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Steenwyk JL, King N. The promise and pitfalls of synteny in phylogenomics. PLoS Biol 2024; 22:e3002632. [PMID: 38768403 PMCID: PMC11105162 DOI: 10.1371/journal.pbio.3002632] [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] [Indexed: 05/22/2024] Open
Abstract
Reconstructing the tree of life remains a central goal in biology. Early methods, which relied on small numbers of morphological or genetic characters, often yielded conflicting evolutionary histories, undermining confidence in the results. Investigations based on phylogenomics, which use hundreds to thousands of loci for phylogenetic inquiry, have provided a clearer picture of life's history, but certain branches remain problematic. To resolve difficult nodes on the tree of life, 2 recent studies tested the utility of synteny, the conserved collinearity of orthologous genetic loci in 2 or more organisms, for phylogenetics. Synteny exhibits compelling phylogenomic potential while also raising new challenges. This Essay identifies and discusses specific opportunities and challenges that bear on the value of synteny data and other rare genomic changes for phylogenomic studies. Synteny-based analyses of highly contiguous genome assemblies mark a new chapter in the phylogenomic era and the quest to reconstruct the tree of life.
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Affiliation(s)
- Jacob L. Steenwyk
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Nicole King
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
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Balakrishnan S, Bhasker R, Ramasamy Y, Dev SA. Genome-wide analysis of cellulose synthase gene superfamily in Tectona grandis L.f. 3 Biotech 2024; 14:86. [PMID: 38385141 PMCID: PMC10876501 DOI: 10.1007/s13205-024-03927-6] [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: 04/05/2023] [Accepted: 01/08/2024] [Indexed: 02/23/2024] Open
Abstract
This study aimed to explore Cellulose synthase gene superfamily of teak, and its evolutionary relationship with homologous genes of other woody species. The incidence of evolutionary events like gene duplication and gene loss, influence of the selection pressure, and consequent adaptive functional divergence of the duplicated TgCes gene were assessed alongside it's role in wood coloration. This study identified 39 full-length non-redundant proteins belonging to CesA and Csl gene families. TgCesA and TgCsl proteins with Cellulose synthase domain repeats indicated tandem gene duplication and probable genetic variability, enabling local adaptation. Further, multi-domain protein (MYB-like DNA-binding domain and CesA domain) with maximum introns was also identified indicating gene fusion and formation of complex protein with novel functions. Phylogenetic analysis grouped the genes into seven subfamilies (CesA, CslA, CslC, CslD, CslE, CslG, and CslM) with each undergoing gene duplication and loss along their evolutionary history. Post-species gene duplications and probable neofunctionalization were identified in TgCesA and TgCsl gene families. Each subfamily was found to be under strong purifying selection with a few or no sites under positive selection. Functional divergence analysis further revealed site-specific selective constraints in CesA and Csl genes of the teak Cellulose synthase gene family. Furthermore, protein-protein interaction network analysis identified co-expression of Cellulose synthase gene with flavonoid 3',5'-hydroxylase (F3'5'H, CYP75A), involved in the biosynthesis of xylem anthocyanin compounds, probably responsible for wood coloration. This study thus offers a foundation for future research in wood formation and wood property traits specific to teak and its provenances. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03927-6.
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Affiliation(s)
- Swathi Balakrishnan
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
- Cochin University of Science and Technology, Kochi, Kerala India
| | - Reshma Bhasker
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
- Cochin University of Science and Technology, Kochi, Kerala India
| | - Yasodha Ramasamy
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002 India
| | - Suma Arun Dev
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
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Xu X, Yang L, Deng X, Xiao Q, Huang X, Wang C, Zhou Y, Luo X, Zhang Y, Xu X, Qin Q, Liu S. Expression and localization of HPG axis-related genes in Carassius auratus with different ploidy. Front Endocrinol (Lausanne) 2024; 15:1336679. [PMID: 38410696 PMCID: PMC10894961 DOI: 10.3389/fendo.2024.1336679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/16/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction In the Dongting water system, the Carassius auratus (Crucian carp) complex is characterized by the coexistence of diploid forms (2n=100, 2nCC) and polyploidy forms. The diploid (2nCC) and triploid C.auratus (3n=150, 3nCC) had the same fertility levels, reaching sexual maturity at one year. Methods The nucleotide sequence, gene expression, methylation, and immunofluorescence of the gonadotropin releasing hormone 2(Gnrh2), Gonadotropin hormone beta(Gthβ), and Gonadotropin-releasing hormone receptor(Gthr) genes pivotal genes of the hypothalamic-pituitary-gonadal (HPG) axis were analyzed. Results The analysis results indicated that Gnrh2, follicle-stimulating hormone receptor(Fshr), and Lethal hybrid rescue(Lhr) genes increased the copy number and distinct structural differentiation in 3nCC compared to that in 2nCC. The transcript levels of HPG axis genes in 3nCC were higher than 2nCC (P<0.05), which could promote the production and secretion of sex steroid hormones conducive to the gonadal development of 3nCC. Meanwhile, the DNA methylation levels in the promoter regions of the HPG axis genes were lower in 3nCC than in 2nCC. These results suggested that methylation of the promoter region had a potential regulatory effect on gene expression after triploidization. Immunofluorescence showed that the localization of the Fshβ, Lhβ, and Fshr genes between 3nCC and 2nCC remained unchanged, ensuring the normal expression of these genes at the corresponding sites after triploidization. Discussion Relevant research results provide cell and molecular biology evidence for normal reproductive activities such as gonad development and gamete maturation in triploid C. auratus, and contribute to further understanding of the genetic basis for fertility restoration in triploid C. auratus.
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Affiliation(s)
- Xiaowei Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xinyi Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Qingwen Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yue Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xiang Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yuxin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xidan Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
- Hunan Yuelu Mountain Science and Technology Co., Ltd., for Aquatic Breeding, Changsha, Hunan, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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Ma F, Zou Y, Chen X, Ma L, Ma R. Evolution, characterization, and expression profile of Egl-9 family hypoxia-inducible factor ( egln) in rainbow trout ( Oncorhynchus mykiss) under hypoxia stress. Anim Biotechnol 2023; 34:1753-1762. [PMID: 35289728 DOI: 10.1080/10495398.2022.2047994] [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: 11/01/2022]
Abstract
Egl-9 family hypoxia-inducible factor (egln), an oxygen-sensing enzyme family, has been thoroughly characterized in mammals and certain fishes, but there is few research on its involvement in reproductive development and hypoxic stress in rainbow trout. In this study, we investigated the gene structure, physicochemical properties, and evolutionary connection of the egln gene family. The expression profile of egln gene family and their regulatory mechanism were explored using bioinformatics analysis and hypoxia treatment experiments. Five egln genes were discovered in the rainbow trout genome in this investigation (egln1, egln2a, egln2b, egln3a, and egln3b). Domain prediction revealed that all egln proteins have p4hc conserved domains, and phylogenetic analysis revealed that rainbow trout egln2 and egln3 were closely related to Atlantic salmon. The results of real-time quantitative PCR (RT-qPCR) showed that egln genes were generally expressed in all detected tissues, and higher in the ovary, testis, and brain in normoxia. Under hypoxia, the expression level of eglns was significantly down-regulated in most tissues except the liver. Our research contributes to future research on the functional properties of egln genes, as well as the evolution of teleosts and the impact of hypoxia on biological immunity.
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Affiliation(s)
- Fang Ma
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu, China
| | - Yali Zou
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu, China
| | - Xin Chen
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu, China
| | - Lanfang Ma
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu, China
| | - Ruilin Ma
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu, China
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Hou ZS, Liu MQ, Wen HS, Gao QF, Li Z, Yang XD, Xiang KW, Yang Q, Hu X, Qian MZ, Li JF. Identification, characterization, and transcription of serotonin receptors in rainbow trout (Oncorhynchus mykiss) in response to bacterial infection and salinity changes. Int J Biol Macromol 2023; 249:125930. [PMID: 37481174 DOI: 10.1016/j.ijbiomac.2023.125930] [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: 05/10/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023]
Abstract
Serotonergic system is involved in the regulation of physiological functions and behavioral traits including cognition, memory, aggression, stress coping, appetite and immunomodulation. Serotonin exerts its functions via binding distinct serotonin receptors which are classified into 7 groups. Salmonid exhibits expanded functional gene copies due to salmonid-specific whole genome duplication. However, serotonin receptor (htr) repertoire is not fully identified in rainbow trout (Oncorhynchus mykiss). In this study, we identified 39 htr genes, including 14 htr1, 4 htr2, 4 htr2 like, 3 htr3, 4 htr4, 2 htr5, 2 htr6, and 6 htr7 subtypes. We investigated physiological functions of serotonin receptors in response to bacterial pathogens exposure and salinity changes. We showed htr1, htr2, htr4 and htr7 subtypes were associated with immunomodulation in response to Vibrio anguillarum or Aeromonas salmonicida infection. Saltwater (salinity of 15) transfer significantly altered htr1, htr2, htr4, and htr7 subtypes, suggesting trout Htr was associated with osmoregulation. We further showed residues interacted with inverse agonist (methiothepin) and serotonin analogue (5-Carboxamidotryptamine) were conserved between trout and human, suggesting exogenous ligands targeting human HTRs might have a role in aquaculture. This study showed duplicated trout Htrs might be physiologically neofunctionalized and potentially exhibit pleiotropic effects in regulating immunomodulation and osmoregulation.
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Affiliation(s)
- Zhi-Shuai Hou
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China.
| | - Meng-Qun Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China
| | - Hai-Shen Wen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China.
| | - Qin-Feng Gao
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China.
| | - Zhao Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China
| | - Xiao-Dong Yang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China
| | - Kai-Wen Xiang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China
| | - Qian Yang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China
| | - Xin Hu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China.
| | - Meng-Zhi Qian
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China
| | - Ji-Fang Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao 266003, China.
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Glunčić M, Vlahović I, Rosandić M, Paar V. Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly. Sci Rep 2023; 13:14420. [PMID: 37660151 PMCID: PMC10475015 DOI: 10.1038/s41598-023-41517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023] Open
Abstract
It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.
