the risk of alcoholism and are under positive selection in multiple human populations. The advent of Neolithic agriculture and associated increase in fermented foods and beverages is hypothesized to have been a selective force acting on such variants. However, this hypothesis has not been tested in populations outside of Asia. Here, we use genome-wide selection scans to show that the ADH gene region is enriched for variants showing strong signals of positive selection in multiple Afroasiatic-speaking, agriculturalist populations from Ethiopia, and that this signal is unique among sub-Saharan Africans. We also observe strong selection signals at putatively functional variants in nearby lipid metabolism genes, which may influence evolutionary dynamics at the ADH region. Finally, we show that haplotypes carrying these selected variants were introduced into Northeast Africa from a West-Eurasian source within the last ∼2,000 years and experienced positive selection following admixture. These selection signals are not evident in nearby, genetically similar populations that practice hunting/gathering or pastoralist subsistence lifestyles, supporting the hypothesis that the emergence of agriculture shapes patterns of selection at ADH genes. Together, these results enhance our understanding of how adaptations to diverse environments and diets have influenced the African genomic landscape.
Collapse
Affiliation(s)
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| | | | - Shaohua Fan
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dawit Woldemeskel
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
31
|
Li C, Feng Y, Fu Z, Deng J, Gu Y, Wang H, Wu X, Huang Z, Zhu Y, Liu Z, Huang M, Wang T, Hu S, Yao B, Zeng Y, Zhou CJ, Brown SDM, Liu Y, Vidal-Puig A, Dong Y, Xu Y. Human-specific gene CT47 blocks PRMT5 degradation to lead to meiosis arrest. Cell Death Discov 2022; 8:345. [PMID: 35918318 PMCID: PMC9345867 DOI: 10.1038/s41420-022-01139-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Exploring the functions of human-specific genes (HSGs) is challenging due to the lack of a tractable genetic model system. Testosterone is essential for maintaining human spermatogenesis and fertility, but the underlying mechanism is unclear. Here, we identified Cancer/Testis Antigen gene family 47 (CT47) as an essential regulator of human-specific spermatogenesis by stabilizing arginine methyltransferase 5 (PRMT5). A humanized mouse model revealed that CT47 functions to arrest spermatogenesis by interacting with and regulating CT47/PRMT5 accumulation in the nucleus during the leptotene/zygotene-to-pachytene transition of meiosis. We demonstrate that testosterone induces nuclear depletion of CT47/PRMT5 and rescues leptotene-arrested spermatocyte progression in humanized testes. Loss of CT47 in human embryonic stem cells (hESCs) by CRISPR/Cas9 led to an increase in haploid cells but blocked the testosterone-induced increase in haploid cells when hESCs were differentiated into haploid spermatogenic cells. Moreover, CT47 levels were decreased in nonobstructive azoospermia. Together, these results established CT47 as a crucial regulator of human spermatogenesis by preventing meiosis initiation before the testosterone surge.
Collapse
Affiliation(s)
- Chao Li
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Yuming Feng
- Department of Reproductive Medical Center, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Zhenxin Fu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Junjie Deng
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Yue Gu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Hanben Wang
- State Key Laboratory of Reproductive Medicine (SKLRM), Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine (SKLRM), Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Zhengyun Huang
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Yichen Zhu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhiwei Liu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Moli Huang
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Tao Wang
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, Suzhou, 215000, China
| | - Bing Yao
- Department of Reproductive Medical Center, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Yizhun Zeng
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA, USA
| | - Steve D M Brown
- Medical Research Council (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, UK
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRC, Cambridge, UK
| | - Yingying Dong
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China.
| |
Collapse
|
32
|
Bulbul Ahmed M, Humayan Kabir A. Understanding of the various aspects of gene regulatory networks related to crop improvement. Gene 2022; 833:146556. [PMID: 35609798 DOI: 10.1016/j.gene.2022.146556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/14/2022] [Accepted: 05/06/2022] [Indexed: 12/30/2022]
Abstract
The hierarchical relationship between transcription factors, associated proteins, and their target genes is defined by a gene regulatory network (GRN). GRNs allow us to understand how the genotype and environment of a plant are incorporated to control the downstream physiological responses. During plant growth or environmental acclimatization, GRNs are diverse and can be differently regulated across tissue types and organs. An overview of recent advances in the development of GRN that speed up basic and applied plant research is given here. Furthermore, the overview of genome and transcriptome involving GRN research along with the exciting advancement and application are discussed. In addition, different approaches to GRN predictions were elucidated. In this review, we also describe the role of GRN in crop improvement, crop plant manipulation, stress responses, speed breeding and identifying genetic variations/locus. Finally, the challenges and prospects of GRN in plant biology are discussed.
