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Ranjan G, Scaria V, Sivasubbu S. Syntenic lncRNA locus exhibits DNA regulatory functions with sequence evolution. Gene 2025; 933:148988. [PMID: 39378975 DOI: 10.1016/j.gene.2024.148988] [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: 04/17/2024] [Revised: 07/12/2024] [Accepted: 10/04/2024] [Indexed: 10/10/2024]
Abstract
Syntenic long non-coding RNAs (lncRNAs) often show limited sequence conservation across species, prompting concern in the field. This study delves into functional signatures of syntenic lncRNAs between humans and zebrafish. Syntenic lncRNAs are highly expressed in zebrafish, with ∼90 % located near protein-coding genes, either in sense or antisense orientation. During early zebrafish development and in human embryonic stem cells (H1-hESC), syntenic lncRNA loci are enriched with cis-regulatory repressor signatures, influencing the expression of development-associated genes. In later zebrafish developmental stages and specific human cell lines, these syntenic lncRNA loci function as enhancers or transcription start sites (TSS) for protein-coding genes. Analysis of transposable elements (TEs) in syntenic lncRNA sequences revealed intriguing patterns: human lncRNAs are enriched in simple repeat elements, while their zebrafish counterparts show enrichment in LTR elements. This sequence evolution likely arises from post-rearrangement mutations that enhance DNA elements or cis-regulatory functions. It may also contribute to vertebrate innovation by creating novel transcription factor binding sites within the locus. This study highlights the conserved functionality of syntenic lncRNA loci through DNA elements, emphasizing their conserved roles across species despite sequence divergence.
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Affiliation(s)
- Gyan Ranjan
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Vishwanath Cancer Care Foundation, Mumbai, India.; Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Vishwanath Cancer Care Foundation, Mumbai, India.; Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
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SoundharaPandiyan N, Alphonse CRW, Thanumalaya S, Vincent SGP, Kannan RR. Genome sequencing of Caridina pseudogracilirostris and its comparative analysis with malacostracan crustaceans. 3 Biotech 2024; 14:276. [PMID: 39464522 PMCID: PMC11499489 DOI: 10.1007/s13205-024-04121-4] [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: 03/13/2023] [Accepted: 10/04/2024] [Indexed: 10/29/2024] Open
Abstract
The Caridina pseudogracilirostris is commonly found in the brackish waters of the southwestern coastal regions of India. This study provides a comprehensive genomic investigation of the shrimp species C. pseudogracilirostris, offering insights into its genetic makeup, evolutionary dynamics, and functional annotations. The genomic DNA was isolated from tissue samples, sequenced using next-generation sequencing (NGS), and stored in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (Accession No: PRJNA847710). De novo sequencing indicated a genome size of 1.31 Gbp with a low heterozygosity of about 0.81%. Repeat masking and annotation revealed that repeated elements constitute 24.60% of the genome, with simple sequence repeats (SSRs) accounting for 7.26%. Gene prediction identified 14,101 genes, with functional annotations indicating involvement in critical biological processes such as development, cellular function, immunological responses, and reproduction. Furthermore, phylogenetic analysis revealed genomic links among Malacostraca species, indicating gene duplication as a strategy for genetic diversity and adaptation. C. pseudogracilirostris has 1,856 duplicated genes, reflecting a distinct genomic architecture and evolutionary strategy within the Malacostraca branch. These findings enhance our understanding of the genetic characteristics and evolutionary relationships of C. pseudogracilirostris, providing significant insights into the overall evolutionary dynamics of the Malacostraca group. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04121-4.
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Affiliation(s)
- NandhaGopal SoundharaPandiyan
- Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu 600119 India
| | - Carlton Ranjith Wilson Alphonse
- Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu 600119 India
| | | | | | - Rajaretinam Rajesh Kannan
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Plot No, 32, 34, Knowledge Park III, Greater Noida, Uttar Pradesh 201306 India
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Souza TBD, Parteka LM, Kuo YT, Nascimento T, Schubert V, Pedrosa-Harand A, Marques A, Houben A, Vanzela ALL. Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges ( Eleocharis, Cyperaceae). Genome 2024. [PMID: 39284229 DOI: 10.1139/gen-2024-0089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
Eleocharis R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. High intra- and interspecific variations in chromosome numbers and genome sizes are documented for different Eleocharis species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in this genus. In our study, we confirmed the holocentricity of Eleocharis chromosomes by immunostaining against the kinetochore protein KNL1 and the cell-cycle dependent posttranslational modifications histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in the newly sequenced species Eleocharis maculosa, Eleocharis geniculata, Eleocharis parodii, Eleocharis elegans, and Eleocharis montana. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was distributed irregularly along the chromatid length in a line-like manner. EmaSAT14 monomers were present in a few copies in few species across the Eleocharis phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus Eleocharis. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.
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Affiliation(s)
- Thaíssa Boldieri de Souza
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570 Paraná, Brazil
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Letícia Maria Parteka
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570 Paraná, Brazil
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Yi-Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Thiago Nascimento
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife-PE, Brazil
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife-PE, Brazil
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - André Luís Laforga Vanzela
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570 Paraná, Brazil
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Fukuda K. The role of transposable elements in human evolution and methods for their functional analysis: current status and future perspectives. Genes Genet Syst 2024; 98:289-304. [PMID: 37866889 DOI: 10.1266/ggs.23-00140] [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] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) are mobile DNA sequences that can insert themselves into various locations within the genome, causing mutations that may provide advantages or disadvantages to individuals and species. The insertion of TEs can result in genetic variation that may affect a wide range of human traits including genetic disorders. Understanding the role of TEs in human biology is crucial for both evolutionary and medical research. This review discusses the involvement of TEs in human traits and disease susceptibility, as well as methods for functional analysis of TEs.
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Affiliation(s)
- Kei Fukuda
- Integrative Genomics Unit, The University of Melbourne
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Mendez-Dorantes C, Burns KH. LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities. Genes Dev 2023; 37:948-967. [PMID: 38092519 PMCID: PMC10760644 DOI: 10.1101/gad.351051.123] [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] [Indexed: 12/28/2023]
Abstract
Long interspersed element 1 (LINE-1) is the only protein-coding transposon that is active in humans. LINE-1 propagates in the genome using RNA intermediates via retrotransposition. This activity has resulted in LINE-1 sequences occupying approximately one-fifth of our genome. Although most copies of LINE-1 are immobile, ∼100 copies are retrotransposition-competent. Retrotransposition is normally limited via epigenetic silencing, DNA repair, and other host defense mechanisms. In contrast, LINE-1 overexpression and retrotransposition are hallmarks of cancers. Here, we review mechanisms of LINE-1 regulation and how LINE-1 may promote genetic heterogeneity in tumors. Finally, we discuss therapeutic strategies to exploit LINE-1 biology in cancers.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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Lin Y, Darolti I, van der Bijl W, Morris J, Mank JE. Extensive variation in germline de novo mutations in Poecilia reticulata. Genome Res 2023; 33:1317-1324. [PMID: 37442578 PMCID: PMC10547258 DOI: 10.1101/gr.277936.123] [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: 03/30/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023]
Abstract
The rate of germline mutation is fundamental to evolutionary processes, as it generates the variation upon which selection acts. The guppy, Poecilia reticulata, is a model of rapid adaptation, however the relative contribution of standing genetic variation versus de novo mutation (DNM) to evolution in this species remains unclear. Here, we use pedigree-based approaches to quantify and characterize germline DNMs in three large guppy families. Our results suggest germline mutation rate in the guppy varies substantially across individuals and families. Most DNMs are shared across multiple siblings, suggesting they arose during early embryonic development. DNMs are randomly distributed throughout the genome, and male-biased mutation rate is low, as would be expected from the short guppy generation time. Overall, our study shows remarkable variation in germline mutation rate and provides insights into rapid evolution of guppies.
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Affiliation(s)
- Yuying Lin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada;
| | - Iulia Darolti
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Wouter van der Bijl
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jake Morris
- School of Biological Science, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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7
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Jin D, Li C, Chen X, Byerly A, Stover NA, Zhang T, Shao C, Wang Y. Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:300-315. [PMID: 37637252 PMCID: PMC10449743 DOI: 10.1007/s42995-023-00175-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/12/2023] [Indexed: 08/29/2023]
Abstract
One of the most diverse clades of ciliated protozoa, the class Spirotrichea, displays a series of unique characters in terms of eukaryotic macronuclear (MAC) genome, including high fragmentation that produces nanochromosomes. However, the genomic diversity and evolution of nanochromosomes and gene families for spirotrich MAC genomes are poorly understood. In this study, we assemble the MAC genome of a representative euplotid (a new model organism in Spirotrichea) species, Euplotes aediculatus. Our results indicate that: (a) the MAC genome includes 35,465 contigs with a total length of 97.3 Mb and a contig N50 of 3.4 kb, and contains 13,145 complete nanochromosomes and 43,194 predicted genes, with the majority of these nanochromosomes containing tiny introns and harboring only one gene; (b) genomic comparisons between E. aediculatus and other reported spirotrichs indicate that average GC content and genome fragmentation levels exhibit interspecific variation, and chromosome breaking sites (CBSs) might be lost during evolution, resulting in the increase of multi-gene nanochromosome; (c) gene families associated with chitin metabolism and FoxO signaling pathway are expanded in E. aediculatus, suggesting their potential roles in environment adaptation and survival strategies of E. aediculatus; and (d) a programmed ribosomal frameshift (PRF) with a conservative motif 5'-AAATAR-3' tends to occur in longer genes with more exons, and PRF genes play an important role in many cellular regulation processes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00175-0.