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Affiliation(s)
- Matko Glunčić
- Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia.
| | | | - Marija Rosandić
- University Hospital Centre Zagreb (Ret.), 10000, Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
| | - Vladimir Paar
- Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
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Soto DC, Uribe-Salazar JM, Shew CJ, Sekar A, McGinty S, Dennis MY. Genomic structural variation: A complex but important driver of human evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181 Suppl 76:118-144. [PMID: 36794631 PMCID: PMC10329998 DOI: 10.1002/ajpa.24713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/21/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.
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Affiliation(s)
- Daniela C. Soto
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - José M. Uribe-Salazar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Aarthi Sekar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Sean McGinty
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
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Vaill M, Kawanishi K, Varki N, Gagneux P, Varki A. Comparative physiological anthropogeny: exploring molecular underpinnings of distinctly human phenotypes. Physiol Rev 2023; 103:2171-2229. [PMID: 36603157 PMCID: PMC10151058 DOI: 10.1152/physrev.00040.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Anthropogeny is a classic term encompassing transdisciplinary investigations of the origins of the human species. Comparative anthropogeny is a systematic comparison of humans and other living nonhuman hominids (so-called "great apes"), aiming to identify distinctly human features in health and disease, with the overall goal of explaining human origins. We begin with a historical perspective, briefly describing how the field progressed from the earliest evolutionary insights to the current emphasis on in-depth molecular and genomic investigations of "human-specific" biology and an increased appreciation for cultural impacts on human biology. While many such genetic differences between humans and other hominids have been revealed over the last two decades, this information remains insufficient to explain the most distinctive phenotypic traits distinguishing humans from other living hominids. Here we undertake a complementary approach of "comparative physiological anthropogeny," along the lines of the preclinical medical curriculum, i.e., beginning with anatomy and considering each physiological system and in each case considering genetic and molecular components that are relevant. What is ultimately needed is a systematic comparative approach at all levels from molecular to physiological to sociocultural, building networks of related information, drawing inferences, and generating testable hypotheses. The concluding section will touch on distinctive considerations in the study of human evolution, including the importance of gene-culture interactions.
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Affiliation(s)
- Michael Vaill
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
| | - Kunio Kawanishi
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nissi Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Pascal Gagneux
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Ajit Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
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Denti L, Khorsand P, Bonizzoni P, Hormozdiari F, Chikhi R. SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads. Nat Methods 2023; 20:550-558. [PMID: 36550274 DOI: 10.1038/s41592-022-01674-1] [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: 02/23/2022] [Accepted: 10/08/2022] [Indexed: 12/24/2022]
Abstract
Structural variants (SVs) account for a large amount of sequence variability across genomes and play an important role in human genomics and precision medicine. Despite intense efforts over the years, the discovery of SVs in individuals remains challenging due to the diploid and highly repetitive structure of the human genome, and by the presence of SVs that vastly exceed sequencing read lengths. However, the recent introduction of low-error long-read sequencing technologies such as PacBio HiFi may finally enable these barriers to be overcome. Here we present SV discovery with sample-specific strings (SVDSS)-a method for discovery of SVs from long-read sequencing technologies (for example, PacBio HiFi) that combines and effectively leverages mapping-free, mapping-based and assembly-based methodologies for overall superior SV discovery performance. Our experiments on several human samples show that SVDSS outperforms state-of-the-art mapping-based methods for discovery of insertion and deletion SVs in PacBio HiFi reads and achieves notable improvements in calling SVs in repetitive regions of the genome.
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Affiliation(s)
- Luca Denti
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France
| | | | - Paola Bonizzoni
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.
| | - Fereydoun Hormozdiari
- Genome Center, UC Davis, Davis, CA, USA.
- UC Davis MIND Institute, Sacramento, CA, USA.
- Department of Biochemistry and Molecular Medicine, Sacramento, UC Davis, Sacramento, CA, USA.
| | - Rayan Chikhi
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France.
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Jahan K, Nie H, Yan X. Revealing the potential regulatory relationship between HSP70, HSP90 and HSF genes under temperature stress. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108607. [PMID: 36758653 DOI: 10.1016/j.fsi.2023.108607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/04/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Heat Shock Protein (HSPs) gene family members play fundamental roles in different environmental stress tolerances, protect the structure and function of cells, and perform a significant task in cellular homeostasis. In this study, we conducted a genome-wide identification, evolutionary relationship analysis and gene expression analysis of the HSP70, HSP90, and HSF gene families in Ruditapes philippinarum. We identified 83 RpHSP70, 6 RpHSP90, and 3 RpHSF genes in R. philippinarum. The structural characteristics, chromosomal localization, and the gene structure map were constructed to reveal the characteristics of protein structures. Furthermore, the expression profiling of transcriptome data showed the expression pattern of HSP70, HSP90 and HSF genes in Manila clam from different populations, and under high and low temperature stress. In addition, we performed protein-protein interaction network analysis between HSP70, HSP90, and HSF gene family which enabled us to recognize the regulatory relationship between the two HSP gene families and the HSF gene family. Furthermore, the predicted sub-cellular location revealed a diversified subcellular distribution of HSP70, HSP90, and HSF proteins, which may be directly or indirectly associated with functional diversification under heat stress condition.
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Affiliation(s)
- Kifat Jahan
- College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023, Dalian, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023, Dalian, China.
| | - Xiwu Yan
- College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023, Dalian, China
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11
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Vanderhaeghen P, Polleux F. Developmental mechanisms underlying the evolution of human cortical circuits. Nat Rev Neurosci 2023; 24:213-232. [PMID: 36792753 PMCID: PMC10064077 DOI: 10.1038/s41583-023-00675-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 02/17/2023]
Abstract
The brain of modern humans has evolved remarkable computational abilities that enable higher cognitive functions. These capacities are tightly linked to an increase in the size and connectivity of the cerebral cortex, which is thought to have resulted from evolutionary changes in the mechanisms of cortical development. Convergent progress in evolutionary genomics, developmental biology and neuroscience has recently enabled the identification of genomic changes that act as human-specific modifiers of cortical development. These modifiers influence most aspects of corticogenesis, from the timing and complexity of cortical neurogenesis to synaptogenesis and the assembly of cortical circuits. Mutations of human-specific genetic modifiers of corticogenesis have started to be linked to neurodevelopmental disorders, providing evidence for their physiological relevance and suggesting potential relationships between the evolution of the human brain and its sensitivity to specific diseases.
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Affiliation(s)
- Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium.
| | - Franck Polleux
- Department of Neuroscience, Columbia University Medical Center, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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12
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Eftekhar M, Panahi Y, Eskandari MR, Pedram M. Association Study between DUF1220 Copy Number and Severity of Social Impairment in Sex-balanced Simplex Cases of Autism. Noro Psikiyatr Ars 2023; 60:43-48. [PMID: 36911566 PMCID: PMC9999218 DOI: 10.29399/npa.28020] [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: 09/16/2021] [Accepted: 04/01/2022] [Indexed: 11/07/2022] Open
Abstract
Introduction Copy number variations (CNVs), which are genetic factors responsible for human evolution, have emerged as underlying pathogenic factors for a number of diseases such as autism spectrum disorders (ASD). DUF1220 coding sequences have been shown to be positively associated with the severity of symptoms in familial/multiplex cases of autism. However, this association has not been confirmed in simplex autism, and the potential impact of gender/sex has not been studied. Methods Using saliva samples taken from Iranian children with non-syndromic simplex autism, different ethnicity/race and genetic backgrounds from previous studies, we assessed the association between DUF1220 CNVs and Autism Diagnostic Interview-Revised (ADI-R) domain scores in both males and females. Results In the male and female combined group with autism, in line with previous reports, our findings showed that there were no significant associations between DUF1220 CNVs with either total ADI-R score, social, communication, or repetitive diagnostic scores in simplex autism cases. Interestingly, however, in sex classified groups, despite the insignificant results, our findings in girls with autism showed a negative trend between DUF1220 CNVs and severity of symptoms for the social interaction and communication domains. By contrast, in male children with autism, the results showed a positive trend. Conclusion It seems that association of DUF1220 CNV with the severity of symptoms in simplex children with autism may follow a sexually dimorphic pattern that needs to be re-examined in prospective studies.
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Affiliation(s)
- Mohammad Eftekhar
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Yasin Panahi
- Department of Pharmacology and Toxicology, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mohammad Reza Eskandari
- Department of Psychiatry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehrdad Pedram
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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13
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Pokrovac I, Pezer Ž. Recent advances and current challenges in population genomics of structural variation in animals and plants. Front Genet 2022; 13:1060898. [PMID: 36523759 PMCID: PMC9745067 DOI: 10.3389/fgene.2022.1060898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/15/2022] [Indexed: 05/02/2024] Open
Abstract
The field of population genomics has seen a surge of studies on genomic structural variation over the past two decades. These studies witnessed that structural variation is taxonomically ubiquitous and represent a dominant form of genetic variation within species. Recent advances in technology, especially the development of long-read sequencing platforms, have enabled the discovery of structural variants (SVs) in previously inaccessible genomic regions which unlocked additional structural variation for population studies and revealed that more SVs contribute to evolution than previously perceived. An increasing number of studies suggest that SVs of all types and sizes may have a large effect on phenotype and consequently major impact on rapid adaptation, population divergence, and speciation. However, the functional effect of the vast majority of SVs is unknown and the field generally lacks evidence on the phenotypic consequences of most SVs that are suggested to have adaptive potential. Non-human genomes are heavily under-represented in population-scale studies of SVs. We argue that more research on other species is needed to objectively estimate the contribution of SVs to evolution. We discuss technical challenges associated with SV detection and outline the most recent advances towards more representative reference genomes, which opens a new era in population-scale studies of structural variation.