Collapse
Affiliation(s)
- Md Bulbul Ahmed
- Plant Science Department, McGill University, 21111 lakeshore Road, Ste. Anne de Bellevue H9X3V9, Quebec, Canada; Institut de Recherche en Biologie Végétale (IRBV), University of Montreal, Montréal, Québec H1X 2B2, Canada.
| | | |
Collapse
|
33
|
Malmström E, Khan HN, Veer CV‘, Stunnenberg M, Meijer MT, Matsumoto H, Otto NA, Geijtenbeek TBH, de Vos AF, van der Poll T, Scicluna BP. The Long Non-Coding Antisense RNA JHDM1D-AS1 Regulates Inflammatory Responses in Human Monocytes. Front Cell Infect Microbiol 2022; 12:934313. [PMID: 35903199 PMCID: PMC9315269 DOI: 10.3389/fcimb.2022.934313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/10/2022] [Indexed: 12/04/2022] Open
Abstract
Monocytes are key players in innate immunity, with their ability to regulate inflammatory responses and combat invading pathogens. There is a growing body of evidence indicating that long non-coding RNA (lncRNA) participate in various cellular biological processes, including the innate immune response. The immunoregulatory properties of numerous lncRNAs discovered in monocytes remain largely unexplored. Here, by RNA sequencing, we identified a lncRNA JHDM1D-AS1, which was upregulated in blood monocytes obtained from patients with sepsis relative to healthy controls. JHDM1D-AS1 expression was induced in primary human monocytes exposed to Toll-like receptor ligands, such as lipopolysaccharide (LPS), or bacteria. The inducibility of JHDM1D-AS1 expression in monocytes depended, at least in part, on nuclear factor-κB activation. JHDM1D-AS1 knockdown experiments in human monocyte-derived macrophages revealed significantly enhanced expression of inflammatory mediators, before and after exposure to LPS, relative to control cells. Specifically, genes involved in inflammatory responses were upregulated (e.g., CXCL2, CXCL8, IL1RN, TREM1, TNF, and IL6), whereas genes involved in anti-inflammatory pathways were downregulated (e.g., SOCS1 and IL10RA). JHDM1D-AS1 overexpression in a pro-monocytic cell line revealed diminished pro-inflammatory responses subsequent to LPS challenge. Collectively, these findings identify JHDM1D-AS1 as a potential anti-inflammatory mediator induced in response to inflammatory stimuli.
Collapse
Affiliation(s)
- Erik Malmström
- Amsterdam University Medical Centers, Center for Experimental and Molecular Medicine, University of Amsterdam, Amsterdam, Netherlands
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
- Emergency Medicine, Department of Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Hina N. Khan
- Amsterdam University Medical Centers, Center for Experimental and Molecular Medicine, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam University Medical Centers, Clinical Epidemiology and Data Science, University of Amsterdam, Amsterdam, Netherlands
| | - Cornelis van ‘t Veer
- Amsterdam University Medical Centers, Center for Experimental and Molecular Medicine, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Melissa Stunnenberg
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Amsterdam University Medical Centers, Experimental Immunology, University of Amsterdam, Amsterdam, Netherlands
| | - Mariska T. Meijer
- Amsterdam University Medical Centers, Center for Experimental and Molecular Medicine, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Hisatake Matsumoto
- Amsterdam University Medical Centers, Center for Experimental and Molecular Medicine, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Natasja A. Otto
- Amsterdam University Medical Centers, Center for Experimental and Molecular Medicine, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Teunis B. H. Geijtenbeek
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Amsterdam University Medical Centers, Experimental Immunology, University of Amsterdam, Amsterdam, Netherlands
| | - Alex F. de Vos
- Amsterdam University Medical Centers, Center for Experimental and Molecular Medicine, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Tom van der Poll
- Amsterdam University Medical Centers, Center for Experimental and Molecular Medicine, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Amsterdam University Medical Centers, Division of Infectious Diseases, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Brendon P. Scicluna
- Amsterdam University Medical Centers, Center for Experimental and Molecular Medicine, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam University Medical Centers, Clinical Epidemiology and Data Science, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Department of Applied Biomedical Science, Faculty of Health Sciences, Mater Dei hospital, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| |
Collapse
|
34
|
Shimizu K, Takeuchi T, Negishi L, Kurumizaka H, Kuriyama I, Endo K, Suzuki M. Evolution of EGF-like and Zona pellucida domains containing shell matrix proteins in mollusks. Mol Biol Evol 2022; 39:6633355. [PMID: 35796746 PMCID: PMC9290575 DOI: 10.1093/molbev/msac148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several types of shell matrix proteins (SMPs) have been identified in molluskan shells. Their diversity is the consequence of various molecular processes, including domain shuffling and gene duplication. However, the evolutionary origin of most SMPs remains unclear. In this study, we investigated the evolutionary process EGF-like and zona pellucida (ZP) domains containing SMPs. Two types of the proteins (EGF-like protein (EGFL) and EGF-like and ZP domains containing protein (EGFZP)) were found in the pearl oyster, Pinctada fucata. In contrast, only EGFZP was identified in the gastropods. Phylogenetic analysis and genomic arrangement studies showed that EGFL and EGFZP formed a clade in bivalves, and their encoding genes were localized in tandem repeats on the same scaffold. In P. fucata, EGFL genes were expressed in the outer part of mantle epithelial cells are related to the calcitic shell formation. However, in both P. fucata and the limpet Nipponacmea fuscoviridis, EGFZP genes were expressed in the inner part of the mantle epithelial cells are related to aragonitic shell formation. Furthermore, our analysis showed that in P. fucata, the ZP domain interacts with eight SMPs that have various functions in the nacreous shell mineralization. The data suggest that the ZP domain can interact with other SMPs, and EGFL evolution in pterimorph bivalves represents an example of neo-functionalization that involves the acquisition of a novel protein through gene duplication.