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Affiliation(s)
- Didi Jin
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
| | - Chao Li
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
| | - Adam Byerly
- Department of Computer Science and Information Systems, Bradley University, Peoria, 61625 USA
| | - Naomi A. Stover
- Department of Biology, Bradley University, Peoria, 61625 USA
| | - Tengteng Zhang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
| | - Chen Shao
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
| | - Yurui Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
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Korotkov E, Suvorova Y, Kostenko D, Korotkova M. Search for Dispersed Repeats in Bacterial Genomes Using an Iterative Procedure. Int J Mol Sci 2023; 24:10964. [PMID: 37446142 DOI: 10.3390/ijms241310964] [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: 06/11/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
We have developed a de novo method for the identification of dispersed repeats based on the use of random position-weight matrices (PWMs) and an iterative procedure (IP). The created algorithm (IP method) allows detection of dispersed repeats for which the average number of substitutions between any two repeats per nucleotide (x) is less than or equal to 1.5. We have shown that all previously developed methods and algorithms (RED, RECON, and some others) can only find dispersed repeats for x ≤ 1.0. We applied the IP method to find dispersed repeats in the genomes of E. coli and nine other bacterial species. We identify three families of approximately 1.09 × 106, 0.64 × 106, and 0.58 × 106 DNA bases, respectively, constituting almost 50% of the complete E. coli genome. The length of the repeats is in the range of 400 to 600 bp. Other analyzed bacterial genomes contain one to three families of dispersed repeats with a total number of 103 to 6 × 103 copies. The existence of such highly divergent repeats could be associated with the presence of a single-type triplet periodicity in various genes or with the packing of bacterial DNA into a nucleoid.
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Affiliation(s)
- Eugene Korotkov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld. 2, 33 Leninsky Ave., 119071 Moscow, Russia
| | - Yulia Suvorova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld. 2, 33 Leninsky Ave., 119071 Moscow, Russia
| | - Dimitry Kostenko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld. 2, 33 Leninsky Ave., 119071 Moscow, Russia
| | - Maria Korotkova
- Moscow Engineering Physics Institute, National Research Nuclear University MEPhI, 31 Kashirskoye Shosse, 115409 Moscow, Russia
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Nip Y, Bennett SR, Smith AA, Jones TI, Jones PL, Tapscott SJ. Human DUX4 and porcine DUXC activate similar early embryonic programs in pig muscle cells: implications for preclinical models of FSHD. Hum Mol Genet 2023; 32:1864-1874. [PMID: 36728804 PMCID: PMC10196675 DOI: 10.1093/hmg/ddad021] [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: 08/29/2022] [Revised: 01/10/2023] [Accepted: 01/29/2023] [Indexed: 02/03/2023] Open
Abstract
Human DUX4 and its mouse ortholog Dux are normally expressed in the early embryo-the 4-cell or 2-cell cleavage stage embryo, respectively-and activate a portion of the first wave of zygotic gene expression. DUX4 is epigenetically suppressed in nearly all somatic tissue, whereas facioscapulohumeral dystrophy (FSHD)-causing mutations result in its aberrant expression in skeletal muscle, transcriptional activation of the early embryonic program and subsequent muscle pathology. Although DUX4 and Dux both activate an early totipotent transcriptional program, divergence of their DNA binding domains limits the use of DUX4 expressed in mice as a preclinical model for FSHD. In this study, we identify the porcine DUXC messenger ribonucleic acid expressed in early development and show that both pig DUXC and human DUX4 robustly activate a highly similar early embryonic program in pig muscle cells. These results support further investigation of pig preclinical models for FSHD.
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Affiliation(s)
- Yee Nip
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sean R Bennett
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew A Smith
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Takako I Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Peter L Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Neurology, University of Washington School of Medicine, Seattle, WA 98105, USA
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Hubley R, Wheeler TJ, Smit AFA. Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families. NAR Genom Bioinform 2022; 4:lqac040. [PMID: 35591887 PMCID: PMC9112768 DOI: 10.1093/nargab/lqac040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/29/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
The construction of a high-quality multiple sequence alignment (MSA) from copies of a transposable element (TE) is a critical step in the characterization of a new TE family. Most studies of MSA accuracy have been conducted on protein or RNA sequence families, where structural features and strong signals of selection may assist with alignment. Less attention has been given to the quality of sequence alignments involving neutrally evolving DNA sequences such as those resulting from TE replication. Transposable element sequences are challenging to align due to their wide divergence ranges, fragmentation, and predominantly-neutral mutation patterns. To gain insight into the effects of these properties on MSA accuracy, we developed a simulator of TE sequence evolution, and used it to generate a benchmark with which we evaluated the MSA predictions produced by several popular aligners, along with Refiner, a method we developed in the context of our RepeatModeler software. We find that MAFFT and Refiner generally outperform other aligners for low to medium divergence simulated sequences, while Refiner is uniquely effective when tasked with aligning high-divergent and fragmented instances of a family.
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Affiliation(s)
- Robert Hubley
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Travis J Wheeler
- Department of Computer Science, University of Montana, Missoula, MT 59801, USA
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Genes and evolutionary fates of the amanitin biosynthesis pathway in poisonous mushrooms. Proc Natl Acad Sci U S A 2022; 119:e2201113119. [PMID: 35533275 PMCID: PMC9171917 DOI: 10.1073/pnas.2201113119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Why do unrelated poisonous mushrooms (Amanita, Galerina, and Lepiota) make the same deadly toxin, α-amanitin? One of the most effective and fast strategies for organisms to acquire new abilities is through horizontal gene transfer (HGT). With the help of genome sequencing and the finding of two genes for the amanitin biosynthetic pathway, we demonstrate that the pathway distribution resulted from HGT probably through an unknown ancestral fungal donor. In Amanita mushrooms, the pathway evolved, through a series of gene manipulations, to produce very high levels of toxins, generating “the deadliest mushroom known to mankind.” The deadly toxin α-amanitin is a bicyclic octapeptide biosynthesized on ribosomes. A phylogenetically disjunct group of mushrooms in Agaricales (Amanita, Lepiota, and Galerina) synthesizes α-amanitin. This distribution of the toxin biosynthetic pathway is possibly related to the horizontal transfer of metabolic gene clusters among taxonomically unrelated mushrooms with overlapping habitats. Here, our work confirms that two biosynthetic genes, P450-29 and FMO1, are oxygenases important for amanitin biosynthesis. Phylogenetic and genetic analyses of these genes strongly support their origin through horizontal transfer, as is the case for the previously characterized biosynthetic genes MSDIN and POPB. Our analysis of multiple genomes showed that the evolution of the α-amanitin biosynthetic pathways in the poisonous agarics in the Amanita, Lepiota, and Galerina clades entailed distinct evolutionary pathways including gene family expansion, biosynthetic genes, and genomic rearrangements. Unrelated poisonous fungi produce the same deadly amanitin toxins using variations of the same pathway. Furthermore, the evolution of the amanitin biosynthetic pathway(s) in Amanita species generates a much wider range of toxic cyclic peptides. The results reported here expand our understanding of the genetics, diversity, and evolution of the toxin biosynthetic pathway in fungi.
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Storer JM, Hubley R, Rosen J, Smit AFA. Methodologies for the De novo Discovery of Transposable Element Families. Genes (Basel) 2022; 13:709. [PMID: 35456515 PMCID: PMC9025800 DOI: 10.3390/genes13040709] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023] Open
Abstract
The discovery and characterization of transposable element (TE) families are crucial tasks in the process of genome annotation. Careful curation of TE libraries for each organism is necessary as each has been exposed to a unique and often complex set of TE families. De novo methods have been developed; however, a fully automated and accurate approach to the development of complete libraries remains elusive. In this review, we cover established methods and recent developments in de novo TE analysis. We also present various methodologies used to assess these tools and discuss opportunities for further advancement of the field.
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Affiliation(s)
| | | | | | - Arian F. A. Smit
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.M.S.); (R.H.); (J.R.)
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Liu S, Cheng H, Ashraf J, Zhang Y, Wang Q, Lv L, He M, Song G, Zuo D. Interpretation of convolutional neural networks reveals crucial sequence features involving in transcription during fiber development. BMC Bioinformatics 2022; 23:91. [PMID: 35291940 PMCID: PMC8922751 DOI: 10.1186/s12859-022-04619-9] [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: 03/16/2021] [Accepted: 02/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upland cotton provides the most natural fiber in the world. During fiber development, the quality and yield of fiber were influenced by gene transcription. Revealing sequence features related to transcription has a profound impact on cotton molecular breeding. We applied convolutional neural networks to predict gene expression status based on the sequences of gene transcription start regions. After that, a gradient-based interpretation and an N-adjusted kernel transformation were implemented to extract sequence features contributing to transcription. RESULTS Our models had approximate 80% accuracies, and the area under the receiver operating characteristic curve reached over 0.85. Gradient-based interpretation revealed 5' untranslated region contributed to gene transcription. Furthermore, 6 DOF binding motifs and 4 transcription activator binding motifs were obtained by N-adjusted kernel-motif transformation from models in three developmental stages. Apart from 10 general motifs, 3 DOF5.1 genes were also detected. In silico analysis about these motifs' binding proteins implied their potential functions in fiber formation. Besides, we also found some novel motifs in plants as important sequence features for transcription. CONCLUSIONS In conclusion, the N-adjusted kernel transformation method could interpret convolutional neural networks and reveal important sequence features related to transcription during fiber development. Potential functions of motifs interpreted from convolutional neural networks could be validated by further wet-lab experiments and applied in cotton molecular breeding.