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Affiliation(s)
| | - Željka Pezer
- Laboratory for Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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14
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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [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: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
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15
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Glunčić M, Vlahović I, Rosandić M, Paar V. Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution. Life Sci Alliance 2022; 6:6/1/e202101306. [PMID: 36261226 PMCID: PMC9584774 DOI: 10.26508/lsa.202101306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
Previously it was found that the neuroblastoma breakpoint family (NBPF) gene repeat units of ∼1.6 kb have an important role in human brain evolution and function. The higher order organization of these repeat units has been discovered by both methods, the higher order repeat (HOR)-searching method and the HLS searching method. Using the HOR searching method with global repeat map algorithm, here we identified the tandemly organized NBPF HORs in the human and nonhuman primate NCBI reference genomes. We identified 50 tandemly organized canonical 3mer NBPF HOR copies (Olduvai triplets), but none in nonhuman primates chimpanzee, gorilla, orangutan, and Rhesus macaque. This discontinuous jump in tandemly organized HOR copy number is in sharp contrast to the known gradual increase in the number of Olduvai domains (NBPF monomers) from nonhuman primates to human, especially from ∼138 in chimpanzee to ∼300 in human genome. Using the same global repeat map algorithm method we have also determined the 3mer tandems of canonical 3mer HOR copies in 20 randomly chosen human genomes (10 male and 10 female). In all cases, we found the same 3mer HOR copy numbers as in the case of the reference human genome, with no mutation. On the other hand, some point mutations with respect to reference genome are found for some NBPF monomers which are not tandemly organized in canonical HORs.
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Affiliation(s)
- Matko Glunčić
- Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Marija Rosandić
- University Hospital Centre Zagreb (ret), Zagreb, Croatia,Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Vladimir Paar
- Faculty of Science, University of Zagreb, Zagreb, Croatia,Croatian Academy of Sciences and Arts, Zagreb, Croatia
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16
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Li T, Bian J, Tang M, Shangguan H, Zeng Y, Luo R, Sun H, Ke Q, Nie X, Li Y, Cui L. BGFD: an integrated multi-omics database of barley gene families. BMC PLANT BIOLOGY 2022; 22:454. [PMID: 36131236 PMCID: PMC9490965 DOI: 10.1186/s12870-022-03846-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND A gene family comprises a group of genes with similar functional domains that play various roles in plant growth, development, and responses to environmental stimuli. Barley (Hordeum vulgare L.) is the fourth most cultivated cereal crop worldwide, and it is an important model species for genetic studies. Systematic identification and annotation of gene families are key for studies of molecular function and evolutionary history. RESULTS We constructed a multi-omics database containing 5593 genes of 77 gene families called the Barley Gene Family Database (BGFD: http://barleygfdb.com ). BGFD is a free, user-friendly, and web-accessible platform that provides data on barley family genes. BGFD provides intuitive visual displays to facilitate studies of the physicochemical properties, gene structure, phylogenetic relationships, and motif organization of genes. Massive multi-omics datasets have been acquired and processed to generate an atlas of expression pattern profiles and genetic variation in BGFD. The platform offers several practical toolkits to conduct searches, browse, and employ BLAST functions, and the data are downloadable. CONCLUSIONS BGFD will aid research on the domestication and adaptive evolution of barley; it will also facilitate the screening of candidate genes and exploration of important agronomic traits in barley.
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Affiliation(s)
- Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325 Shandong China
| | - Minqiang Tang
- College of Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Hongbin Shangguan
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Huifan Sun
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Qinglin Ke
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
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17
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Espinós A, Fernández‐Ortuño E, Negri E, Borrell V. Evolution of genetic mechanisms regulating cortical neurogenesis. Dev Neurobiol 2022; 82:428-453. [PMID: 35670518 PMCID: PMC9543202 DOI: 10.1002/dneu.22891] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/26/2022] [Accepted: 05/24/2022] [Indexed: 11/20/2022]
Abstract
The size of the cerebral cortex increases dramatically across amniotes, from reptiles to great apes. This is primarily due to different numbers of neurons and glial cells produced during embryonic development. The evolutionary expansion of cortical neurogenesis was linked to changes in neural stem and progenitor cells, which acquired increased capacity of self‐amplification and neuron production. Evolution works via changes in the genome, and recent studies have identified a small number of new genes that emerged in the recent human and primate lineages, promoting cortical progenitor proliferation and increased neurogenesis. However, most of the mammalian genome corresponds to noncoding DNA that contains gene‐regulatory elements, and recent evidence precisely points at changes in expression levels of conserved genes as key in the evolution of cortical neurogenesis. Here, we provide an overview of basic cellular mechanisms involved in cortical neurogenesis across amniotes, and discuss recent progress on genetic mechanisms that may have changed during evolution, including gene expression regulation, leading to the expansion of the cerebral cortex.
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Affiliation(s)
- Alexandre Espinós
- Instituto de Neurociencias CSIC ‐ UMH, 03550 Sant Joan d'Alacant Spain
| | | | - Enrico Negri
- Instituto de Neurociencias CSIC ‐ UMH, 03550 Sant Joan d'Alacant Spain
| | - Víctor Borrell
- Instituto de Neurociencias CSIC ‐ UMH, 03550 Sant Joan d'Alacant Spain
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18
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Ma F, Zou Y, Ma L, Ma R, Chen X. Evolution, characterization, and immune response function of long-chain acyl-CoA synthetase genes in rainbow trout (Oncorhynchus mykiss) under hypoxic stress. Comp Biochem Physiol B Biochem Mol Biol 2022; 260:110737. [PMID: 35385771 DOI: 10.1016/j.cbpb.2022.110737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/16/2022] [Accepted: 03/31/2022] [Indexed: 11/30/2022]
Abstract
Long-chain acyl-CoA synthetases (Acsls), members of the acyl-activating enzyme superfamily, haves been systematically characterized in mammals and certain fishes, but the research on their involvement in reproductive development and hypoxic stress response in rainbow trout remains limited. In this study, we investigated the acsl gene structure and physical and chemical characteristics and the evolutionary relationship among acsl genes using the NCBI/Ensembl database. Using hypoxia treatment experiment, acsl gene expression in various organs and its regulation were investigated. A total of 11 acsl genes were identified in rainbow trout. Phylogenetic analyses found that acsl genes in rainbow trout were clustered into two clades: acsl3/4 and acsl1/2/5/6, and the additional gene duplication observed resulted from the third round of genome duplication unique to teleosts. Multiple sequence alignment and conserved motif analyses showed that the sequence of acsl proteins was highly conserved. Real-time quantitative PCR (RT-qPCR) showed that the acsl genes were highly expressed in immune tissues (liver and head kidney). Under hypoxia, the expression of acsl genes was upregulated, suggesting that they enhance the tolerance to hypoxia and are involved in the immune response in rainbow trout. Our study provides valuable insights into teleost evolution and effects of hypoxia on biological immunity and form a basis for further research on the functional characteristics of acsl genes.
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Affiliation(s)
- Fang Ma
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu Province, PR China.
| | - Yali Zou
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu Province, PR China
| | - Langfang Ma
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu Province, PR China
| | - Ruilin Ma
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu Province, PR China
| | - Xin Chen
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, Tianshui, Gansu Province, PR China
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19
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Sándor S, Jónás D, Tátrai K, Czeibert K, Kubinyi E. Poly(A) RNA sequencing reveals age-related differences in the prefrontal cortex of dogs. GeroScience 2022; 44:1269-1293. [PMID: 35288843 PMCID: PMC9213612 DOI: 10.1007/s11357-022-00533-3] [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: 08/24/2021] [Accepted: 02/17/2022] [Indexed: 12/02/2022] Open
Abstract
Dogs may possess a unique translational potential to investigate neural aging and dementia because they are prone to age-related cognitive decline, including an Alzheimer’s disease–like pathological condition. Yet very little is known about the molecular mechanisms underlying canine cognitive decline. The goal of the current study was to explore the transcriptomic differences between young and old dogs’ frontal cortex, which is a brain region often affected by various forms of age-related dementia in humans. RNA isolates from the frontal cortical brain area of 13 pet dogs, which represented 7 different breeds and crossbreds, were analyzed. The dogs were euthanized for medical reasons, and their bodies had been donated by their owners for scientific purposes. The poly(A) tail RNA subfraction of the total transcriptome was targeted in the sequencing analysis. Cluster analyses, differential gene expression analyses, and gene ontology analyses were carried out to assess which genes and genetic regulatory mechanisms were mostly affected by aging. Age was the most prominent factor in the clustering of the animals, indicating the presence of distinct gene expression patterns related to aging in a genetically variable population. A total of 3436 genes were found to be differentially expressed between the age groups, many of which were linked to neural function, immune system, and protein synthesis. These findings are in accordance with previous human brain aging RNA sequencing studies. Some genes were found to behave more similarly to humans than to rodents, further supporting the applicability of dogs in translational aging research.
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Affiliation(s)
- Sára Sándor
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.
| | - Dávid Jónás
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kitti Tátrai
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.,Department of Genetics, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kálmán Czeibert
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Eniko Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
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20
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Schmidt ERE, Polleux F. Genetic Mechanisms Underlying the Evolution of Connectivity in the Human Cortex. Front Neural Circuits 2022; 15:787164. [PMID: 35069126 PMCID: PMC8777274 DOI: 10.3389/fncir.2021.787164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/09/2021] [Indexed: 12/22/2022] Open
Abstract
One of the most salient features defining modern humans is our remarkable cognitive capacity, which is unrivaled by any other species. Although we still lack a complete understanding of how the human brain gives rise to these unique abilities, the past several decades have witnessed significant progress in uncovering some of the genetic, cellular, and molecular mechanisms shaping the development and function of the human brain. These features include an expansion of brain size and in particular cortical expansion, distinct physiological properties of human neurons, and modified synaptic development. Together they specify the human brain as a large primate brain with a unique underlying neuronal circuit architecture. Here, we review some of the known human-specific features of neuronal connectivity, and we outline how novel insights into the human genome led to the identification of human-specific genetic modifiers that played a role in the evolution of human brain development and function. Novel experimental paradigms are starting to provide a framework for understanding how the emergence of these human-specific genomic innovations shaped the structure and function of neuronal circuits in the human brain.