Collapse
Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Isao Kuriyama
- Mie Prefecture Fisheries Research Institute, 3564-3 Hamajima, Hamajima-cho, Shima-city, Mie 517-0404, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| |
Collapse
|
35
|
Detecting signatures of selection on gene expression. Nat Ecol Evol 2022; 6:1035-1045. [PMID: 35551249 DOI: 10.1038/s41559-022-01761-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
A substantial amount of phenotypic diversity results from changes in gene expression levels and patterns. Understanding how the transcriptome evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of gene expression evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene expression are subject to biases that can lead to false signatures of selection. Here we first outline the main approaches for describing expression evolution and their inherent biases. Next, we bridge the gap between the fields of phylogenetic comparative methods and transcriptomics to reinforce the main pitfalls of inferring selection on expression patterns and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of transcriptional variation and identifying major unanswered questions in disentangling how selection acts on the transcriptome.
Collapse
|
36
|
Mahmoudi A, Moadab F, Safdarian E, Navashenaq JG, Rezaee M, Gheibihayat SM. MicroRNAs and Efferocytosis: Implications for Diagnosis and Therapy. Mini Rev Med Chem 2022; 22:2641-2660. [PMID: 35362375 DOI: 10.2174/1389557522666220330150937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/24/2021] [Accepted: 01/19/2022] [Indexed: 11/22/2022]
Abstract
About 10-100 billion cells are generated in the human body in a day, and accordingly, 10-100 billion cells predominantly die for maintaining homeostasis. Dead cells generated by apoptosis are also rapidly engulfed by macrophages (Mθs) to be degraded. In case of the inefficient engulfment of apoptotic cells (ACs) via Mθs, they experience secondary necrosis and thus release intracellular materials, which display damage-associated molecular patterns (DAMPs) and result in diseases. Over the last decades, researchers have also reflected on the significant contribution of microRNAs (miRNAs) to autoimmune diseases through the regulation of Mθs functions. Moreover, miRNAs have shown intricate involvement with completely adjusting basic Mθs functions, such as phagocytosis, inflammation, efferocytosis, tumor promotion, and tissue repair. In this review, the mechanism of efferocytosis containing "Find-Me", "Eat-Me", and "Digest-Me" signals is summarized and the biogenesis of miRNAs is briefly described. Finally, the role of miRNAs in efferocytosis is discussed. It is concluded that miRNAs represent promising treatments and diagnostic targets in impaired phagocytic clearance, which leads to different diseases.
Collapse
Affiliation(s)
- Ali Mahmoudi
- Department of medical biotechnology and nanotechnology, faculty of medicine, Mashhad University of Medical science, Iran
| | - Fatemeh Moadab
- Medical student, Student Research Committee, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Esmat Safdarian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran Iran
| | | | - Mehdi Rezaee
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran;
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Seyed Mohammad Gheibihayat
- Department of Medical Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| |
Collapse
|
37
|
Qiu S, Li B, Xia Y, Xuan Z, Li Z, Xie L, Gu C, Lv J, Lu C, Jiang T, Fang L, Xu P, Yang J, Li Y, Chen Z, Zhang L, Wang L, Zhang D, Xu H, Wang W, Xu Z. CircTHBS1 drives gastric cancer progression by increasing INHBA mRNA expression and stability in a ceRNA- and RBP-dependent manner. Cell Death Dis 2022; 13:266. [PMID: 35338119 PMCID: PMC8949653 DOI: 10.1038/s41419-022-04720-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 12/15/2022]
Abstract
Circular RNAs (circRNAs) play vital regulatory roles in the progression of multiple cancers. In our study, transcriptome analysis and self-organizing maps (SOM) were applied to screen backbone circRNAs in gastric cancer (GC). Upon validation of the expression patterns of screened circRNAs, gain- and loss-of-function assays were performed in vitro and in vivo. Underlying mechanisms were investigated using RNA pull-down, luciferase reporter assay and RNA immunoprecipitation. The expression of circTHBS1 was significantly increased in GC and associated with poor prognosis. CircTHBS1 facilitated the malignant behavior and epithelial-to-mesenchymal transition of GC cells. Mechanistically, circTHBS1 sponged miR-204-5p to promote the expression of Inhibin Subunit Beta A (INHBA). Moreover, circTHBS1 could enhance the HuR-mediated mRNA stability of INHBA, which subsequently activated the TGF-β pathway. Our research identified circTHBS1 as an oncogenic circRNA that enhances GC malignancy by elevating INHBA expression, providing new insight and a feasible target for the diagnosis and treatment of GC.