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Affiliation(s)
- Shang Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hailiang Cheng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Javaria Ashraf
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Punjab, 63100, Pakistan
| | - Youping Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Qiaolian Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Limin Lv
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Man He
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Guoli Song
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Dongyun Zuo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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14
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PRDM9-directed recombination hotspots depleted near meiotically transcribed genes. Gene 2021; 813:146123. [PMID: 34952174 DOI: 10.1016/j.gene.2021.146123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/22/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022]
Abstract
PRDM9 drives recombination hotspots in some mammals, including mice and apes. Non-functional orthologs of PRDM9 are present in a wide variety of vertebrates, but why it is functionally maintained in some lineages is not clear. One possible explanation is that PRDM9 plays a role in ensuring that meiosis is successful. During meiosis, available DNA may be a limiting resource given the tight packaging of chromosomes and could lead to competition between two key processes: meiotic transcription and recombination. Here we explore this potential competition and the role that PRDM9 might play in their interaction. Leveraging existing mouse genomic data, we use resampling schemes that simulate shuffled features along the genome and models that account for the rarity of features in the genome, to test if PRDM9 influences interactions between recombination hotspots and meiotic transcription in a whole genome framework. We also explored possible DNA sequence motifs associated to clusters of hotspots not tied to transcription or PRDM9. We find evidence of competition between meiotic transcription and recombination, with PRDM9 appearing to relocate recombination to avoid said conflict. We also find that retrotransposons may be playing a role in directing hotspots in the absence of other factors.
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15
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Takahashi O, Tanahashi M, Yokoi S, Kaneko M, Yanaka K, Nakagawa S, Maita H. The cell type-specific ER membrane protein UGS148 is not essential in mice. Genes Cells 2021; 27:43-60. [PMID: 34897904 DOI: 10.1111/gtc.12910] [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: 09/30/2021] [Revised: 11/30/2021] [Accepted: 12/09/2021] [Indexed: 12/01/2022]
Abstract
Genomes of higher eukaryotes encode many uncharacterized proteins, and the functions of these proteins cannot be predicted from the primary sequences due to a lack of conserved functional domains. In this study, we focused on a poorly characterized protein UGS148 that is highly expressed in a specialized cell type called tanycytes that line the ventral wall of the third ventricle in the hypothalamus. Immunostaining of UGS148 revealed the fine morphology of tanycytes with highly branched apical ER membranes. Immunoprecipitation revealed that UGS148 associated with mitochondrial ATPase at least in vitro, and ER and mitochondrial signals occasionally overlapped in tanycytes. Mutant mice lacking UGS148 did not exhibit overt phenotypes, suggesting that UGS148 was not essential in mice reared under normal laboratory conditions. We also found that RNA probes that were predicted to uniquely detect UGS148 mRNA cross-reacted with uncharacterized RNAs, highlighting the importance of experimental validation of the specificity of probes during the hybridization-based study of RNA localization.
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Affiliation(s)
- Osamu Takahashi
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Mayuko Tanahashi
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Saori Yokoi
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Kaori Yanaka
- Liver Cancer Prevention Research Unit, RIKEN, Wako, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hiroshi Maita
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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16
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Ahmed Z, Renart EG, Zeeshan S. Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping. PeerJ 2021; 9:e11724. [PMID: 34395068 PMCID: PMC8320519 DOI: 10.7717/peerj.11724] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics applications have been developed, and many of those are freely available and published. Timely finding and interpreting genetic variants are still challenging tasks among diagnostic laboratories and clinicians. In this study, we are interested in understanding, evaluating, and reporting the current state of solutions available to process the NGS data of variable lengths and types for the identification of variants, alleles, and haplotypes. Residing within the scope, we consulted high quality peer reviewed literature published in last 10 years. We were focused on the standalone and networked bioinformatics applications proposed to efficiently process WGS and WES data, and support downstream analysis for gene-variant discovery, annotation, prediction, and interpretation. We have discussed our findings in this manuscript, which include but not are limited to the set of operations, workflow, data handling, involved tools, technologies and algorithms and limitations of the assessed applications.
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Affiliation(s)
- Zeeshan Ahmed
- Institute for Health, Health Care Policy and Aging Research, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Eduard Gibert Renart
- Institute for Health, Health Care Policy and Aging Research, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Saman Zeeshan
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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17
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Yang N, Zhao B, Chen Y, D'Alessandro E, Chen C, Ji T, Wu X, Song C. Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus). Genome Biol Evol 2021; 13:6322960. [PMID: 34270728 PMCID: PMC8346653 DOI: 10.1093/gbe/evab168] [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] [Accepted: 07/12/2021] [Indexed: 12/22/2022] Open
Abstract
Although the rabbit genome has already been annotated, it is mobilome remains largely unknown. Here, multiple pipelines were used to de novo mine and annotate the mobilome in rabbit. Four families and 19 subfamilies of LINE1s, two families and nine subfamilies of SINEs, and 12 ERV families were defined in rabbit based on sequence identity, structural organization, and phylogenetic tree. The analysis of insertion age and polymerase chain reaction suggests that a number of families are very young and may remain active, such as L1B, L1D, OcuSINEA, and OcuERV1. RepeatMasker annotation revealed a distinct transposable element landscape within the genome, with approximately two million copies of SINEs, representing the greatest proportion of the genome (19.61%), followed by LINEs (15.44%), and LTRs (4.11%), respectively, considerably different from most other mammal mobilomes except hedgehog and tree shrew, in which LINEs have the highest proportion. Furthermore, a very high rate of insertion polymorphisms (>85%) for the youngest subfamily (OcuSINEA1) was identified by polymerase chain reaction. The majority of retrotransposon insertions overlapped with protein-coding regions (>80%) and lncRNA (90%) genes. Genomic distribution bias was observed for retrotransposons, with those immediately upstream (-1 kb) and downstream (1 kb) of genes significantly depleted. Local GC content in 50-kb widows had significantly negative correlations with LINE (rs=-0.996) and LTR (rs=-0.829) insertions. The current study revealed a distinct mobilome landscape in rabbit, which will assist in the elucidation of the evolution of the genome of lagomorphs, and even other mammals.
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Affiliation(s)
- Naisu Yang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Bohao Zhao
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Yang Chen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | | | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Ting Ji
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Xinsheng Wu
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
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18
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Pérez RF, Tejedor JR, Santamarina-Ojeda P, Martínez VL, Urdinguio RG, Villamañán L, Candiota AP, Sarró NMV, Barradas M, Fernandez-Marcos PJ, Serrano M, Fernández AF, Fraga MF. Conservation of Aging and Cancer Epigenetic Signatures across Human and Mouse. Mol Biol Evol 2021; 38:3415-3435. [PMID: 33871658 PMCID: PMC8321527 DOI: 10.1093/molbev/msab112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aging and cancer are two interrelated processes, with aging being a major risk factor for the development of cancer. Parallel epigenetic alterations have been described for both, although differences, especially within the DNA hypomethylation scenario, have also been recently reported. Although many of these observations arise from the use of mouse models, there is a lack of systematic comparisons of human and mouse epigenetic patterns in the context of disease. However, such comparisons are significant as they allow to establish the extent to which some of the observed similarities or differences arise from pre-existing species-specific epigenetic traits. Here, we have used reduced representation bisulfite sequencing to profile the brain methylomes of young and old, tumoral and nontumoral brain samples from human and mouse. We first characterized the baseline epigenomic patterns of the species and subsequently focused on the DNA methylation alterations associated with cancer and aging. Next, we described the functional genomic and epigenomic context associated with the alterations, and finally, we integrated our data to study interspecies DNA methylation levels at orthologous CpG sites. Globally, we found considerable differences between the characteristics of DNA methylation alterations in cancer and aging in both species. Moreover, we describe robust evidence for the conservation of the specific cancer and aging epigenomic signatures in human and mouse. Our observations point toward the preservation of the functional consequences of these alterations at multiple levels of genomic regulation. Finally, our analyses reveal a role for the genomic context in explaining disease- and species-specific epigenetic traits.
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Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Pablo Santamarina-Ojeda
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Virginia López Martínez
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Lucía Villamañán
- Unitat de Bioquímica de Biociències, Departament de Bioquímica i Biologia Molecular, Edifici Cs, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ana Paula Candiota
- Unitat de Bioquímica de Biociències, Departament de Bioquímica i Biologia Molecular, Edifici Cs, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - N Mí Vidal Sarró
- Servicio Anatomía Patológica, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Spain
| | - Marta Barradas
- Metabolic Syndrome Group-BIOPROMET, Madrid Institute for Advanced Studies-IMDEA Food, CEI UAM+CSIC, Madrid, Spain
| | - Pablo Jose Fernandez-Marcos
- Metabolic Syndrome Group-BIOPROMET, Madrid Institute for Advanced Studies-IMDEA Food, CEI UAM+CSIC, Madrid, Spain
| | - Manuel Serrano
- Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Cellular Plasticity and Disease Group, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Agusín F Fernández
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Mario F Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
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19
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Ansere VA, Ali-Mondal S, Sathiaseelan R, Garcia DN, Isola JVV, Henseb JD, Saccon TD, Ocañas SR, Tooley KB, Stout MB, Schneider A, Freeman WM. Cellular hallmarks of aging emerge in the ovary prior to primordial follicle depletion. Mech Ageing Dev 2021; 194:111425. [PMID: 33383072 PMCID: PMC8279026 DOI: 10.1016/j.mad.2020.111425] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/02/2020] [Accepted: 12/22/2020] [Indexed: 01/10/2023]
Abstract
Decline in ovarian reserve with advancing age is associated with reduced fertility and the emergence of metabolic disturbances, osteoporosis, and neurodegeneration. Recent studies have provided insight into connections between ovarian insufficiency and systemic aging, although the basic mechanisms that promote ovarian reserve depletion remain unknown. Here, we sought to determine if chronological age is linked to changes in ovarian cellular senescence, transcriptomic, and epigenetic mechanisms in a mouse model. Histological assessments and transcriptional analyses revealed the accumulation of lipofuscin aggresomes and senescence-related transcripts (Cdkn1a, Cdkn2a, Pai-1 and Hmgb1) significantly increased with advancing age. Transcriptomic profiling and pathway analyses following RNA sequencing, revealed an upregulation of genes related to pro-inflammatory stress and cell-cycle inhibition, whereas genes involved in cell-cycle progression were downregulated; which could be indicative of senescent cell accumulation. The emergence of these senescence-related markers preceded the dramatic decline in primordial follicle reserve observed. Whole Genome Oxidative Bisulfite Sequencing (WGoxBS) found no genome-wide or genomic context-specific DNA methylation and hydroxymethylation changes with advancing age. These findings suggest that cellular senescence may contribute to ovarian aging, and thus, declines in ovarian follicular reserve. Cell-type-specific analyses across the reproductive lifespan are needed to fully elucidate the mechanisms that promote ovarian insufficiency.