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Affiliation(s)
- Ewoud R. E. Schmidt
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
- *Correspondence: Ewoud R. E. Schmidt
| | - Franck Polleux
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Kavli Institute for Brain Science, Columbia University, New York, NY, United States
- Franck Polleux
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21
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Liu F, Zhou L, Zhang J, Wang Y, Wang Z, Liu X, Cai M. Genome-wide identification and transcriptome-based expression profiling of the Sox gene family in the spinyhead croaker (Collichthys lucidus). JOURNAL OF FISH BIOLOGY 2022; 100:15-24. [PMID: 34553785 DOI: 10.1111/jfb.14913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Sox genes encode transcription factors with a high-mobility group (HMG) box, playing critical roles in the initiation and maintenance of a variety of developmental processes, such as sex determination and differentiation. In the present study, we identified 26 Sox genes in the genome of spinyhead croaker Collichthys lucidus (Richardson, 1844) with homology-based analysis of the HMG box. The transcriptome-based expression profiles revealed that the expression of the Sox gene in gonads began to differ between sexes when the body length was 2.74 ± 0.24 cm. At that time, three Sox genes (Sox11b, Sox8a and Sox19) were significantly upregulated, accompanied by the downregulation of 12 Sox genes in the ovary, and six Sox genes were temporarily significantly upregulated in the testis. Afterwards, the expression profile of Sox genes changed only with a small amplitude in both the ovary and testis. For adult tissues, huge differences were observed in the expression profiles of Sox genes between ovaries and testes, as well as small differences in somatic tissues between sexes. These results provide clues to further decipher the role of Sox genes in the processes of sex determination and differentiation in spinyhead croaker and other teleosts.
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Affiliation(s)
- Fujiang Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Li Zhou
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Jing Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Xiande Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Mingyi Cai
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
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22
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Schmidt ERE, Zhao HT, Park JM, Dipoppa M, Monsalve-Mercado MM, Dahan JB, Rodgers CC, Lejeune A, Hillman EMC, Miller KD, Bruno RM, Polleux F. A human-specific modifier of cortical connectivity and circuit function. Nature 2021; 599:640-644. [PMID: 34707291 PMCID: PMC9161439 DOI: 10.1038/s41586-021-04039-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 09/17/2021] [Indexed: 01/04/2023]
Abstract
The cognitive abilities that characterize humans are thought to emerge from unique features of the cortical circuit architecture of the human brain, which include increased cortico-cortical connectivity. However, the evolutionary origin of these changes in connectivity and how they affected cortical circuit function and behaviour are currently unknown. The human-specific gene duplication SRGAP2C emerged in the ancestral genome of the Homo lineage before the major phase of increase in brain size1,2. SRGAP2C expression in mice increases the density of excitatory and inhibitory synapses received by layer 2/3 pyramidal neurons (PNs)3-5. Here we show that the increased number of excitatory synapses received by layer 2/3 PNs induced by SRGAP2C expression originates from a specific increase in local and long-range cortico-cortical connections. Mice humanized for SRGAP2C expression in all cortical PNs displayed a shift in the fraction of layer 2/3 PNs activated by sensory stimulation and an enhanced ability to learn a cortex-dependent sensory-discrimination task. Computational modelling revealed that the increased layer 4 to layer 2/3 connectivity induced by SRGAP2C expression explains some of the key changes in sensory coding properties. These results suggest that the emergence of SRGAP2C at the birth of the Homo lineage contributed to the evolution of specific structural and functional features of cortical circuits in the human cortex.
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Affiliation(s)
- Ewoud R E Schmidt
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, USA
| | - Hanzhi T Zhao
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA
| | - Jung M Park
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Mario Dipoppa
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Center for Theoretical Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mauro M Monsalve-Mercado
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Center for Theoretical Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jacob B Dahan
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Chris C Rodgers
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - Amélie Lejeune
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Elizabeth M C Hillman
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA
| | - Kenneth D Miller
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Center for Theoretical Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - Randy M Bruno
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - Franck Polleux
- Department of Neuroscience, Columbia University, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
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23
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Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development. Genes (Basel) 2021; 12:genes12101628. [PMID: 34681022 PMCID: PMC8535579 DOI: 10.3390/genes12101628] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/23/2022] Open
Abstract
Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.
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24
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Libé-Philippot B, Vanderhaeghen P. Cellular and Molecular Mechanisms Linking Human Cortical Development and Evolution. Annu Rev Genet 2021; 55:555-581. [PMID: 34535062 DOI: 10.1146/annurev-genet-071719-020705] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cerebral cortex is at the core of brain functions that are thought to be particularly developed in the human species. Human cortex specificities stem from divergent features of corticogenesis, leading to increased cortical size and complexity. Underlying cellular mechanisms include prolonged patterns of neuronal generation and maturation, as well as the amplification of specific types of stem/progenitor cells. While the gene regulatory networks of corticogenesis appear to be largely conserved among all mammals including humans, they have evolved in primates, particularly in the human species, through the emergence of rapidly divergent transcriptional regulatory elements, as well as recently duplicated novel genes. These human-specific molecular features together control key cellular milestones of human corticogenesis and are often affected in neurodevelopmental disorders, thus linking human neural development, evolution, and diseases. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Baptiste Libé-Philippot
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium; .,Institut de Recherches Interdisciplinaires en Biologie Humaine et Moléculaire (IRIBHM) and ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium; .,Institut de Recherches Interdisciplinaires en Biologie Humaine et Moléculaire (IRIBHM) and ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
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25
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Thomas GWC, Wang RJ, Nguyen J, Alan Harris R, Raveendran M, Rogers J, Hahn MW. Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques. Mol Biol Evol 2021; 38:1460-1471. [PMID: 33226085 PMCID: PMC8042740 DOI: 10.1093/molbev/msaa303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutations play a key role in the development of disease in an individual and the evolution of traits within species. Recent work in humans and other primates has clarified the origins and patterns of single-nucleotide variants, showing that most arise in the father’s germline during spermatogenesis. It remains unknown whether larger mutations, such as deletions and duplications of hundreds or thousands of nucleotides, follow similar patterns. Such mutations lead to copy-number variation (CNV) within and between species, and can have profound effects by deleting or duplicating genes. Here, we analyze patterns of CNV mutations in 32 rhesus macaque individuals from 14 parent–offspring trios. We find the rate of CNV mutations per generation is low (less than one per genome) and we observe no correlation between parental age and the number of CNVs that are passed on to offspring. We also examine segregating CNVs within the rhesus macaque sample and compare them to a similar data set from humans, finding that both species have far more segregating deletions than duplications. We contrast this with long-term patterns of gene copy-number evolution between 17 mammals, where the proportion of deletions that become fixed along the macaque lineage is much smaller than the proportion of segregating deletions. These results suggest purifying selection acting on deletions, such that the majority of them are removed from the population over time. Rhesus macaques are an important biomedical model organism, so these results will aid in our understanding of this species and the disease models it supports.
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Affiliation(s)
- Gregg W C Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Richard J Wang
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Jelena Nguyen
- Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN, USA.,Department of Computer Science, Indiana University, Bloomington, IN, USA
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26
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Kundu S, Ray MD, Sharma A. Interplay between genome organization and epigenomic alterations of pericentromeric DNA in cancer. J Genet Genomics 2021; 48:184-197. [PMID: 33840602 DOI: 10.1016/j.jgg.2021.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/07/2021] [Accepted: 02/20/2021] [Indexed: 12/16/2022]
Abstract
In eukaryotic genome biology, the genomic organization inside the three-dimensional (3D) nucleus is highly complex, and whether this organization governs gene expression is poorly understood. Nuclear lamina (NL) is a filamentous meshwork of proteins present at the lining of inner nuclear membrane that serves as an anchoring platform for genome organization. Large chromatin domains termed as lamina-associated domains (LADs), play a major role in silencing genes at the nuclear periphery. The interaction of the NL and genome is dynamic and stochastic. Furthermore, many genes change their positions during developmental processes or under disease conditions such as cancer, to activate certain sorts of genes and/or silence others. Pericentromeric heterochromatin (PCH) is mostly in the silenced region within the genome, which localizes at the nuclear periphery. Studies show that several genes located at the PCH are aberrantly expressed in cancer. The interesting question is that despite being localized in the pericentromeric region, how these genes still manage to overcome pericentromeric repression. Although epigenetic mechanisms control the expression of the pericentromeric region, recent studies about genome organization and genome-nuclear lamina interaction have shed light on a new aspect of pericentromeric gene regulation through a complex and coordinated interplay between epigenomic remodeling and genomic organization in cancer.
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Affiliation(s)
- Subhadip Kundu
- Laboratory of Chromatin and Cancer Epigenetics, Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - M D Ray
- Department of Surgical Oncology, IRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ashok Sharma
- Laboratory of Chromatin and Cancer Epigenetics, Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India.
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27
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Ma D, Guo Z, Ding Q, Zhao Z, Shen Z, Wei M, Gao C, Zhang L, Li H, Zhang S, Li J, Zhu X, Zheng HL. Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies. Mol Ecol Resour 2021; 21:1593-1607. [PMID: 33550674 DOI: 10.1111/1755-0998.13347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/22/2021] [Accepted: 02/02/2021] [Indexed: 12/18/2022]
Abstract
Aegiceras corniculatum is a major mangrove plant species adapted to waterlogging and saline conditions, grows in the coastal intertidal zone of tropical and subtropical regions. Here, we present a chromosome-level genome assembly of A. corniculatum by incorporating PacBio long-read sequencing and Hi-C technology. The results showed that the PacBio draft genome size is 906.63 Mb. Hi-C scaffolding anchored 885.06 Mb contigs (97.62% of draft assembly) onto 24 pseudochromosomes. The contig N50 and scaffold N50 were 7.1 Mb and 37.74 Mb, respectively. Out of 40,727 protein-coding genes predicted in the study, 89% have functional annotations in public databases. We also showed that of the 603.93 Mb repetitive sequences predicted in the assembled genome, long terminal repeat retrotransposons constitute 41.52%. The genome evolution analysis showed that the A. corniculatum genome experienced two whole-genome duplication events and shared the ancient γ whole-genome triplication event. A comparative genomic analysis revealed an incidence of expansion in 1,488 gene families associated with essential metabolism and biosynthetic pathways, including photosynthesis, oxidative phosphorylation, phenylalanine, glyoxylate, dicarboxylate metabolism, and DNA replication, which probably constitute adaptation traits that allow the A. corniculatum to survive in the intertidal zone. Also, the systematic characterization of genes associated with flavonoid biosynthesis pathway and the AcNHX gene family conducted in this study will provide insight into the adaptation mechanism of A. corniculatum to intertidal environments. The high-quality genome reported here can provide historical insights into genomic transformations that support the survival of A. corniculatum under harsh intertidal habitats.