Collapse
Affiliation(s)
- Shengkui Qiu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China.,Department of General Surgery, The Second Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Bowen Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Yiwen Xia
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Zhe Xuan
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Zheng Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Li Xie
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Chao Gu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Jialun Lv
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Chen Lu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Tianlu Jiang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Lang Fang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Penghui Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Jing Yang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Ying Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Zetian Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Lu Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Linjun Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Diancai Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Hao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Weizhi Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China.
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China. .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu Province, China.
| |
Collapse
|
38
|
Ma J, Zhang T, Wang W, Chen Y, Cai W, Zhu B, Xu L, Gao H, Zhang L, Li J, Gao X. Comparative Transcriptome Analyses of Gayal (Bos frontalis), Yak (Bos grunniens), and Cattle (Bos taurus) Reveal the High-Altitude Adaptation. Front Genet 2022; 12:778788. [PMID: 35087567 PMCID: PMC8789257 DOI: 10.3389/fgene.2021.778788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Gayal and yak are well adapted to their local high-altitude environments, yet the transcriptional regulation difference of the plateau environment among them remains obscure. Herein, cross-tissue and cross-species comparative transcriptome analyses were performed for the six hypoxia-sensitive tissues from gayal, yak, and cattle. Gene expression profiles for all single-copy orthologous genes showed tissue-specific expression patterns. By differential expression analysis, we identified 3,020 and 1,995 differentially expressed genes (DEGs) in at least one tissue of gayal vs. cattle and yak vs. cattle, respectively. Notably, we found that the adaptability of the gayal to the alpine canyon environment is highly similar to the yak living in the Qinghai-Tibet Plateau, such as promoting red blood cell development, angiogenesis, reducing blood coagulation, immune system activation, and energy metabolism shifts from fatty acid β-oxidation to glycolysis. By further analyzing the common and unique DEGs in the six tissues, we also found that numerous expressed regulatory genes related to these functions are unique in the gayal and yak, which may play important roles in adapting to the corresponding high-altitude environment. Combined with WGCNA analysis, we found that UQCRC1 and COX5A are the shared differentially expressed hub genes related to the energy supply of myocardial contraction in the heart-related modules of gayal and yak, and CAPS is a shared differential hub gene among the hub genes of the lung-related module, which is related to pulmonary artery smooth muscle contraction. Additionally, EDN3 is the unique differentially expressed hub gene related to the tracheal epithelium and pulmonary vasoconstriction in the lung of gayal. CHRM2 is a unique differentially expressed hub gene that was identified in the heart of yak, which has an important role in the autonomous regulation of the heart. These results provide a basis for further understanding the complex transcriptome expression pattern and the regulatory mechanism of high-altitude domestication of gayal and yak.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Junya Li
- *Correspondence: Junya Li, ; Xue Gao,
| | - Xue Gao
- *Correspondence: Junya Li, ; Xue Gao,
| |
Collapse
|
39
|
Rostami Azar A, Maroufi A. Identification of Long Non-coding RNA Transcripts in Glycyrrhiza uralensis. IRANIAN JOURNAL OF BIOTECHNOLOGY 2022; 20:e2607. [PMID: 35891954 PMCID: PMC9284242 DOI: 10.30498/ijb.2021.205469.2607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Chinese liquorice (Glycyrrhiza uralensis), an important medicinal plant, contains various valuable secondary metabolites. Secondary metabolites biosynthesis is
very tightly regulated; therefore, elucidation and manipulation of the biosynthetic pathways are of great interest. Recent studies have shown that lncRNAs play important
regulatory roles in many biological processes, thus identification and modification of their expression is essential to metabolic pathways for biosynthesis of secondary metabolites. Objectives: In this study we attempted to identify non-coding RNA transcripts (lncRNAs) that may act as important regulators of diverse biological processes, including stress responses
and developmental programs in Glycyrrhiza uralensis. Materials and Methods: Identification of potential lncRNAs in Chinese liquorice was performed using a bioinformatics pipeline from the available EST dataset of G. uralensis. Results: Bioinformatics analysis revealed that 1365 identical sequences in the range of 200 to 1286 base pair are putative lncRNAs. Only less than one percent of the
predicted lncRNAs display sequence conservation with lncRNAs from other species. Moreover, 13 lncRNAs were detected as the potential precursors of 16 miRNAs.
From this analysis, we also detected possible target genes of 16 known miRNA genes. The majority of the predicted miRNA target genes have important role in response
to plant disease and a couple of them contribute to signalling and metabolic pathways. Conclusion: This study demonstrates the existence of lncRNAs in G. uralensis which has not been found before and provides valuable resources for further understanding and characterizing
of lncRNAs and also a basis for additional investigation to reveal specific roles of lncRNAs in various biological processes and particularly in response to plant diseases.