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Affiliation(s)
- Victor A Ansere
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Samim Ali-Mondal
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Roshini Sathiaseelan
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Driele N Garcia
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - José V V Isola
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jéssica D Henseb
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Tatiana D Saccon
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael B Stout
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Willard M Freeman
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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20
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Storer J, Hubley R, Rosen J, Wheeler TJ, Smit AF. The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob DNA 2021; 12:2. [PMID: 33436076 PMCID: PMC7805219 DOI: 10.1186/s13100-020-00230-y] [Citation(s) in RCA: 286] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/28/2020] [Indexed: 02/02/2023] Open
Abstract
Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0-3.3 releases of Dfam ( https://dfam.org ) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam's new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.
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Affiliation(s)
| | - Robert Hubley
- Institute for Systems Biology, Seattle, WA, 98109, USA.
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Arian F Smit
- Institute for Systems Biology, Seattle, WA, 98109, USA.
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21
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Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation. Genes (Basel) 2020; 11:genes11111241. [PMID: 33105659 PMCID: PMC7716205 DOI: 10.3390/genes11111241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/10/2020] [Accepted: 10/20/2020] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can “jump” and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10−6% to 5.63 × 10−2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.
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22
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Bogema DR, Yam J, Micallef ML, Gholipourkanani H, Go J, Jenkins C, Dang C. Draft genomes of Perkinsus olseni and Perkinsus chesapeaki reveal polyploidy and regional differences in heterozygosity. Genomics 2020; 113:677-688. [PMID: 33017625 DOI: 10.1016/j.ygeno.2020.09.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022]
Abstract
Perkinsus spp. parasites have significant impact on aquaculture and wild mollusc populations. We sequenced the genomes of five monoclonal isolates of Perkinsus olseni and one Perkinsus chesapeaki from international sources. Sequence analysis revealed similar levels of repetitive sequence within species, a polyploid genome structure, and substantially higher heterozygosity in Oceanian-sourced isolates. We also identified tandem replication of the rRNA transcriptional unit, with high strain variation. Characterized gene content was broadly similar amongst all Perkinsus spp. but P. olseni Oceanian isolates contained an elevated number of genes compared to other P. olseni isolates and cox3 could not be identified in any Perkinsus spp. sequence. Phylogenetics and average nucleotide identity scans were consistent with all P. olseni isolates being within one species. These are the first genome sequences generated for both P. olseni and P. chesapeaki and will allow future advances in diagnostic design and population genomics of these important aquatic parasites.
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Affiliation(s)
- Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia.
| | - Jerald Yam
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia; The Ithree Institute, University of Technology Sydney, NSW 2007, Australia
| | - Melinda L Micallef
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Hosna Gholipourkanani
- Department of Primary Industries and Regional Development, Government of Western Australia, Perth, WA, Australia
| | - Jeffrey Go
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Cheryl Jenkins
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Cecile Dang
- Department of Primary Industries and Regional Development, Government of Western Australia, Perth, WA, Australia
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23
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Gao GF, Parker JS, Reynolds SM, Silva TC, Wang LB, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z, Liang H, Noble MS. Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data. Cell Syst 2020; 9:24-34.e10. [PMID: 31344359 DOI: 10.1016/j.cels.2019.06.006] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/18/2019] [Accepted: 06/13/2019] [Indexed: 01/09/2023]
Abstract
We present a systematic analysis of the effects of synchronizing a large-scale, deeply characterized, multi-omic dataset to the current human reference genome, using updated software, pipelines, and annotations. For each of 5 molecular data platforms in The Cancer Genome Atlas (TCGA)-mRNA and miRNA expression, single nucleotide variants, DNA methylation and copy number alterations-comprehensive sample, gene, and probe-level studies were performed, towards quantifying the degree of similarity between the 'legacy' GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as 'harmonized' by the Genomic Data Commons. We offer gene lists to elucidate differences that remained after controlling for confounders, and strategies to mitigate their impact on biological interpretation. Our results demonstrate that the hg19 and hg38 TCGA datasets are very highly concordant, promote informed use of either legacy or harmonized omics data, and provide a rubric that encourages similar comparisons as new data emerge and reference data evolve.
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Affiliation(s)
- Galen F Gao
- Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; The University of Texas Southwestern Medical School, Dallas, TX 75390, USA
| | - Joel S Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Tiago C Silva
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14.040-905, Brazil
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Bailey
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Saianand Balu
- Lineberger Comprehensive Cancer Center, Bioinformatics Core, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Faculty of Medicine, Department of Developmental Biology and Cancer Research, the Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Denise Brooks
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Hu Chen
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew D Cherniack
- Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Li Ding
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Ina Felau
- National Cancer Institute, Bethesda, MD 20892, USA
| | - Sharon Gaheen
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | | | - David I Heiman
- Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Kyle M Hernandez
- Department of Pediatrics, the University of Chicago, Chicago, IL 60637, USA; Center for Research Informatics, the University of Chicago, Chicago, IL 60637, USA
| | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Reyka Jayasinghe
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Anab Kemal
- National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | - Zhining Wang
- National Cancer Institute, Bethesda, MD 20892, USA
| | - Matthew Wyczalkowski
- Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA
| | - Liming Yang
- National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Zhenyu Zhang
- Center for Translational Data Science, the University of Chicago, Chicago, IL 60615, USA
| | | | - Han Liang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Systems Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Michael S Noble
- Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
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24
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Zhuang QKW, Galvez JH, Xiao Q, AlOgayil N, Hyacinthe J, Taketo T, Bourque G, Naumova AK. Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver. Cells 2020; 9:E1436. [PMID: 32527045 PMCID: PMC7349295 DOI: 10.3390/cells9061436] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Sex biases in the genome-wide distribution of DNA methylation and gene expression levels are some of the manifestations of sexual dimorphism in mammals. To advance our understanding of the mechanisms that contribute to sex biases in DNA methylation and gene expression, we conducted whole genome bisulfite sequencing (WGBS) as well as RNA-seq on liver samples from mice with different combinations of sex phenotype and sex-chromosome complement. We compared groups of animals with different sex phenotypes, but the same genetic sexes, and vice versa, same sex phenotypes, but different sex-chromosome complements. We also compared sex-biased DNA methylation in mouse and human livers. Our data show that sex phenotype, X-chromosome dosage, and the presence of Y chromosome shape the differences in DNA methylation between males and females. We also demonstrate that sex bias in autosomal methylation is associated with sex bias in gene expression, whereas X-chromosome dosage-dependent methylation differences are not, as expected for a dosage-compensation mechanism. Furthermore, we find partial conservation between the repertoires of mouse and human genes that are associated with sex-biased methylation, an indication that gene function is likely to be an important factor in this phenomenon.
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Affiliation(s)
- Qinwei Kim-Wee Zhuang
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
| | - Jose Hector Galvez
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada;
| | - Qian Xiao
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA;
| | - Najla AlOgayil
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
| | - Jeffrey Hyacinthe
- Department of Quantitative Life Sciences, McGill University, Montréal, QC H3A 0G4, Canada;
| | - Teruko Taketo
- The Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada;
- Department of Surgery, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada;
| | - Anna K. Naumova
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
- The Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada;
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC H4A 3J1, Canada
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25
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Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet 2020; 16:e1008742. [PMID: 32392208 PMCID: PMC7241854 DOI: 10.1371/journal.pgen.1008742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 05/21/2020] [Accepted: 03/27/2020] [Indexed: 01/01/2023] Open
Abstract
The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources of genomic diversity within and between species and a widely recognized cause of inter-individual differences in disease risk. However, copy number differences among rhesus macaques and between the human and macaque genomes, as well as the relevance of this diversity to research involving this nonhuman primate, remain understudied. Here we present a high-resolution map of sequence copy number for the rhesus macaque genome constructed from a dataset of 198 individuals. Our results show that about one-eighth of the rhesus macaque reference genome is composed of recently duplicated regions, either copy number variable regions or fixed duplications. Comparison with human genomic copy number maps based on previously published data shows that, despite overall similarities in the genome-wide distribution of these regions, there are specific differences at the chromosome level. Some of these create differences in the copy number profile between human disease genes and their rhesus macaque orthologs. Our results highlight the importance of addressing the number of copies of target genes in the design of experiments and cautions against human-centered assumptions in research conducted with model organisms. Overall, we present a genome-wide copy number map from a large sample of rhesus macaque individuals representing an important novel contribution concerning the evolution of copy number in primate genomes.