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Affiliation(s)
- Dongna Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zejun Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qiansu Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhizhu Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhijun Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Mingyue Wei
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Changhao Gao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ludan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Huan Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Shan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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28
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Franchini LF. Genetic Mechanisms Underlying Cortical Evolution in Mammals. Front Cell Dev Biol 2021; 9:591017. [PMID: 33659245 PMCID: PMC7917222 DOI: 10.3389/fcell.2021.591017] [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: 08/03/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
The remarkable sensory, motor, and cognitive abilities of mammals mainly depend on the neocortex. Thus, the emergence of the six-layered neocortex in reptilian ancestors of mammals constitutes a fundamental evolutionary landmark. The mammalian cortex is a columnar epithelium of densely packed cells organized in layers where neurons are generated mainly in the subventricular zone in successive waves throughout development. Newborn cells move away from their site of neurogenesis through radial or tangential migration to reach their specific destination closer to the pial surface of the same or different cortical area. Interestingly, the genetic programs underlying neocortical development diversified in different mammalian lineages. In this work, I will review several recent studies that characterized how distinct transcriptional programs relate to the development and functional organization of the neocortex across diverse mammalian lineages. In some primates such as the anthropoids, the neocortex became extremely large, especially in humans where it comprises around 80% of the brain. It has been hypothesized that the massive expansion of the cortical surface and elaboration of its connections in the human lineage, has enabled our unique cognitive capacities including abstract thinking, long-term planning, verbal language and elaborated tool making capabilities. I will also analyze the lineage-specific genetic changes that could have led to the modification of key neurodevelopmental events, including regulation of cell number, neuronal migration, and differentiation into specific phenotypes, in order to shed light on the evolutionary mechanisms underlying the diversity of mammalian brains including the human brain.
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Affiliation(s)
- Lucía Florencia Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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29
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Ihnatovych I, Birkaya B, Notari E, Szigeti K. iPSC-Derived Microglia for Modeling Human-Specific DAMP and PAMP Responses in the Context of Alzheimer's Disease. Int J Mol Sci 2020; 21:ijms21249668. [PMID: 33352944 PMCID: PMC7765962 DOI: 10.3390/ijms21249668] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/08/2020] [Accepted: 12/15/2020] [Indexed: 12/25/2022] Open
Abstract
Neuroinflammation in Alzheimer’s disease (AD) has been the focus for identifying targetable pathways for drug development. The role of amyloid beta (Aβ), a prototype of damage-associated molecular patterns (DAMPs), has been implicated in triggering an inflammatory response. As alpha7 nicotinic acetylcholine receptor (α7 nAChR) binds Aβ with high affinity, α7 nAChR may play a role in Aβ-induced neuroinflammation. The conundrum of how α7 nAChR as the mediator of the cholinergic anti-inflammatory response may trigger an inflammatory response has not been resolved. CHRFAM7A, the uniquely human fusion gene between ULK4 and CHRNA7, is a negative regulator of α7 nAChR ionotropic function. To provide the human context, isogenic induced pluripotent stem cell (iPSC) lines were developed from CHRFAM7A null and carrier individuals by genome-editing the null line using TALENs to knock-in CHRFAM7A. In iPSC-derived microglia-like cells, CHRFAM7A mitigated Aβ uptake through the α7 nAChR. Despite the lower Aβ uptake, the presence of CHRFAM7A was associated with an innate immune response that was characterized by NF-κB activation and NF-κB target transcription (TNFA, IL6, and IL1B). LPS, a prototype PAMP, induced a heightened immune response in CHRFAM7A carriers. CHRFAM7A modified the dynamics of NF-κB translocation by prolonging its nuclear presence. CHRFAM7A modified the α7 nAChR metabotropic function, resulting in a human-specific innate immune response. This iPSC model provided an opportunity to elucidate the mechanism and establish high throughput screens.
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30
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Okawa Y, Kohara S, Uchiyama A, Yamazaki H, Uno Y. Evaluation of domain of unknown function 1220 (DUF1220) for detection of human genome by quantitative polymerase chain reaction: Potential use in assessing the biodistribution of transplanted therapeutic human cells. Drug Metab Pharmacokinet 2020; 38:100366. [PMID: 33714132 DOI: 10.1016/j.dmpk.2020.11.001] [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: 03/28/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
The biodistribution profile of cell-based therapy products in animal models is important for evaluation of their safety and efficacy. Because of its quantitative nature and sensitivity, the quantitative polymerase chain reaction (qPCR) is a useful method for detecting and quantifying xenogeneic cell-derived DNA in animal models, thereby allowing a biodistribution profile to be established. Although the restriction endonuclease family from Arthrobacter luteus (Alu) of repetitive elements in human genome sequences has been used to assess the biodistribution of human cells, high background signals are detected. In the present study, we evaluate the potential of domain of unknown function 1220 (DUF1220), which is a human lineage-specific, multiple-copy gene similar to Alu sequences, for such analysis. Using qPCR analysis for DUF1220, human genome could be detected against a mouse genome background at a level comparable to that of Alu sequences with no detectable background signals. Moreover, using this approach, the human genome could be distinguished from the cynomolgus monkey genome. Further investigation of the quantitative aspects of this DUF1220-based qPCR assay might prove its usefulness for biodistribution studies of human cells transplanted into animals in the future.
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Affiliation(s)
- Yurie Okawa
- Drug Safety Research Laboratories, Shin Nippon Biomedical Laboratories, Ltd., Kagoshima, Japan.
| | - Sakae Kohara
- Pharmacokinetics and Bioanalysis Center, Shin Nippon Biomedical Laboratories, Ltd., Kainan, Japan
| | - Asako Uchiyama
- Drug Safety Research Laboratories, Shin Nippon Biomedical Laboratories, Ltd., Kagoshima, Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Japan.
| | - Yasuhiro Uno
- Pharmacokinetics and Bioanalysis Center, Shin Nippon Biomedical Laboratories, Ltd., Kainan, Japan; Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.
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31
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Liu Y, Konopka G. An integrative understanding of comparative cognition: lessons from human brain evolution. Integr Comp Biol 2020; 60:991-1006. [PMID: 32681799 PMCID: PMC7608741 DOI: 10.1093/icb/icaa109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A comprehensive understanding of animal cognition requires the integration of studies on behavior, electrophysiology, neuroanatomy, development, and genomics. Although studies of comparative cognition are receiving increasing attention from organismal biologists, most current studies focus on the comparison of behaviors and anatomical structures to understand their adaptative values. However, to understand the most potentially complex cognitive program of the human brain a greater synthesis of a multitude of disciplines is needed. In this review, we start with extensive neuroanatomic comparisons between humans and other primates. One likely specialization of the human brain is the expansion of neocortex, especially in regions for high-order cognition (e.g., prefrontal cortex). We then discuss how such an expansion can be linked to heterochrony of the brain developmental program, resulting in a greater number of neurons and enhanced computational capacity. Furthermore, alteration of gene expression in the human brain has been associated with positive selection in DNA sequences of gene regulatory regions. These results not only imply that genes associated with brain development are a major factor in the evolution of cognition, but also that high-quality whole-genome sequencing and gene manipulation techniques are needed for an integrative and functional understanding of comparative cognition in non-model organisms.
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Affiliation(s)
- Yuxiang Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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32
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Suntsova MV, Buzdin AA. Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species. BMC Genomics 2020; 21:535. [PMID: 32912141 PMCID: PMC7488140 DOI: 10.1186/s12864-020-06962-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
Chimpanzees are the closest living relatives of humans. The divergence between human and chimpanzee ancestors dates to approximately 6,5-7,5 million years ago. Genetic features distinguishing us from chimpanzees and making us humans are still of a great interest. After divergence of their ancestor lineages, human and chimpanzee genomes underwent multiple changes including single nucleotide substitutions, deletions and duplications of DNA fragments of different size, insertion of transposable elements and chromosomal rearrangements. Human-specific single nucleotide alterations constituted 1.23% of human DNA, whereas more extended deletions and insertions cover ~ 3% of our genome. Moreover, much higher proportion is made by differential chromosomal inversions and translocations comprising several megabase-long regions or even whole chromosomes. However, despite of extensive knowledge of structural genomic changes accompanying human evolution we still cannot identify with certainty the causative genes of human identity. Most structural gene-influential changes happened at the level of expression regulation, which in turn provoked larger alterations of interactome gene regulation networks. In this review, we summarized the available information about genetic differences between humans and chimpanzees and their potential functional impacts on differential molecular, anatomical, physiological and cognitive peculiarities of these species.
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Affiliation(s)
- Maria V Suntsova
- Institute for personalized medicine, I.M. Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow, Russia
| | - Anton A Buzdin
- Institute for personalized medicine, I.M. Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, Moscow, Russia. .,Omicsway Corp, Walnut, CA, USA. .,Moscow Institute of Physics and Technology (National Research University), 141700, Moscow, Russia.