Collapse
Affiliation(s)
- Arash Rostami Azar
- Department of Plant Production and Genetics, University of Kurdistan, Sanandaj, Iran
| | - Asad Maroufi
- Department of Plant Production and Genetics, University of Kurdistan, Sanandaj, Iran.,Research Center for Medicinal Plant Breeding and Development, University of Kurdistan, Sanandaj, Iran
| |
Collapse
|
40
|
Laverre A, Tannier E, Necsulea A. Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness. Genome Res 2021; 32:280-296. [PMID: 34930799 PMCID: PMC8805723 DOI: 10.1101/gr.275901.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022]
Abstract
Gene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements are rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Here, we address these questions by comparing genome-wide maps of promoter-centered chromatin contacts in mouse and human. We show that there is significant evolutionary conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter–enhancer contacts, illustrating how the structure of regulatory landscapes constrains large-scale genome evolution. We show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny, or contacts with target genes, is significantly associated with gene expression evolution.
Collapse
Affiliation(s)
- Alexandre Laverre
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive
| | - Eric Tannier
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Centre de recherche Inria de Lyon
| | | |
Collapse
|
41
|
Troskie RL, Faulkner GJ, Cheetham SW. Processed pseudogenes: A substrate for evolutionary innovation: Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome. Bioessays 2021; 43:e2100186. [PMID: 34569081 DOI: 10.1002/bies.202100186] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022]
Abstract
Processed pseudogenes may serve as a genetic reservoir for evolutionary innovation. Here, we argue that through the activity of long interspersed element-1 retrotransposons, processed pseudogenes disperse coding and noncoding sequences rich with regulatory potential throughout the human genome. While these sequences may appear to be non-functional, a lack of contemporary function does not prohibit future development of biological activity. Here, we discuss the dynamic evolution of certain processed pseudogenes into coding and noncoding genes and regulatory elements, and their implication in wide-ranging biological and pathological processes. Also see the video abstract here: https://youtu.be/iUY_mteVoPI.
Collapse
Affiliation(s)
- Robin-Lee Troskie
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, Australia.,Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Seth W Cheetham
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
| |
Collapse
|
42
|
Gene expression levels modulate germline mutation rates through the compound effects of transcription-coupled repair and damage. Hum Genet 2021; 141:1211-1222. [PMID: 34482438 DOI: 10.1007/s00439-021-02355-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/25/2021] [Indexed: 12/16/2022]
Abstract
Of all mammalian organs, the testis has long been observed to have the most diverse gene expression profile. To account for this widespread gene expression, we have proposed a mechanism termed 'transcriptional scanning', which reduces germline mutation rates through transcription-coupled repair (TCR). Our hypothesis contrasts with an earlier observation that mutation rates are overall positively correlated with gene expression levels in yeast, implying that transcription is mutagenic due to effects dominated by transcription-coupled damage (TCD). Here we report evidence that the compound effects of both TCR and TCD during spermatogenesis modulate human germline mutation rates, with TCR dominating in most genes, thus supporting the transcriptional scanning hypothesis. Our analyses address potentially confounding factors, distinguish the differential mutagenic effects acting on the highly expressed genes and the low-to-moderately expressed genes, and resolve concerns relating to the validation of the results using a de novo mutation dataset. We also discuss the theoretical possibility of transcriptional scanning hypothesis from an evolutionary perspective. Together, these analyses support a model by which the coupling of transcription-coupled repair and damage establishes the pattern of germline mutation rates and provide an evolutionary explanation for widespread gene expression during spermatogenesis.
Collapse
|
43
|
Rivard EL, Ludwig AG, Patel PH, Grandchamp A, Arnold SE, Berger A, Scott EM, Kelly BJ, Mascha GC, Bornberg-Bauer E, Findlay GD. A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster. PLoS Genet 2021; 17:e1009787. [PMID: 34478447 PMCID: PMC8445463 DOI: 10.1371/journal.pgen.1009787] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/16/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes with testis-enriched expression in Drosophila melanogaster and identified one gene, atlas, required for male fertility. Detailed genetic and cytological analyses showed that atlas is required for proper chromatin condensation during the final stages of spermatogenesis. Atlas protein is expressed in spermatid nuclei and facilitates the transition from histone- to protamine-based chromatin packaging. Complementary evolutionary analyses revealed the complex evolutionary history of atlas. The protein-coding portion of the gene likely arose at the base of the Drosophila genus on the X chromosome but was unlikely to be essential, as it was then lost in several independent lineages. Within the last ~15 million years, however, the gene moved to an autosome, where it fused with a conserved non-coding RNA and evolved a non-redundant role in male fertility. Altogether, this study provides insight into the integration of novel genes into biological processes, the links between genomic innovation and functional evolution, and the genetic control of a fundamental developmental process, gametogenesis.