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Affiliation(s)
- Marina Brasó-Vives
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Inna S. Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Diego A. Hartasánchez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Xavier Farré
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Marcos Fernandez-Callejo
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Douglas L. Rosene
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Belen Lorente-Galdos
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- National Institute for Bioinformatics (INB), Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
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26
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Li C, Huang R, Nie F, Li J, Zhu W, Shi X, Guo Y, Chen Y, Wang S, Zhang L, Chen L, Li R, Liu X, Zheng C, Zhang C, Ma RZ. Organization of the Addax Major Histocompatibility Complex Provides Insights Into Ruminant Evolution. Front Immunol 2020; 11:260. [PMID: 32161588 PMCID: PMC7053375 DOI: 10.3389/fimmu.2020.00260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/31/2020] [Indexed: 12/22/2022] Open
Abstract
Ruminants are critical as prey in transferring solar energy fixed by plants into carnivorous species, yet the genetic signature of the driving forces leading to the evolutionary success of the huge number of ruminant species remains largely unknown. Here we report a complete DNA map of the major histocompatibility complex (MHC) of the addax (Addax nasomaculatus) genome by sequencing a total of 47 overlapping BAC clones previously mapped to cover the MHC region. The addax MHC is composed of 3,224,151 nucleotides, harboring a total of 150 coding genes, 50 tRNA genes, and 14 non-coding RNA genes. The organization of addax MHC was found to be highly conserved to those of sheep and cattle, highlighted by a large piece of chromosome inversion that divided the MHC class II into IIa and IIb subregions. It is now highly possible that all of the ruminant species in the family of Bovidae carry the same chromosome inversion in the MHC region, inherited from a common ancestor of ruminants. Phylogenetic analysis indicated that DY, a ruminant-specific gene located at the boundary of the inversion and highly expressed in dendritic cells, was possibly evolved from DQ, with an estimated divergence time ~140 million years ago. Homology modeling showed that the overall predicted structure of addax DY was similar to that of HLA-DQ2. However, the pocket properties of P1, P4, P6, and P9, which were critical for antigen binding in the addax DY, showed certain distinctive features. Structural analysis suggested that the populations of peptide antigens presented by addax DY and HLA-DQ2 were quite diverse, which in theory could serve to promote microbial regulation in the rumen by ruminant species, contributing to enhanced grass utilization ability. In summary, the results of our study helped to enhance our understanding of the MHC evolution and provided additional supportive evidence to our previous hypothesis that an ancient chromosome inversion in the MHC region of the last common ancestor of ruminants may have contributed to the evolutionary success of current ruminants on our planet.
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Affiliation(s)
- Chaokun Li
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Rui Huang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fangyuan Nie
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiujie Li
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Zhu
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoqian Shi
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yu Guo
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chen
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shiyu Wang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Limeng Zhang
- Molecular Biology Laboratory of Zhengzhou Normal University, Zhengzhou, China
| | - Longxin Chen
- Molecular Biology Laboratory of Zhengzhou Normal University, Zhengzhou, China
| | - Runting Li
- Molecular Biology Laboratory of Zhengzhou Normal University, Zhengzhou, China
| | - Xuefeng Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Changming Zheng
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Runlin Z Ma
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Molecular Biology Laboratory of Zhengzhou Normal University, Zhengzhou, China
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27
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Pan B, Chen X, Hou L, Zhang Q, Qu Z, Warren A, Miao M. Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage. Front Microbiol 2019; 10:2819. [PMID: 31921016 PMCID: PMC6920121 DOI: 10.3389/fmicb.2019.02819] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/20/2019] [Indexed: 11/13/2022] Open
Abstract
Ciliated protists (ciliates) are widely used for investigating evolution, mostly due to their successful radiation after their early evolutionary branching. In this study, we employed high-throughput sequencing technology to reveal the phylogenetic position of Synhymenia, as well as two classes Nassophorea and Phyllopharyngea, which have been a long-standing puzzle in the field of ciliate systematics and evolution. We obtained genomic and transcriptomic data from single cells of one synhymenian (Chilodontopsis depressa) and six other species of phyllopharyngeans (Chilodochona sp., Dysteria derouxi, Hartmannula sinica, Trithigmostoma cucullulus, Trochilia petrani, and Trochilia sp.). Phylogenomic analysis based on 157 orthologous genes comprising 173,835 amino acid residues revealed the affiliation of C. depressa within the class Phyllopharyngea, and the monophyly of Nassophorea, which strongly support the assignment of Synhymenia as a subclass within the class Phyllopharyngea. Comparative genomic analyses further revealed that C. depressa shares more orthologous genes with the class Nassophorea than with Phyllopharyngea, and the stop codon usage in C. depressa resembles that of Phyllopharyngea. Functional enrichment analysis demonstrated that biological pathways in C. depressa are more similar to Phyllopharyngea than Nassophorea. These results suggest that genomic and transcriptomic data can be used to provide insights into the evolutionary relationships within the "Nassophorea-Synhymenia-Phyllopharyngea" assemblage.
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Affiliation(s)
- Bo Pan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, United States
| | - Lina Hou
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhishuai Qu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Miao Miao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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28
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Abstract
Long interspersed element-1s (L1s) encode 2 proteins (ORF1p and ORF2p) that preferentially mobilize (i.e., retrotranspose) their encoding messenger RNA (mRNA) transcript. ORF1p and/or ORF2p can also mobilize other cellular RNAs, including short interspersed elements (SINEs), U6 small nuclear RNA (snRNA), and mRNAs. Here, we demonstrate the RNA ligase RtcB can join U6 snRNA to L1 or other cellular RNAs to create chimeric RNAs; retrotransposition of the resultant chimeric RNAs leads to chimeric pseudogene formation; and chimeric U6/L1 RNAs are part of the transcriptome in multiple human cells. These data suggest RNA ligation contributes to the plasticity of the transcriptome and that the retrotransposition of chimeric RNAs can generate genetic variation in the human genome. Long interspersed element-1 (LINE-1 or L1) amplifies via retrotransposition. Active L1s encode 2 proteins (ORF1p and ORF2p) that bind their encoding transcript to promote retrotransposition in cis. The L1-encoded proteins also promote the retrotransposition of small-interspersed element RNAs, noncoding RNAs, and messenger RNAs in trans. Some L1-mediated retrotransposition events consist of a copy of U6 RNA conjoined to a variably 5′-truncated L1, but how U6/L1 chimeras are formed requires elucidation. Here, we report the following: The RNA ligase RtcB can join U6 RNAs ending in a 2′,3′-cyclic phosphate to L1 RNAs containing a 5′-OH in vitro; depletion of endogenous RtcB in HeLa cell extracts reduces U6/L1 RNA ligation efficiency; retrotransposition of U6/L1 RNAs leads to U6/L1 pseudogene formation; and a unique cohort of U6/L1 chimeric RNAs are present in multiple human cell lines. Thus, these data suggest that U6 small nuclear RNA (snRNA) and RtcB participate in the formation of chimeric RNAs and that retrotransposition of chimeric RNA contributes to interindividual genetic variation.
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29
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Vuong LM, Pan S, Donovan PJ. Proteome Profile of Endogenous Retrotransposon-Associated Complexes in Human Embryonic Stem Cells. Proteomics 2019; 19:e1900169. [PMID: 31219246 PMCID: PMC8054700 DOI: 10.1002/pmic.201900169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/11/2019] [Indexed: 01/25/2023]
Abstract
Long Interspersed Element-1 (LINE-1 or L1) are transposable elements similar to retroviruses that have existed in the genome of primates for millions of years. They encode two Open Reading Frame (ORF) proteins (ORF1p and ORF2p) that bind L1 RNA to form a ribonucleoprotein (RNP) complex and are required for L1 integration into the host genome. Humans have evolved with L1 and found ways to limit L1 activity. To identify partners of the L1 RNP, previous studies used ectopic expression of L1 ORF1/2p or RNA in various cancer cells, which express low levels of the ORF proteins. Whether naturally occurring L1 RNP interacts with the same proteins in non-cancer cells is unknown. Here, the aim is to examine the natural assembly of endogenous L1 RNPs in normal human cells. L1 elements are expressed in human embryonic stem cells (hESCs), derived from pre-implantation embryos. Therefore, these cells are used to immunoprecipitate ORF1p followed by MS to identify proteins that associate with the naturally-occurring L1 ORF1p. Some of the same proteins as well as unique proteins are found interacting with the endogenous L1 ORF1p complexes. The analysis of ORF1p-associated proteins in hESCs can help address important questions in both retrotransposon biology and the biology of hESCs.