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33
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Huang X, Wu C, Gong K, Chen Q, Gu Q, Qin H, Zhao C, Yu T, Yang L, Fu W, Wang Y, Qin Q, Liu S. Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus. Front Genet 2020; 11:804. [PMID: 32849805 PMCID: PMC7399338 DOI: 10.3389/fgene.2020.00804] [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: 04/22/2020] [Accepted: 07/06/2020] [Indexed: 11/29/2022] Open
Abstract
The Sox gene family encoded transcription factors that played key roles in developmental processes in vertebrates. To further understand the evolutionary fate of the Sox gene family in teleosts, the Sox genes were comprehensively characterized in fish of different ploidy levels, including blunt snout bream (2n = 48, Megalobrama amblycephala, BSB), goldfish (2n = 100, Carassius auratus red var., 2nRCC), and autotetraploid C. auratus (4n = 200, 4nRCC). The 4nRCC, which derived from the whole genome duplication (WGD) of 2nRCC, were obtained through the distant hybridization of 2nRCC (♀) × BSB (♂). Compared with the 26 Sox genes in zebrafish (2n = 50, Danio rerio), 26, 47, and 92 putative Sox genes were identified in the BSB, 2nRCC, and 4nRCC genomes, respectively, and classified into seven subfamilies (B1, B2, C, D, E, F, and K). Comparative analyses showed that 89.36% (42/47) of Sox genes were duplicated in 2nRCC compared with those in BSB, while 97.83% (90/92) of Sox genes were duplicated in 4nRCC compared with those in 2nRCC, meaning the Sox gene family had undergone an expansion in BSB, 2nRCC, and 4nRCC, respectively, following polyploidization events. In addition, potential gene loss, genetic variations, and paternal parent SNP locus insertion occurred during the polyploidization events. Our data provided new insights into the evolution of the Sox gene family in polyploid vertebrates after several rounds of WGD events.
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Affiliation(s)
- Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Kaijun Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qian Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qianhong Gu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Wen Fu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
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34
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Ma F, Liu Z, Kang Y, Quan J. Genome-Wide Identification of hsp90 Gene in Rainbow Trout ( Oncorhynchus mykiss) and Their Regulated Expression in Response to Heat Stress. DNA Cell Biol 2020; 39:428-440. [PMID: 31977244 DOI: 10.1089/dna.2019.4936] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In this study, we analyzed the gene structure, chemical characterizations, chromosome locations, evolutionary relationship, and expression profile of hsp90 genes with online database. In addition, the expression levels of hsp90s were also investigated under heat stress by quantitative real-time (qRT)-PCR. A total of eight hsp90 genes were identified from the rainbow trout genome. They were all distributed on chromosomes 2, 4, 8, and 13. The molecular weight ranged from 78.93 to 91.39 kDa, and the isoelectric point ranged from 4.84 to 4.96. The eight hsp90 genes were clustered into six subfamilies (A, B, C, D, E, and F). Genetic structure and conserved domain analysis revealed that all eight hsp90 genes had only one exon, and motif 1-motif 10 was shared by most genes. According to RNA-seq analysis of rainbow trout liver and head kidney, a total of seven out of eight genes were significantly upregulated under heat stress, and qRT-PCR was carried out on these seven genes; the expression levels of these genes were significantly upregulated under heat stress. The significantly regulated expressions of hsp90 genes under heat stress indicated that hsp90 genes are involved in heat stress response in rainbow trout. This study provides a theoretical basis for further study on the role of hsp90 in the heat stress tolerance of rainbow trout.
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Affiliation(s)
- Fang Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yujun Kang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jinqiang Quan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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35
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Yang J, Hu Y, Han J, Xiao K, Liu X, Tan C, Zeng Q, Du H. Genome-wide analysis of the Chinese sturgeon sox gene family: identification, characterisation and expression profiles of different tissues. JOURNAL OF FISH BIOLOGY 2020; 96:175-184. [PMID: 31713865 DOI: 10.1111/jfb.14199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
The sox family is assumed to be responsible for a number of developmental systems. Genome sequencing technology makes it possible to scan sox genes and conduct characteristic analyses of different species. In fish, full characterisation of sox genes at the genome-wide level has been reported for pufferfish Takifugu rubripes, medaka Oryzias latipes, tilapia Oreochromis niloticus and channel catfish Ictalurus punctatus. However, no systematic investigation of the sox family in sturgeons (Acipenseridae) has been reported to date. This study conducted genome-wide identification of the sox genes in the Chinese sturgeon Acipenser sinensis and profiled their tissue distribution between male and female individuals. In total, 19 sox genes were identified, including soxb1, b2, c, d, e, f and h, in the Chinese sturgeon. Genomic structure analysis indicated relatively conserved exon-intron structures in each sox group and phylogenetic analysis supported the previous classification of the sox family. Most of the sox genes showed a tissue-specific expression pattern, indicating the possible involvement of Chinese sturgeon sox genes at different developmental processes such as cardiac and gonadal development. This study provides a comprehensive resource of Chinese sturgeon sox genes and enables a better understanding of the evolution and function of the sox family.
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Affiliation(s)
- Jing Yang
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Yacheng Hu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Jilu Han
- China Three Gorges Corporation, Yichang, China
| | - Kan Xiao
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Xueqing Liu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Chun Tan
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Qingkai Zeng
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Hejun Du
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
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36
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Heft IE, Mostovoy Y, Levy-Sakin M, Ma W, Stevens AJ, Pastor S, McCaffrey J, Boffelli D, Martin DI, Xiao M, Kennedy MA, Kwok PY, Sikela JM. The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome. Genetics 2020; 214:179-191. [PMID: 31754017 PMCID: PMC6944415 DOI: 10.1534/genetics.119.302782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/05/2019] [Indexed: 11/18/2022] Open
Abstract
Sequences encoding Olduvai protein domains (formerly DUF1220) show the greatest human lineage-specific increase in copy number of any coding region in the genome and have been associated, in a dosage-dependent manner, with brain size, cognitive aptitude, autism, and schizophrenia. Tandem intragenic duplications of a three-domain block, termed the Olduvai triplet, in four NBPF genes in the chromosomal 1q21.1-0.2 region, are primarily responsible for the striking human-specific copy number increase. Interestingly, most of the Olduvai triplets are adjacent to, and transcriptionally coregulated with, three human-specific NOTCH2NL genes that have been shown to promote cortical neurogenesis. Until now, the underlying genomic events that drove the Olduvai hyperamplification in humans have remained unexplained. Here, we show that the presence or absence of an alternative first exon of the Olduvai triplet perfectly discriminates between amplified (58/58) and unamplified (0/12) triplets. We provide sequence and breakpoint analyses that suggest the alternative exon was produced by an nonallelic homologous recombination-based mechanism involving the duplicative transposition of an existing Olduvai exon found in the CON3 domain, which typically occurs at the C-terminal end of NBPF genes. We also provide suggestive in vitro evidence that the alternative exon may promote instability through a putative G-quadraplex (pG4)-based mechanism. Lastly, we use single-molecule optical mapping to characterize the intragenic structural variation observed in NBPF genes in 154 unrelated individuals and 52 related individuals from 16 families and show that the presence of pG4-containing Olduvai triplets is strongly correlated with high levels of Olduvai copy number variation. These results suggest that the same driver of genomic instability that allowed the evolutionarily recent, rapid, and extreme human-specific Olduvai expansion remains highly active in the human genome.
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Affiliation(s)
- Ilea E Heft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Yulia Mostovoy
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Walfred Ma
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Aaron J Stevens
- Department of Pathology, University of Otago, Christchurch, New Zealand 8140
| | - Steven Pastor
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, California 94609
| | - David I Martin
- Children's Hospital Oakland Research Institute, Oakland, California 94609
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104
| | - Martin A Kennedy
- Department of Pathology, University of Otago, Christchurch, New Zealand 8140
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, California
- Department of Dermatology, University of California, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, California
| | - James M Sikela
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado 80045
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37
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Aamodt CM, Farias-Virgens M, White SA. Birdsong as a window into language origins and evolutionary neuroscience. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190060. [PMID: 31735151 DOI: 10.1098/rstb.2019.0060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Humans and songbirds share the key trait of vocal learning, manifested in speech and song, respectively. Striking analogies between these behaviours include that both are acquired during developmental critical periods when the brain's ability for vocal learning peaks. Both behaviours show similarities in the overall architecture of their underlying brain areas, characterized by cortico-striato-thalamic loops and direct projections from cortical neurons onto brainstem motor neurons that control the vocal organs. These neural analogies extend to the molecular level, with certain song control regions sharing convergent transcriptional profiles with speech-related regions in the human brain. This evolutionary convergence offers an unprecedented opportunity to decipher the shared neurogenetic underpinnings of vocal learning. A key strength of the songbird model is that it allows for the delineation of activity-dependent transcriptional changes in the brain that are driven by learned vocal behaviour. To capitalize on this advantage, we used previously published datasets from our laboratory that correlate gene co-expression networks to features of learned vocalization within and after critical period closure to probe the functional relevance of genes implicated in language. We interrogate specific genes and cellular processes through converging lines of evidence: human-specific evolutionary changes, intelligence-related phenotypes and relevance to vocal learning gene co-expression in songbirds. This article is part of the theme issue 'What can animal communication teach us about human language?'
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Affiliation(s)
- Caitlin M Aamodt
- Neuroscience Interdepartmental Program, University of California Los Angeles, CA 90095-7239, USA
| | - Madza Farias-Virgens
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California Los Angeles, CA 90095-7239, USA
| | - Stephanie A White
- Neuroscience Interdepartmental Program, University of California Los Angeles, CA 90095-7239, USA.,Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California Los Angeles, CA 90095-7239, USA.,Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095-7239, USA
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38
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Glinsky GV. A Catalogue of 59,732 Human-Specific Regulatory Sequences Reveals Unique-to-Human Regulatory Patterns Associated with Virus-Interacting Proteins, Pluripotency, and Brain Development. DNA Cell Biol 2019; 39:126-143. [PMID: 31730374 DOI: 10.1089/dna.2019.4988] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Extensive searches for genomic regions harboring various types of candidate human-specific regulatory sequences (HSRS) identified thousands' HSRS using high-resolution next-generation sequencing technologies and methodologically diverse comparative analyses of human and nonhuman primates' (NHPs) reference genomes. In this study, a comprehensive catalogue of 59,732 genomic loci harboring candidate HSRS has been assembled to facilitate the systematic analyses of genomic sequences that were either inherited from extinct common ancestors (ECAs) or created de novo in human genomes. These analyses identified thousands of candidate HSRS and HSRS-harboring loci that appear inherited from ECAs, yet absent in genomes of our closest evolutionary relatives, chimpanzee and bonobo, presumably due to the incomplete lineage sorting and/or species-specific loss or regulatory DNA. This pattern is particularly prominent for HSRS-harboring loci that have been putatively associated with human-specific gene expression changes in cerebral organoid models. A prominent majority of regions harboring human-specific mutations associated with human-specific expression changes during brain development is highly conserved in chimpanzee, bonobo, and gorilla genomes. Among NHPs, dominant fractions of HSRS-harboring loci associated with human-specific gene expression in both excitatory neurons (347 loci; 67%) and radial glia (683 loci; 72%) are highly conserved in the gorilla genome. Analysis of 4433 genes encoding virus-interacting proteins (VIPs) revealed that 95.9% of human VIPs are components of human-specific regulatory networks that appear to operate in distinct types of human cells from preimplantation embryos to adult dorsolateral prefrontal cortex. These analyses demonstrate that modern humans captured unique genome-wide combinations of regulatory sequences, divergent subsets of which are highly conserved in distinct species of six NHP separated by 30 million years of evolution. Concurrently, this unique-to-human mosaic of genomic regulatory patterns inherited from ECAs was supplemented with 12,486 created de novo HSRS. Genes encoding VIPs appear to represent a principal genomic target during evolution of human-specific regulatory networks, which contribute to fitness of Homo sapiens and affect a functionally diverse spectrum of biological and cellular processes controlled by VIP-containing liquid-liquid phase-separated condensates.