Collapse
Affiliation(s)
- Emily L. Rivard
- College of the Holy Cross, Worcester, Massachusetts, United States of America
| | - Andrew G. Ludwig
- College of the Holy Cross, Worcester, Massachusetts, United States of America
| | - Prajal H. Patel
- College of the Holy Cross, Worcester, Massachusetts, United States of America
| | | | - Sarah E. Arnold
- College of the Holy Cross, Worcester, Massachusetts, United States of America
| | | | - Emilie M. Scott
- College of the Holy Cross, Worcester, Massachusetts, United States of America
| | - Brendan J. Kelly
- College of the Holy Cross, Worcester, Massachusetts, United States of America
| | - Grace C. Mascha
- College of the Holy Cross, Worcester, Massachusetts, United States of America
| | - Erich Bornberg-Bauer
- University of Münster, Münster, Germany
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Geoffrey D. Findlay
- College of the Holy Cross, Worcester, Massachusetts, United States of America
| |
Collapse
|
44
|
Parnigoni A, Caon I, Moretto P, Viola M, Karousou E, Passi A, Vigetti D. The role of the multifaceted long non-coding RNAs: A nuclear-cytosolic interplay to regulate hyaluronan metabolism. Matrix Biol Plus 2021; 11:100060. [PMID: 34435179 PMCID: PMC8377009 DOI: 10.1016/j.mbplus.2021.100060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
In the extracellular matrix (ECM), the glycosaminoglycan (GAG) hyaluronan (HA) has different physiological roles favouring hydration, elasticity and cell survival. Three different isoforms of HA synthases (HAS1, 2, and 3) are responsible for the production of HA. In several pathologies the upregulation of HAS enzymes leads to an abnormal HA accumulation causing cell dedifferentiation, proliferation and migration thus favouring cancer progression, fibrosis and vascular wall thickening. An intriguing new player in HAS2 gene expression regulation and HA production is the long non-coding RNA (lncRNA) hyaluronan synthase 2 antisense 1 (HAS2-AS1). A significant part of mammalian genomes corresponds to genes that transcribe lncRNAs; they can regulate gene expression through several mechanisms, being involved not only in maintaining the normal homeostasis of cells and tissues, but also in the onset and progression of different diseases, as demonstrated by the increasing number of studies published through the last decades. HAS2-AS1 is no exception: it can be localized both in the nucleus and in the cytosol, regulating cancer cells as well as vascular smooth muscle cells behaviour. Hyaluronan is a component of the extracellular matrix and is synthetised by three isoenzymes named HAS1, 2, and 3. In several pathologies an upregulation of HAS2 leads to an abnormal accumulation of HA. The long non-coding RNA is a new specific epigenetic regulator of HAS2. In the nucleus HAS2-AS1 modulates chromatin structure around HAS2 promoter increasing transcription. In the cytosol, HAS2-AS1 can interact with several miRNAs altering the expression of several genes as well as can stabilise HAS2 mRNA forming RNA: RNA duplex.
Collapse
Key Words
- 4-MU, 4-methylubelliferone
- 4-MUG, 4-methylumbelliferyl glucuronide
- Atherosclerosis
- Cancer
- ECM, extracellular matrix
- EMT, epithelial to mesenchymal transition
- Epigenetics
- Extracellular matrix
- GAG, glycosaminoglycans
- Glycosaminoglycans
- HA, hyaluronan
- HAS2
- HAS2, hyaluronan synthase 2
- HAS2-AS1
- HAS2–AS1, hyaluronan synthase 2 natural antisense 1
- HIFs, hypoxia-inducible factors
- NF-κB, nuclear factor κ–light-chain enhancer of activated B cell
- PG, proteoglycan
- PTM, post-translational modification
- Proteoglycans
- RBP, RNA-binding protein
- SIRT1, sirtuin 1
- SMCs, smooth muscle cells
- TNF-α, tumour necrosis factor alpha
- UDP-GlcNAc, UDP-N-acetylglucosamine
- UDP-GlcUA, UDP-glucuronic acid
- ceRNA, competitive endogenous RNA
- lncRNA, long non-coding RNA
- miRNA, micro-RNA
Collapse
Affiliation(s)
- Arianna Parnigoni
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Ilaria Caon
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Paola Moretto
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Manuela Viola
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Evgenia Karousou
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Alberto Passi
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Davide Vigetti
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| |
Collapse
|
45
|
Policarpo R, Sierksma A, De Strooper B, d'Ydewalle C. From Junk to Function: LncRNAs in CNS Health and Disease. Front Mol Neurosci 2021; 14:714768. [PMID: 34349622 PMCID: PMC8327212 DOI: 10.3389/fnmol.2021.714768] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/25/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.
Collapse
Affiliation(s)
- Rafaela Policarpo
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Annerieke Sierksma
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,UK Dementia Research Institute, University College London, London, United Kingdom
| | - Constantin d'Ydewalle
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| |
Collapse
|
46
|
Winkelmüller TM, Entila F, Anver S, Piasecka A, Song B, Dahms E, Sakakibara H, Gan X, Kułak K, Sawikowska A, Krajewski P, Tsiantis M, Garrido-Oter R, Fukushima K, Schulze-Lefert P, Laurent S, Bednarek P, Tsuda K. Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. THE PLANT CELL 2021; 33:1863-1887. [PMID: 33751107 PMCID: PMC8290292 DOI: 10.1093/plcell/koab073] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/24/2021] [Indexed: 05/20/2023]
Abstract
Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species to investigate PTI responses, we identified a set of genes that commonly respond to the MAMP flg22 and genes that exhibit species-specific expression signatures. Variation in flg22-triggered transcriptome responses across Brassicaceae species was incongruent with their phylogeny, while expression changes were strongly conserved within A. thaliana. We found the enrichment of WRKY transcription factor binding sites in the 5'-regulatory regions of conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene expression patterns during PTI. Our findings advance our understanding of the evolution of the transcriptome during biotic stress.