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Affiliation(s)
- Linh M. Vuong
- Departments of Developmental and Cell Biology
- Departments of Biological Chemistry, UCI
| | - Songqin Pan
- W.M. Keck Proteomics Laboratory, Institute of Integrated Genome Biology, Department of Botany and Plant Sciences, UCR
| | - Peter J. Donovan
- Departments of Developmental and Cell Biology
- Departments of Biological Chemistry, UCI
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30
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Yang L, Scott L, Wichman HA. Tracing the history of LINE and SINE extinction in sigmodontine rodents. Mob DNA 2019; 10:22. [PMID: 31139266 PMCID: PMC6530004 DOI: 10.1186/s13100-019-0164-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background L1 retrotransposons have co-evolved with their mammalian hosts for the entire history of mammals and currently compose ~ 20% of a mammalian genome. B1 retrotransposons are dependent on L1 for retrotransposition and span the evolutionary history of rodents since their radiation. L1s were found to have lost their activity in a group of South American rodents, the Sigmodontinae, and B1 inactivation preceded the extinction of L1 in the same group. Consequently, a basal group of sigmodontines have active L1s but inactive B1s and a derived clade have both inactive L1s and B1s. It has been suggested that B1s became extinct during a long period of L1 quiescence and that L1s subsequently reemerged in the basal group. Results Here we investigate the evolutionary histories of L1 and B1 in the sigmodontine rodents and show that L1 activity continued until after the L1-extinct clade and the basal group diverged. After the split, L1 had a small burst of activity in the former group, followed by extinction. In the basal group, activity was initially low but was followed by a dramatic increase in L1 activity. We found the last wave of B1 retrotransposition was large and probably preceded the split between the two rodent clades. Conclusions Given that L1s had been steadily retrotransposing during the time corresponding to B1 extinction and that the burst of B1 activity preceding B1 extinction was large, we conclude that B1 extinction was not a result of L1 quiescence. Rather, the burst of B1 activity may have contributed to L1 extinction both by competition with L1 and by putting strong selective pressure on the host to control retrotransposition. Electronic supplementary material The online version of this article (10.1186/s13100-019-0164-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lei Yang
- 1Department of Biological Sciences, University of Idaho, Moscow, ID USA.,2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID USA
| | - LuAnn Scott
- 1Department of Biological Sciences, University of Idaho, Moscow, ID USA.,2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID USA
| | - Holly A Wichman
- 1Department of Biological Sciences, University of Idaho, Moscow, ID USA.,2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID USA
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Tang Y, Ma X, Zhao S, Xue W, Zheng X, Sun H, Gu P, Zhu Z, Sun C, Liu F, Tan L. Identification of an active miniature inverted-repeat transposable element mJing in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:639-653. [PMID: 30689248 PMCID: PMC6850418 DOI: 10.1111/tpj.14260] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/01/2019] [Accepted: 01/18/2019] [Indexed: 05/27/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are structurally homogeneous non-autonomous DNA transposons with high copy numbers that play important roles in genome evolution and diversification. Here, we analyzed the rice high-tillering dwarf (htd) mutant in an advanced backcross population between cultivated and wild rice, and identified an active MITE named miniature Jing (mJing). The mJing element belongs to the PIF/Harbinger superfamily. japonica rice var. Nipponbare and indica var. 93-11 harbor 72 and 79 mJing family members, respectively, have undergone multiple rounds of amplification bursts during the evolution of Asian cultivated rice (Oryza sativa L.). A heterologous transposition experiment in Arabidopsis thaliana indicated that the autonomous element Jing is likely to have provides the transposase needed for mJing mobilization. We identified 297 mJing insertion sites and their presence/absence polymorphism among 71 rice samples through targeted high-throughput sequencing. The results showed that the copy number of mJing varies dramatically among Asian cultivated rice (O. sativa), its wild ancestor (O. rufipogon), and African cultivated rice (O. glaberrima) and that some mJing insertions are subject to directional selection. These findings suggest that the amplification and removal of mJing elements have played an important role in rice genome evolution and species diversification.
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Affiliation(s)
- Yanyan Tang
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xin Ma
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Shuangshuang Zhao
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Wei Xue
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xu Zheng
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Hongying Sun
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Ping Gu
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Zuofeng Zhu
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Fengxia Liu
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Lubin Tan
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
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Zeeshan S, Xiong R, Liang BT, Ahmed Z. 100 Years of evolving gene-disease complexities and scientific debutants. Brief Bioinform 2019; 21:885-905. [PMID: 30972412 DOI: 10.1093/bib/bbz038] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/22/2022] Open
Abstract
It's been over 100 years since the word `gene' is around and progressively evolving in several scientific directions. Time-to-time technological advancements have heavily revolutionized the field of genomics, especially when it's about, e.g. triple code development, gene number proposition, genetic mapping, data banks, gene-disease maps, catalogs of human genes and genetic disorders, CRISPR/Cas9, big data and next generation sequencing, etc. In this manuscript, we present the progress of genomics from pea plant genetics to the human genome project and highlight the molecular, technical and computational developments. Studying genome and epigenome led to the fundamentals of development and progression of human diseases, which includes chromosomal, monogenic, multifactorial and mitochondrial diseases. World Health Organization has classified, standardized and maintained all human diseases, when many academic and commercial online systems are sharing information about genes and linking to associated diseases. To efficiently fathom the wealth of this biological data, there is a crucial need to generate appropriate gene annotation repositories and resources. Our focus has been how many gene-disease databases are available worldwide and which sources are authentic, timely updated and recommended for research and clinical purposes. In this manuscript, we have discussed and compared 43 such databases and bioinformatics applications, which enable users to connect, explore and, if possible, download gene-disease data.
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Affiliation(s)
- Saman Zeeshan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Ruoyun Xiong
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Bruce T Liang
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA.,Pat and Jim Calhoun Cardiology Center, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Zeeshan Ahmed
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
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Novroski NM, Woerner AE, Budowle B. Potential highly polymorphic short tandem repeat markers for enhanced forensic identity testing. Forensic Sci Int Genet 2018; 37:162-171. [DOI: 10.1016/j.fsigen.2018.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/02/2018] [Accepted: 08/21/2018] [Indexed: 01/22/2023]
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Li W, Thanos D, Provata A. Quantifying local randomness in human DNA and RNA sequences using Erdös motifs. J Theor Biol 2018; 461:41-50. [PMID: 30336158 DOI: 10.1016/j.jtbi.2018.09.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/14/2018] [Accepted: 09/25/2018] [Indexed: 10/28/2022]
Abstract
In 1932, Paul Erdös asked whether a random walk constructed from a binary sequence can achieve the lowest possible deviation (lowest discrepancy), for the sequence itself and for all its subsequences formed by homogeneous arithmetic progressions. Although avoiding low discrepancy is impossible for infinite sequences, as recently proven by Terence Tao, attempts were made to construct such sequences with finite lengths. We recognize that such constructed sequences (we call these "Erdös sequences") exhibit certain hallmarks of randomness at the local level: they show roughly equal frequencies of short subsequences, and at the same time exclude trivial periodic patterns. For the human DNA we examine the frequency of a set of Erdös motifs of length-10 using three nucleotides-to-binary mappings. The particular length-10 Erdös sequence is derived from the length-11 Mathias sequence and is identical with the first 10 digits of the Thue-Morse sequence, underscoring the fact that both are deficient in periodicities. Our calculations indicate that: (1) the purine(A and G)/pyridimine(C and T) based Erdös motifs are greatly underrepresented in the human genome, (2) the strong(G and C)/weak(A and T) based Erdös motifs are slightly overrepresented, (3) the densities of the two are negatively correlated, (4) the Erdös motifs based on all three mappings being combined are slightly underrepresented, and (5) the strong/weak based Erdös motifs are greatly overrepresented in the human messenger RNA sequences.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
| | - Dimitrios Thanos
- Department of Mathematics, National and Kapodistrian University of Athens, Athens GR-15784, Greece; Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", Athens GR-15341, Greece
| | - Astero Provata
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", Athens GR-15341, Greece
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Wagstaff BJ, Wang L, Lai S, Derbes RS, Roy-Engel AM. Reviving a 60 million year old LINE-1 element. GENE REPORTS 2018; 11:74-78. [PMID: 30221208 DOI: 10.1016/j.genrep.2018.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Mobile elements have significantly impacted genome structure of most organisms. The continued activity of the mobile element, LINE-1 (L1), through time has contributed to the accumulation of over half a million L1 copies in the human genome. Most copies in the human genome belong to evolutionary older extinct L1s. Here we apply our previous published approach to "revive" the extinct L1 PA13A; an L1 family that was active about 60 million year ago (mya). The reconstructed L1PA13A is retrocompentent in culture, but shows a significantly lower level of activity in HeLa cells when compared to the modern L1 element (L1PA1) and a 40 million year old L1PA8. L1 elements code for two proteins (ORF1p and ORF2p) that are necessary for retrotransposition. Using PA13A-PA1 and PA13A-PA8 L1 chimeric elements, we determined that both the ORF1p and ORF2p contribute to the observed decrease in retrotransposition efficiency of L1PA13A. The lower retrotransposition rate of L1PA13A is consistent in both human and rodent cell lines. However, in rodent cells, the chimeric element L1PA:1-13 containing the modern L1PA1 ORF1p shows a recovery in the retrotransposition rate, suggestive that the L1PA13A ORF2p efficiently drives retrotransposition in these cells. The functionality of the L1PA13A ORF2p was further confirmed by demonstrating its ability to drive Alu retrotransposition in rodent cells. The variation in L1PA13A retrotransposition rates observed between rodent and human cells are suggestive that cellular environment significantly affects retrotransposition efficiency, which may be mediated through an interaction with ORF1p. Based on these observations, we speculate that the observed differences between cell lines may reflect an evolutionary adaptation of the L1 element to its host cell.