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Affiliation(s)
- Gennadi V Glinsky
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California
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39
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Wang X, Lin S, Liu D, Wang Q, McAvoy R, Ding J, Li Y. Characterization and Expression Analysis of ERF Genes in Fragaria vesca Suggest Different Divergences of Tandem ERF Duplicates. Front Genet 2019; 10:805. [PMID: 31572436 PMCID: PMC6752658 DOI: 10.3389/fgene.2019.00805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/31/2019] [Indexed: 01/26/2023] Open
Abstract
Ethylene-responsive factors (ERFs) play important roles in plant growth and development and in responses to abiotic stresses. However, little information was available about the ERF genes in woodland strawberry (Fragaria vesca), a genetic model plant for the Fragaria genus and Rosaceae family. In this study, 91 FveERF genes were identified, including 35 arrayed in tandem, indicating that tandem duplication is a major mechanism for the expansion of the FveERF family. According to their phylogenetic relationships with AtERFs from Arabidopsis thaliana, the tandem FveERF genes could be grouped into ancestral and lineage-specific tandem ones. The ancestral tandem FveERFs are likely derived from tandem duplications that occurred in the common ancestor of F. vesca and A. thaliana, whereas the lineage-specific ones are specifically present in the F. vesca lineage. The lineage-specific tandem FveERF duplicates are more conserved than the ancestral ones in sequence and structure. However, their expression in flowers and fruits is similarly diversified, indicating that tandem FveERFs have diverged rapidly after duplication in this respect. The lineage-specific tandem FveERFs display the same response patterns with only one exception under drought or cold, whereas the ancestral tandem ones are largely differentially expressed, suggesting that divergence of tandem FveERF expression under stress may have occurred later in the reproductive development. Our results provide evidence that the retention of tandem FveERF duplicates soon after their duplication may be related to their divergence in the regulation of reproductive development. In contrast, their further divergence in expression pattern likely contributes to plant response to abiotic stress.
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Affiliation(s)
- Xiaojing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shanshan Lin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Decai Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Quanzhi Wang
- Engineering and Technology Center for Modern Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Richard McAvoy
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, United States
| | - Jing Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, China.,Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, United States
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40
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Moon JM, Capra JA, Abbot P, Rokas A. Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation. Bioessays 2019; 41:e1900072. [PMID: 31373044 DOI: 10.1002/bies.201900072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/03/2019] [Indexed: 11/05/2022]
Abstract
Novel regulatory elements that enabled expression of pre-existing immune genes in reproductive tissues and novel immune genes with pregnancy-specific roles in eutherians have shaped the evolution of mammalian pregnancy by facilitating the emergence of novel mechanisms for immune regulation over its course. Trade-offs arising from conflicting fitness effects on reproduction and host defenses have further influenced the patterns of genetic variation of these genes. These three mechanisms (novel regulatory elements, novel immune genes, and trade-offs) played a pivotal role in refining the regulation of maternal immune systems during pregnancy in eutherians, likely facilitating the establishment of prolonged direct maternal-fetal contact in eutherians without causing immunological rejection of the genetically distinct fetus.
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Affiliation(s)
- Jiyun M Moon
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, 37235, USA.,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, 37235, USA.,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37235, USA
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41
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Boldinova EO, Khairullin RF, Makarova AV, Zharkov DO. Isoforms of Base Excision Repair Enzymes Produced by Alternative Splicing. Int J Mol Sci 2019; 20:ijms20133279. [PMID: 31277343 PMCID: PMC6651865 DOI: 10.3390/ijms20133279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/29/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
Transcripts of many enzymes involved in base excision repair (BER) undergo extensive alternative splicing, but functions of the corresponding alternative splice variants remain largely unexplored. In this review, we cover the studies describing the common alternatively spliced isoforms and disease-associated variants of DNA glycosylases, AP-endonuclease 1, and DNA polymerase beta. We also discuss the roles of alternative splicing in the regulation of their expression, catalytic activities, and intracellular transport.
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Affiliation(s)
| | - Rafil F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 9 Parizhskoy Kommuny Str., 420012 Kazan, Russia
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., 123182 Moscow, Russia.
| | - Dmitry O Zharkov
- Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia.
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
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42
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Gerdol M, Cervelli M, Oliverio M, Modica MV. Piercing Fishes: Porin Expansion and Adaptation to Hematophagy in the Vampire Snail Cumia reticulata. Mol Biol Evol 2019; 35:2654-2668. [PMID: 30099551 PMCID: PMC6231492 DOI: 10.1093/molbev/msy156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cytolytic pore-forming proteins are widespread in living organisms, being mostly involved in both sides of the host-pathogen interaction, either contributing to the innate defense or promoting infection. In venomous organisms, such as spiders, insects, scorpions, and sea anemones, pore-forming proteins are often secreted as key components of the venom. Coluporins are pore-forming proteins recently discovered in the Mediterranean hematophagous snail Cumia reticulata (Colubrariidae), highly expressed in the salivary glands that discharge their secretion at close contact with the host. To understand their putative functional role, we investigated coluporins' molecular diversity and evolutionary patterns. Coluporins is a well-diversified family including at least 30 proteins, with an overall low sequence similarity but sharing a remarkably conserved actinoporin-like predicted structure. Tracking the evolutionary history of the molluscan porin genes revealed a scattered distribution of this family, which is present in some other lineages of predatory gastropods, including venomous conoidean snails. Comparative transcriptomic analyses highlighted the expansion of porin genes as a lineage-specific feature of colubrariids. Coluporins seem to have evolved from a single ancestral porin gene present in the latest common ancestor of all Caenogastropoda, undergoing massive expansion and diversification in this colubrariid lineage through repeated gene duplication events paired with widespread episodic positive selection. As for other parasites, these findings are congruent with a "one-sided arms race," equipping the parasite with multiple variants in order to broaden its host spectrum. Overall, our results pinpoint a crucial adaptive role for coluporins in the evolution of the peculiar trophic ecology of vampire snails.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, Trieste University, Italy
| | | | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Roma, Italy
| | - Maria Vittoria Modica
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.,UMR5247, University of Montpellier, France
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43
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Fiddes IT, Pollen AA, Davis JM, Sikela JM. Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution. Hum Genet 2019; 138:715-721. [PMID: 31087184 PMCID: PMC6611739 DOI: 10.1007/s00439-019-02018-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
Sequences encoding Olduvai (DUF1220) protein domains show the largest human-specific increase in copy number of any coding region in the genome and have been linked to human brain evolution. Most human-specific copies of Olduvai (119/165) are encoded by three NBPF genes that are adjacent to three human-specific NOTCH2NL genes that have been shown to promote cortical neurogenesis. Here, employing genomic, phylogenetic, and transcriptomic evidence, we show that these NOTCH2NL/NBPF gene pairs evolved jointly, as two-gene units, very recently in human evolution, and are likely co-regulated. Remarkably, while three NOTCH2NL paralogs were added, adjacent Olduvai sequences hyper-amplified, adding 119 human-specific copies. The data suggest that human-specific Olduvai domains and adjacent NOTCH2NL genes may function in a coordinated, complementary fashion to promote neurogenesis and human brain expansion in a dosage-related manner.
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Affiliation(s)
| | - Alex A Pollen
- Department of Neurology and the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan M Davis
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics Program and Neuroscience Program, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - James M Sikela
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics Program and Neuroscience Program, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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44
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van der Nest MA, Steenkamp ET, Roodt D, Soal NC, Palmer M, Chan WY, Wilken PM, Duong TA, Naidoo K, Santana QC, Trollip C, De Vos L, van Wyk S, McTaggart AR, Wingfield MJ, Wingfield BD. Genomic analysis of the aggressive tree pathogen Ceratocystis albifundus. Fungal Biol 2019; 123:351-363. [PMID: 31053324 DOI: 10.1016/j.funbio.2019.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 12/13/2022]
Abstract
The overall goal of this study was to determine whether the genome of an important plant pathogen in Africa, Ceratocystis albifundus, is structured into subgenomic compartments, and if so, to establish how these compartments are distributed across the genome. For this purpose, the publicly available genome of C. albifundus was complemented with the genome sequences for four additional isolates using the Illumina HiSeq platform. In addition, a reference genome for one of the individuals was assembled using both PacBio and Illumina HiSeq technologies. Our results showed a high degree of synteny between the five genomes, although several regions lacked detectable long-range synteny. These regions were associated with the presence of accessory genes, lower genetic similarity, variation in read-map depth, as well as transposable elements and genes associated with host-pathogen interactions (e.g. effectors and CAZymes). Such patterns are regarded as hallmarks of accelerated evolution, particularly of accessory subgenomic compartments in fungal pathogens. Our findings thus showed that the genome of C. albifundus is made-up of core and accessory subgenomic compartments, which is an important step towards characterizing its pangenome. This study also highlights the value of comparative genomics for understanding mechanisms that may underly and influence the biology and evolution of pathogens.