Collapse
Affiliation(s)
- Thomas M Winkelmüller
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Frederickson Entila
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Shajahan Anver
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Present address: Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anna Piasecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Baoxing Song
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Present address: Institute for Genomic Diversity, Cornell University, Ithaca, New York
| | - Eik Dahms
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, 230-0045 Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Karolina Kułak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Present address: Department of Computational Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Aneta Sawikowska
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-628 Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
| | - Paul Schulze-Lefert
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, 430070 Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, 430070 Wuhan, China
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Author for correspondence:
| |
Collapse
|
47
|
Chadourne M, Poumerol E, Jouneau L, Passet B, Castille J, Sellem E, Pailhoux E, Mandon-Pépin B. Structural and Functional Characterization of a Testicular Long Non-coding RNA (4930463O16Rik) Identified in the Meiotic Arrest of the Mouse Topaz1 -/- Testes. Front Cell Dev Biol 2021; 9:700290. [PMID: 34277642 PMCID: PMC8281061 DOI: 10.3389/fcell.2021.700290] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/14/2021] [Indexed: 12/23/2022] Open
Abstract
Spermatogenesis involves coordinated processes, including meiosis, to produce functional gametes. We previously reported Topaz1 as a germ cell-specific gene highly conserved in vertebrates. Topaz1 knockout males are sterile with testes that lack haploid germ cells because of meiotic arrest after prophase I. To better characterize Topaz1–/– testes, we used RNA-sequencing analyses at two different developmental stages (P16 and P18). The absence of TOPAZ1 disturbed the expression of genes involved in microtubule and/or cilium mobility, biological processes required for spermatogenesis. Moreover, a quarter of P18 dysregulated genes are long non-coding RNAs (lncRNAs), and three of them are testis-specific and located in spermatocytes, their expression starting between P11 and P15. The suppression of one of them, 4939463O16Rik, did not alter fertility although sperm parameters were disturbed and sperm concentration fell. The transcriptome of P18-4939463O16Rik–/– testes was altered and the molecular pathways affected included microtubule-based processes, the regulation of cilium movement and spermatogenesis. The absence of TOPAZ1 protein or 4930463O16Rik produced the same enrichment clusters in mutant testes despite a contrasted phenotype on male fertility. In conclusion, although Topaz1 is essential for the meiosis in male germ cells and regulate the expression of numerous lncRNAs, these studies have identified a Topaz1 regulated lncRNA (4930463O16Rik) that is key for both sperm production and motility.
Collapse
Affiliation(s)
- Manon Chadourne
- UVSQ, INRAE, BREED, Université Paris-Saclay, Jouy-en-Josas, France
| | - Elodie Poumerol
- UVSQ, INRAE, BREED, Université Paris-Saclay, Jouy-en-Josas, France
| | - Luc Jouneau
- UVSQ, INRAE, BREED, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bruno Passet
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Johan Castille
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Eric Pailhoux
- UVSQ, INRAE, BREED, Université Paris-Saclay, Jouy-en-Josas, France
| | | |
Collapse
|
48
|
Yang W, Qian Y, Gao K, Zheng W, Wu G, He Q, Chen Q, Song Y, Wang L, Wang Y, Gu P, Chen B, Zhai R. LncRNA BRCAT54 inhibits the tumorigenesis of non-small cell lung cancer by binding to RPS9 to transcriptionally regulate JAK-STAT and calcium pathway genes. Carcinogenesis 2021; 42:80-92. [PMID: 32459848 DOI: 10.1093/carcin/bgaa051] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/12/2020] [Accepted: 05/24/2020] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES Increasing evidence suggest that long non-coding RNAs (lncRNAs) play critical roles in cancers. However, the expression pattern and underlying mechanisms of lncRNAs in non-small cell lung cancer (NSCLC) remain incompletely understood. This study aimed to elucidate the functions and molecular mechanisms of a certain lncRNA in NSCLC. METHODS LncRNA microarray was performed to identify differential expressed lncRNAs between pre- and postoperation plasma in NSCLC patients. The expression level of candidate lncRNA in NSCLC tissues, plasma and cells was determined by quantitative real-time PCR (qRT-PCR) and in situ hybridization. The functional roles of lncRNA were assessed in vitro and in vivo. Furthermore, RNA pull-down, RNA immunoprecipitation, microarray, qRT-PCR and rescue assays were conducted to explore the mechanism action of lncRNA in NSCLC cells. RESULTS We identified a novel lncRNA (BRCAT54), which was significantly upregulated in preoperative plasma, NSCLC tissues and NSCLC cells, and its higher expression was associated with better prognosis in patients with NSCLC. Overexpression of BRCAT54 inhibited proliferation, migration and activated apoptosis in NSCLC cells. Conversely, knockdown of BRCAT54 reversed the suppressive effects of BRCAT54. Moreover, overexpression of BRCAT54 repressed NSCLC cell growth in vivo. Mechanistically, BRCAT54 directly bound to RPS9. Knockdown of RPS9 substantially reversed the promoting effects of si-BRCAT54 on cell proliferation and enhanced the inhibitive effect of si-BRCAT54 on BRCAT54 expression. In addition, silencing of RPS9 activated JAK-STAT pathway and suppressed calcium signaling pathway gene expressions. CONCLUSION This study identified BRCAT54 as a tumor suppressor in NSCLC. Targeting the BRCAT54 and RPS9 feedback loop might be a novel therapeutic strategy for NSCLC.