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Affiliation(s)
- Bradley J Wagstaff
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Linda Wang
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Susan Lai
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Rebecca S Derbes
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Astrid M Roy-Engel
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
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Richardson ME, Chong H, Mu W, Conner BR, Hsuan V, Willett S, Lam S, Tsai P, Pesaran T, Chamberlin AC, Park MS, Gray P, Karam R, Elliott A. DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes. Genet Med 2018; 21:683-693. [PMID: 30054569 PMCID: PMC6752314 DOI: 10.1038/s41436-018-0092-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/04/2018] [Indexed: 01/17/2023] Open
Abstract
PURPOSE Gross duplications are ambiguous in terms of clinical interpretation due to the limitations of the detection methods that cannot infer their context, namely, whether they occur in tandem or are duplicated and inserted elsewhere in the genome. We investigated the proportion of gross duplications occurring in tandem in breast cancer predisposition genes with the intent of informing their classifications. METHODS The DNA breakpoint assay (DBA) is a custom, paired-end, next-generation sequencing (NGS) method designed to capture and detect deep-intronic DNA breakpoints in gross duplications in BRCA1, BRCA2, ATM, CDH1, PALB2, and CHEK2. RESULTS DBA allowed us to ascertain breakpoints for 44 unique gross duplications from 147 probands. We determined that the duplications occurred in tandem in 114 (78%) carriers from this cohort, while the remainder have unknown tandem status. Among the tandem gross duplications that were eligible for reclassification, 95% of them were upgraded to pathogenic. CONCLUSION DBA is a novel, high-throughput, NGS-based method that informs the tandem status, and thereby the classification of, gross duplications. This method revealed that most gross duplications in the investigated genes occurred in tandem and resulted in a pathogenic classification, which helps to secure the necessary treatment options for their carriers.
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Affiliation(s)
- Marcy E Richardson
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA.
| | - Hansook Chong
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Wenbo Mu
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Blair R Conner
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Vickie Hsuan
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Sara Willett
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Stephanie Lam
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Pei Tsai
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Tina Pesaran
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Adam C Chamberlin
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Min-Sun Park
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Phillip Gray
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Rachid Karam
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
| | - Aaron Elliott
- Department of Clinical Genomics, Ambry Genetics, 15 Argonaut Drive, Aliso Viejo, California, 92656, USA
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Distinguishing friends, foes, and freeloaders in giant genomes. Curr Opin Genet Dev 2018; 49:49-55. [DOI: 10.1016/j.gde.2018.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 12/11/2022]
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Keidar D, Doron C, Kashkush K. Genome-wide analysis of a recently active retrotransposon, Au SINE, in wheat: content, distribution within subgenomes and chromosomes, and gene associations. PLANT CELL REPORTS 2018; 37:193-208. [PMID: 29164313 PMCID: PMC5787218 DOI: 10.1007/s00299-017-2213-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/05/2017] [Indexed: 05/02/2023]
Abstract
Here, we show that Au SINE elements have strong associations with protein-coding genes in wheat. Most importantly Au SINE insertion within introns causes allelic variation and might induce intron retention. The impact of transposable elements (TEs) on genome structure and function is intensively studied in eukaryotes, especially in plants where TEs can reach up to 90% of the genome in some cases, such as in wheat. Here, we have performed a genome-wide in-silico analysis using the updated publicly available genome draft of bread wheat (T. aestivum), in addition to the updated genome drafts of the diploid donor species, T. urartu and Ae. tauschii, to retrieve and analyze a non-LTR retrotransposon family, termed Au SINE, which was found to be widespread in plant species. Then, we have performed site-specific PCR and realtime RT-PCR analyses to assess the possible impact of Au SINE on gene structure and function. To this end, we retrieved 133, 180 and 1886 intact Au SINE insertions from T. urartu, Ae. tauschii and T. aestivum genome drafts, respectively. The 1886 Au SINE insertions were distributed in the seven homoeologous chromosomes of T. aestivum, while ~ 67% of the insertions were associated with genes. Detailed analysis of 40 genes harboring Au SINE revealed allelic variation of those genes in the Triticum-Aegilops genus. In addition, expression analysis revealed that both regular transcripts and alternative Au SINE-containing transcripts were simultaneously amplified in the same tissue, indicating retention of Au SINE-containing introns. Analysis of the wheat transcriptome revealed that hundreds of protein-coding genes harbor Au SINE in at least one of their mature splice variants. Au SINE might play a prominent role in speciation by creating transcriptome variation.
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Affiliation(s)
- Danielle Keidar
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel
| | - Chen Doron
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel
| | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel.
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Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics 2017; 18:977. [PMID: 29258433 PMCID: PMC5735816 DOI: 10.1186/s12864-017-4318-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/17/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. However, copy number variation (CNV), despite its increasingly recognized importance as a contributor to phenotypic diversity, has not been extensively explored in canids. RESULTS Here, we develop a new accurate probabilistic framework to create fine-scale genomic maps of segmental duplications (SDs), compare patterns of CNV across groups and investigate their role in the evolution of the domestic dog by using information from 34 canine genomes. Our analyses show that duplicated regions are enriched in genes and hence likely possess functional importance. We identify 86 loci with large CNV differences between dogs and wolves, enriched in genes responsible for sensory perception, immune response, metabolic processes, etc. In striking contrast to the observed loss of nucleotide diversity in domestic dogs following the population bottlenecks that occurred during domestication and breed creation, we find a similar proportion of CNV loci in dogs and wolves, suggesting that other dynamics are acting to particularly select for CNVs with potentially functional impacts. CONCLUSIONS This work is the first comparison of genome wide CNV patterns in domestic and wild canids using whole-genome sequencing data and our findings contribute to study the impact of novel kinds of genetic changes on the evolution of the domestic dog.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Inna S Povolotskaya
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Javier Quilez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Oscar Ramirez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Vetgenomics, 08193, Barcelona, Spain
| | - Gabriel Santpere
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Lukas F K Kuderna
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Daniel Gomez-Sanchez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Adam H Freedman
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - John Novembre
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Arcadi Navarro
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain
| | - Adam Boyko
- Cornell University, Department of Biological Statistics and Computational Biology, New York, NY, 14853, USA
| | - Robert Wayne
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Carles Vilà
- Estación Biológica de Doñana EBD-CSIC, Department of Integrative Ecology, 41092, Sevilla, Spain
| | - Belen Lorente-Galdos
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain.
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Zhou W, Laird PW, Shen H. Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res 2017; 45:e22. [PMID: 27924034 PMCID: PMC5389466 DOI: 10.1093/nar/gkw967] [Citation(s) in RCA: 338] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/12/2016] [Indexed: 12/13/2022] Open
Abstract
Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, the recently introduced MethylationEPIC (EPIC) array expands on the utility of this platform, but has not yet been well characterized. We present in this paper an extensive characterization of probes on the EPIC and HM450 microarrays, including mappability to the latest genome build, genomic copy number of the 3΄ nested subsequence and influence of polymorphisms including a previously unrecognized color channel switch for Type I probes. We show empirical evidence for exclusion criteria for underperforming probes, providing a sounder basis than current ad hoc criteria for exclusion. In addition, we describe novel probe uses, exemplified by the addition of a total of 1052 SNP probes to the existing 59 explicit SNP probes on the EPIC array and the use of these probes to predict ethnicity. Finally, we present an innovative out-of-band color channel application for the dual use of 62 371 probes as internal bisulfite conversion controls.
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Affiliation(s)
- Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
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In Silico Identification and Validation of Potential microRNAs in Kinnow Mandarin (Citrus reticulata Blanco). Interdiscip Sci 2017; 10:762-770. [PMID: 28534166 DOI: 10.1007/s12539-017-0235-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 10/19/2022]
Abstract
MicroRNAs (miRNAs) are a large family of 19-25 nucleotides, regulatory, non-coding RNA molecules that control gene expression by cleaving or inhibiting the translation of target gene transcripts in animals and plants. Despite the important functions of miRNAs related to regulation of plant growth and development processes, metabolism, and abiotic and biotic stresses, little is known about the disease-related miRNA. Here, we present a new pipeline for miRNA analysis using expressed sequence tags (ESTs)-based bioinformatics approach in Kinnow mandarin, a commercially important citrus fruit crop. For this, 56,041 raw EST sequences of Citrus reticulata Blanco were retrieved from EST database in NCBI through step-by-step filtering and processing methods and 130 miRNAs were predicted. Upon blast with Citrus sinensis transcriptome data, these produced potential targets related to disease resistance proteins, pectin lyase-like superfamily proteins, lateral organ boundaries (LOB) domain-containing proteins 11, and protein phosphatase 2C family proteins, protein kinases, dehydrogenases, and methyltransferases. Majority of the predicted miRNAs were of 22, 23, and 24 nucleotides in length. To validate these computationally predicted miRNA, poly(A)-tailed Reverse Transcription-PCR was applied to detect the expression of seven miRNA which showed disease-related potential targets, in citrus greening diseased leaf tissues in comparison to the healthy tissues of Kinnow mandarin. Our study provides information on regulatory roles of these potential miRNAs for the citrus greening disease development, miRNA targets, and would be helpful for future research of miRNA function in citrus.
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Agarwal P, Enroth S, Teichmann M, Jernberg Wiklund H, Smit A, Westermark B, Singh U. Growth signals employ CGGBP1 to suppress transcription of Alu-SINEs. Cell Cycle 2017; 15:1558-71. [PMID: 25483050 PMCID: PMC4934077 DOI: 10.4161/15384101.2014.967094] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
CGGBP1 (CGG triplet repeat-binding protein 1) regulates cell proliferation, stress response, cytokinesis, telomeric integrity and transcription. It could affect these processes by modulating target gene expression under different conditions. Identification of CGGBP1-target genes and their regulation could reveal how a transcription regulator affects such diverse cellular processes. Here we describe the mechanisms of differential gene expression regulation by CGGBP1 in quiescent or growing cells. By studying global gene expression patterns and genome-wide DNA-binding patterns of CGGBP1, we show that a possible mechanism through which it affects the expression of RNA Pol II-transcribed genes in trans depends on Alu RNA. We also show that it regulates Alu transcription in cis by binding to Alu promoter. Our results also indicate that potential phosphorylation of CGGBP1 upon growth stimulation facilitates its nuclear retention, Alu-binding and dislodging of RNA Pol III therefrom. These findings provide insights into how Alu transcription is regulated in response to growth signals.