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Affiliation(s)
- Magriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Danielle Roodt
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Nicole C Soal
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai-Yin Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Kershney Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Quentin C Santana
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Conrad Trollip
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Stephanie van Wyk
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Alistair R McTaggart
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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45
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Zhang S, Chen X, Wang M, Zhang W, Pan J, Qin Q, Zhong L, Shao J, Sun M, Jiang H, Bian W. Genome-wide identification, phylogeny and expressional profile of the Sox gene family in channel catfish (Ictalurus punctatus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:17-26. [DOI: 10.1016/j.cbd.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 12/11/2017] [Accepted: 03/05/2018] [Indexed: 01/10/2023]
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46
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Dougherty ML, Underwood JG, Nelson BJ, Tseng E, Munson KM, Penn O, Nowakowski TJ, Pollen AA, Eichler EE. Transcriptional fates of human-specific segmental duplications in brain. Genome Res 2018; 28:1566-1576. [PMID: 30228200 PMCID: PMC6169893 DOI: 10.1101/gr.237610.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/07/2018] [Indexed: 01/27/2023]
Abstract
Despite the importance of duplicate genes for evolutionary adaptation, accurate gene annotation is often incomplete, incorrect, or lacking in regions of segmental duplication. We developed an approach combining long-read sequencing and hybridization capture to yield full-length transcript information and confidently distinguish between nearly identical genes/paralogs. We used biotinylated probes to enrich for full-length cDNA from duplicated regions, which were then amplified, size-fractionated, and sequenced using single-molecule, long-read sequencing technology, permitting us to distinguish between highly identical genes by virtue of multiple paralogous sequence variants. We examined 19 gene families as expressed in developing and adult human brain, selected for their high sequence identity (average >99%) and overlap with human-specific segmental duplications (SDs). We characterized the transcriptional differences between related paralogs to better understand the birth-death process of duplicate genes and particularly how the process leads to gene innovation. In 48% of the cases, we find that the expressed duplicates have changed substantially from their ancestral models due to novel sites of transcription initiation, splicing, and polyadenylation, as well as fusion transcripts that connect duplication-derived exons with neighboring genes. We detect unannotated open reading frames in genes currently annotated as pseudogenes, while relegating other duplicates to nonfunctional status. Our method significantly improves gene annotation, specifically defining full-length transcripts, isoforms, and open reading frames for new genes in highly identical SDs. The approach will be more broadly applicable to genes in structurally complex regions of other genomes where the duplication process creates novel genes important for adaptive traits.
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Affiliation(s)
- Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Jason G Underwood
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Pacific Biosciences (PacBio) of California, Incorporated, Menlo Park, California 94025, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Elizabeth Tseng
- Pacific Biosciences (PacBio) of California, Incorporated, Menlo Park, California 94025, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94158, USA.,Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Alex A Pollen
- Department of Neurology, University of California, San Francisco, San Francisco, California 94158, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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47
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Saha M, Reddy HM, Salih MA, Estrella E, Jones MD, Mitsuhashi S, Cho KA, Suzuki-Hatano S, Rizzo SA, Hamad MH, Mukhtar MM, Hamed AA, Elseed MA, Lek M, Valkanas E, MacArthur DG, Kunkel LM, Pacak CA, Draper I, Kang PB. Impact of PYROXD1 deficiency on cellular respiration and correlations with genetic analyses of limb-girdle muscular dystrophy in Saudi Arabia and Sudan. Physiol Genomics 2018; 50:929-939. [PMID: 30345904 DOI: 10.1152/physiolgenomics.00036.2018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Next-generation sequencing is commonly used to screen for pathogenic mutations in families with Mendelian disorders, but due to the pace of discoveries, gaps have widened for some diseases between genetic and pathophysiological knowledge. We recruited and analyzed 16 families with limb-girdle muscular dystrophy (LGMD) of Arab descent from Saudi Arabia and Sudan who did not have confirmed genetic diagnoses. The analysis included both traditional and next-generation sequencing approaches. Cellular and metabolic studies were performed on Pyroxd1 siRNA C2C12 myoblasts and controls. Pathogenic mutations were identified in eight of the 16 families. One Sudanese family of Arab descent residing in Saudi Arabia harbored a homozygous c.464A>G, p.Asn155Ser mutation in PYROXD1, a gene recently reported in association with myofibrillar myopathy and whose protein product reduces thiol residues. Pyroxd1 deficiency in murine C2C12 myoblasts yielded evidence for impairments of cellular proliferation, migration, and differentiation, while CG10721 (Pyroxd1 fly homolog) knockdown in Drosophila yielded a lethal phenotype. Further investigations indicated that Pyroxd1 does not localize to mitochondria, yet Pyroxd1 deficiency is associated with decreased cellular respiration. This study identified pathogenic mutations in half of the LGMD families from the cohort, including one in PYROXD1. Developmental impairments were demonstrated in vitro for Pyroxd1 deficiency and in vivo for CG10721 deficiency, with reduced metabolic activity in vitro for Pyroxd1 deficiency.
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Affiliation(s)
- Madhurima Saha
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine , Gainesville, Florida
| | - Hemakumar M Reddy
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine , Gainesville, Florida
| | - Mustafa A Salih
- Division of Neurology, Department of Pediatrics, King Saud University , Riyadh , Saudi Arabia
| | - Elicia Estrella
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School , Boston, Massachusetts
| | - Michael D Jones
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine , Gainesville, Florida
| | - Satomi Mitsuhashi
- Department of Neurology, Boston Children's Hospital and Harvard Medical School , Boston, Massachusetts
| | - Kyung-Ah Cho
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine , Gainesville, Florida
| | - Silveli Suzuki-Hatano
- Department of Pediatrics, University of Florida College of Medicine , Gainesville, Florida
| | - Skylar A Rizzo
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine , Gainesville, Florida
| | - Muddathir H Hamad
- Division of Neurology, Department of Pediatrics, King Saud University , Riyadh , Saudi Arabia
| | - Maowia M Mukhtar
- The Institute of Endemic Diseases, University of Khartoum , Khartoum , Sudan
| | - Ahlam A Hamed
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Khartoum , Khartoum , Sudan
| | - Maha A Elseed
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Khartoum , Khartoum , Sudan
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School , Boston, Massachusetts.,Broad Institute of the Massachusetts Institute of Technology and Harvard University , Cambridge, Massachusetts
| | - Elise Valkanas
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School , Boston, Massachusetts.,Broad Institute of the Massachusetts Institute of Technology and Harvard University , Cambridge, Massachusetts
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School , Boston, Massachusetts.,Broad Institute of the Massachusetts Institute of Technology and Harvard University , Cambridge, Massachusetts
| | - Louis M Kunkel
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School , Boston, Massachusetts
| | - Christina A Pacak
- Department of Pediatrics, University of Florida College of Medicine , Gainesville, Florida
| | - Isabelle Draper
- Molecular Cardiology Research Institute, Tufts Medical Center , Boston, Massachusetts
| | - Peter B Kang
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine , Gainesville, Florida.,Department of Neurology and Department of Molecular Genetics and Microbiology, University of Florida College of Medicine , Gainesville, Florida.,Genetics Institute and Myology Institute, University of Florida , Gainesville, Florida
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48
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Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. High-resolution comparative analysis of great ape genomes. Science 2018; 360:eaar6343. [PMID: 29880660 PMCID: PMC6178954 DOI: 10.1126/science.aar6343] [Citation(s) in RCA: 231] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/02/2018] [Indexed: 12/22/2022]
Abstract
Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.
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Affiliation(s)
- Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Shwetha Murali
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Olivia S Meyerson
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jason G Underwood
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Pacific Biosciences (PacBio) of California, Inc., Menlo Park, CA 94025, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Mark J P Chaisson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Fereydoun Hormozdiari
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Nicola Lorusso
- Department of Biology, University of Bari, Aldo Moro, Bari 70121, Italy
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - AnneMarie E Welch
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Robert S Fulton
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Joel Armstrong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tina A Graves-Lindsay
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Ahmet M Denli
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emma R Hoppe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Christopher M Hill
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA 92121, USA
| | | | - Susan K Dutcher
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Fred H Gage
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wesley C Warren
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Han Cao
- Bionano Genomics, San Diego, CA 92121, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Aldo Moro, Bari 70121, Italy
| | - Richard K Wilson
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alex Pollen
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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49
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Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation. Cell 2018; 173:1370-1384.e16. [PMID: 29856955 PMCID: PMC6092419 DOI: 10.1016/j.cell.2018.03.067] [Citation(s) in RCA: 243] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/16/2018] [Accepted: 03/26/2018] [Indexed: 12/03/2022]
Abstract
The cerebral cortex underwent rapid expansion and increased complexity during recent hominid evolution. Gene duplications constitute a major evolutionary force, but their impact on human brain development remains unclear. Using tailored RNA sequencing (RNA-seq), we profiled the spatial and temporal expression of hominid-specific duplicated (HS) genes in the human fetal cortex and identified a repertoire of 35 HS genes displaying robust and dynamic patterns during cortical neurogenesis. Among them NOTCH2NL, human-specific paralogs of the NOTCH2 receptor, stood out for their ability to promote cortical progenitor maintenance. NOTCH2NL promote the clonal expansion of human cortical progenitors, ultimately leading to higher neuronal output. At the molecular level, NOTCH2NL function by activating the Notch pathway through inhibition of cis Delta/Notch interactions. Our study uncovers a large repertoire of recently evolved genes active during human corticogenesis and reveals how human-specific NOTCH paralogs may have contributed to the expansion of the human cortex. Identification of >35 HS protein-coding genes expressed during human corticogenesis NOTCH2NL human-specific paralogs of NOTCH2 expressed in human cortical progenitors NOTCH2NL genes expand human cortical progenitors and their neuronal output NOTCH2NL promotes Notch signaling through cis-inhibition of Delta/Notch interactions
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50
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Evolution and genomics of the human brain. NEUROLOGÍA (ENGLISH EDITION) 2018. [DOI: 10.1016/j.nrleng.2015.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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