Collapse
Affiliation(s)
- Wenhan Yang
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Youhui Qian
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Kaiping Gao
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Wenjing Zheng
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Guodong Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qihan He
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Qianqian Chen
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Yi Song
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Liang Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Yejun Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Peigui Gu
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Bin Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Rihong Zhai
- School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Carson Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| |
Collapse
|
49
|
Kundu M, Basu J. The Role of microRNAs and Long Non-Coding RNAs in the Regulation of the Immune Response to Mycobacterium tuberculosis Infection. Front Immunol 2021; 12:687962. [PMID: 34248974 PMCID: PMC8264550 DOI: 10.3389/fimmu.2021.687962] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022] Open
Abstract
Non-coding RNAs have emerged as critical regulators of the immune response to infection. MicroRNAs (miRNAs) are small non-coding RNAs which regulate host defense mechanisms against viruses, bacteria and fungi. They are involved in the delicate interplay between Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), and its host, which dictates the course of infection. Differential expression of miRNAs upon infection with M. tuberculosis, regulates host signaling pathways linked to inflammation, autophagy, apoptosis and polarization of macrophages. Experimental evidence suggests that virulent M. tuberculosis often utilize host miRNAs to promote pathogenicity by restricting host-mediated antibacterial signaling pathways. At the same time, host- induced miRNAs augment antibacterial processes such as autophagy, to limit bacterial proliferation. Targeting miRNAs is an emerging option for host-directed therapies. Recent studies have explored the role of long non-coding RNA (lncRNAs) in the regulation of the host response to mycobacterial infection. Among other functions, lncRNAs interact with chromatin remodelers to regulate gene expression and also function as miRNA sponges. In this review we attempt to summarize recent literature on how miRNAs and lncRNAs are differentially expressed during the course of M. tuberculosis infection, and how they influence the outcome of infection. We also discuss the potential use of non-coding RNAs as biomarkers of active and latent tuberculosis. Comprehensive understanding of the role of these non-coding RNAs is the first step towards developing RNA-based therapeutics and diagnostic tools for the treatment of TB.
Collapse
Affiliation(s)
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, India
| |
Collapse
|
50
|
Jin L, Tang Q, Hu S, Chen Z, Zhou X, Zeng B, Wang Y, He M, Li Y, Gui L, Shen L, Long K, Ma J, Wang X, Chen Z, Jiang Y, Tang G, Zhu L, Liu F, Zhang B, Huang Z, Li G, Li D, Gladyshev VN, Yin J, Gu Y, Li X, Li M. A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription. Nat Commun 2021; 12:3715. [PMID: 34140474 PMCID: PMC8211698 DOI: 10.1038/s41467-021-23560-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of tissue specialization processes underlying economically valuable traits and accelerate their use as a biomedical model. Here we characterize four transcript types (lncRNAs, TUCPs, miRNAs, and circRNAs) and protein-coding genes in 31 adult pig tissues and two cell lines. We uncover the transcriptomic variability among 47 skeletal muscles, and six adipose depots linked to their different origins, metabolism, cell composition, physical activity, and mitochondrial pathways. We perform comparative analysis of the transcriptomes of seven tissues from pigs and nine other vertebrates to reveal that evolutionary divergence in transcription potentially contributes to lineage-specific biology. Long-range promoter–enhancer interaction analysis in subcutaneous adipose tissues across species suggests evolutionarily stable transcription patterns likely attributable to redundant enhancers buffering gene expression patterns against perturbations, thereby conferring robustness during speciation. This study can facilitate adoption of the pig as a biomedical model for human biology and disease and uncovers the molecular bases of valuable traits. A comprehensive transcriptomic survey of the pig could enable mechanistic understanding of tissue specialization and accelerate its use as a biomedical model. Here the authors characterize four distinct transcript types in 31 adult pig tissues to dissect their distinct structural and transcriptional features and uncover transcriptomic variability related to tissue physiology.
Collapse
Affiliation(s)
- Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Xuming Zhou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bo Zeng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuhao Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lixuan Gui
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Linyuan Shen
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Guoqing Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fei Liu
- Information and Educational Technology Center, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zhang
- Ya'an Digital Economy Operation Company, Ya'an, Sichuan, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guisen Li
- Renal Department and Nephrology Institute, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| |
Collapse
|