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Affiliation(s)
- Prasoon Agarwal
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
| | - Stefan Enroth
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
| | - Martin Teichmann
- b University of Bordeaux, IECB , ARNA laboratory, Equipe Labellisée Contre le Cancer , Pessac , France
| | - Helena Jernberg Wiklund
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
| | - Arian Smit
- c Institute for Systems Biology , Seattle , WA , USA
| | - Bengt Westermark
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
| | - Umashankar Singh
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
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43
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Bao E, Lan L. HALC: High throughput algorithm for long read error correction. BMC Bioinformatics 2017; 18:204. [PMID: 28381259 PMCID: PMC5382505 DOI: 10.1186/s12859-017-1610-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/24/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correction algorithms have been designed to efficiently reduce the error rate to 1%, but they discard large amounts of uncorrected bases and thus lead to low throughput. This loss of bases could limit the completeness of downstream assemblies and the accuracy of analysis. RESULTS Here, we introduce HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region's repeats in the contigs sufficiently similar to it (similar repeat based alignment approach). It then constructs a contig graph and, for each long read, references the other long reads' alignments to find the most accurate alignment and correct it with the aligned contig regions (long read support based validation approach). Even though some long read regions without the true genome regions in the contigs are corrected with their repeats, this approach makes it possible to further refine these long read regions with the initial insufficient short reads and correct the uncorrected regions in between. In our performance tests on E. coli, A. thaliana and Maylandia zebra data sets, HALC was able to obtain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable accuracy. The HALC corrected long reads can thus result in 11.4-60.7% longer assembled contigs than the existing algorithms. CONCLUSIONS The HALC software can be downloaded for free from this site: https://github.com/lanl001/halc .
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Affiliation(s)
- Ergude Bao
- School of Software Engineering, Beijing Jiaotong University, 3 Shangyuan Residence, Haidian District, Beijing, 100044 China
- Department of Botany and Plant Sciences, University of California, Riverside, 900 University Ave., RiversideCA, 92521 USA
| | - Lingxiao Lan
- School of Software Engineering, Beijing Jiaotong University, 3 Shangyuan Residence, Haidian District, Beijing, 100044 China
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44
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Hu T, Zhu X, Pi W, Yu M, Shi H, Tuan D. Hypermethylated LTR retrotransposon exhibits enhancer activity. Epigenetics 2017; 12:226-237. [PMID: 28165867 DOI: 10.1080/15592294.2017.1289300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
LTR retrotransposons are repetitive DNA elements comprising ∼10% of the human genome. They are silenced by hypermethylation of cytosines in CpG dinucleotides and are considered parasitic DNA serving no useful function for the host genome. However, hypermethylated LTRs contain enhancer and promoter sequences and can promote tissue-specific transcription of cis-linked genes. To resolve the apparent paradox of hypermethylated LTRs possessing transcriptional activities, we studied the ERV-9 LTR retrotransposon located at the 5' border of the transcriptionally active β-globin gene locus in human erythroid progenitor and erythroleukemia K562 cells. We found that the ERV-9 LTR, containing 65 CpGs in 1.7 kb DNA, was hypermethylated (with > 90% methylated CpGs). Hypermethylated LTR possessed transcriptional enhancer activity, since in vivo deletion of the LTR by CRISPR-cas9 suppressed transcription of the globin genes by > 50%. ChIP-qPCR and ChIP-seq studies showed that the hypermethylated LTR enhancer spanning recurrent CCAATCG and GATA motifs associated respectively with key transcription factors (TFs) NF-Y and GATA-1 and -2 at reduced levels, compared with the unmethylated LTR in transfected LTR-reporter gene plasmids. Electrophoretic mobility shift assays with methylated LTR enhancer probe showed that the methylated probe bound both NF-Y and GATA-1 and -2 with lower affinities than the unmethylated enhancer probe. Thus, hypermethylation drastically reduced, but did not totally abolish, the binding affinities of the enhancer motifs to the key TFs to assemble the LTR-pol II transcription complex that activated transcription of cis-linked genes at reduced efficiency.
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Affiliation(s)
- Tianxiang Hu
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Xingguo Zhu
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Wenhu Pi
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Miao Yu
- b Georgia Cancer Center , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Huidong Shi
- b Georgia Cancer Center , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Dorothy Tuan
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
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45
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Cardoso AR, Oliveira M, Amorim A, Azevedo L. Major influence of repetitive elements on disease-associated copy number variants (CNVs). Hum Genomics 2016; 10:30. [PMID: 27663310 PMCID: PMC5035501 DOI: 10.1186/s40246-016-0088-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/16/2016] [Indexed: 01/13/2023] Open
Abstract
Copy number variants (CNVs) are important contributors to the human pathogenic genetic diversity as demonstrated by a number of cases reported in the literature. The high homology between repetitive elements may guide genomic stability which will give rise to CNVs either by non-allelic homologous recombination (NAHR) or non-homologous end joining (NHEJ). Here, we present a short guide based on previously documented cases of disease-associated CNVs in order to provide a general view on the impact of repeated elements on the stability of the genomic sequence and consequently in the origin of the human pathogenic variome.
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Affiliation(s)
- Ana R Cardoso
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Luisa Azevedo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal.
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Tefferi A. Genomics Basics: DNA Structure, Gene Expression, Cloning, Genetic Mapping, and Molecular Tests. Semin Cardiothorac Vasc Anesth 2016; 10:282-90. [PMID: 17200086 DOI: 10.1177/1089253206294343] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genomics is the study of the structure and function of the human genome including genes and their surrounding DNA sequences. The over 3 billion base pairs of the human genome have now been sequenced and approximately 25 000 genes acknowledged. However, only 1% of the entire genome has been assigned to protein coding and decades more work is anticipated to define the functional relevance of noncoding DNA as well as the basis and consequences of sequence variations among individuals. For medical scientists, the focus remains on discovering both disease-causing and disease-susceptibility genes. For pharmaceutical companies, the opportunity to develop molecularly targeted therapy is not going unnoticed. For the practicing physician, the prospect of genomic medicine that incorporates molecular diagnosis and pathogenesis-targeted therapy requires basic understanding of terminology and concepts in molecular biology and the corresponding laboratory tests.
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Affiliation(s)
- Ayalew Tefferi
- Division of Hematology, Mayo Clinic, Rochester, MN 55905, USA.
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47
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Huang Y, Chen SY, Deng F. Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction. Comput Struct Biotechnol J 2016; 14:298-303. [PMID: 27536341 PMCID: PMC4975701 DOI: 10.1016/j.csbj.2016.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 07/06/2016] [Accepted: 07/12/2016] [Indexed: 12/31/2022] Open
Abstract
In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools.
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Affiliation(s)
- Ying Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Corresponding author at: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Wenjiang 611130, Sichuan, China.Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural University211# Huimin RoadWenjiangSichuan611130China
| | - Feilong Deng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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48
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Göke J, Ng HH. CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome. EMBO Rep 2016; 17:1131-44. [PMID: 27402545 DOI: 10.15252/embr.201642743] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/20/2016] [Indexed: 12/25/2022] Open
Abstract
The human genome contains millions of fragments from retrotransposons-highly repetitive DNA sequences that were once able to "copy and paste" themselves to other regions in the genome. However, the majority of retrotransposons have lost this capacity through acquisition of mutations or through endogenous silencing mechanisms. Without this imminent threat of transposition, retrotransposons have the potential to act as a major source of genomic innovation. Indeed, large numbers of retrotransposons have been found to be active in specific contexts: as gene regulatory elements and promoters for protein-coding genes or long noncoding RNAs, among others. In this review, we summarise recent findings about retrotransposons, with implications in gene expression regulation, the expansion of gene isoform diversity and the generation of long noncoding RNAs. We highlight key examples that demonstrate their role in cellular identity and their versatility as markers of cell states, and we discuss how their dysregulation may contribute to the formation of and possibly therapeutic response in human cancers.
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Affiliation(s)
- Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Huck Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore Department of Biochemistry, National University of Singapore, Singapore Department of Biological Sciences, National University of Singapore, Singapore School of Biological Sciences, Nanyang Technological University, Singapore
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49
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Godakova SA, Sevast'yanova GA, Semyenova SK. [STRUCTURE AND DISTRIBUTION OF THE RETROTRANSPOSON BOV-B LINE]. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2016; 34:9-12. [PMID: 27183715 DOI: 10.3103/s0891416816010043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The classification of mobile elements was discussed. Special attention was devoted to the retroelement of the LINE group: retrotransposon Bov-B LINE. The history of its origin and distribution in the nature was considered. The results of the phenomenon of horizontal transition of the retrotransposon Bov-B LINE between evolutionally distant classes were discussed.
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50
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Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mob DNA 2016; 7:9. [PMID: 27158268 PMCID: PMC4859970 DOI: 10.1186/s13100-016-0065-9] [Citation(s) in RCA: 437] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022] Open
Abstract
Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans.
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Affiliation(s)
- Dustin C. Hancks
- />Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Haig H. Kazazian
- />McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins School of Medicine, Baltimore, MD USA
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