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Liu A, Wang N, Xie G, Li Y, Yan X, Li X, Zhu Z, Li Z, Yang J, Meng F, Dou M, Chen W, Ma N, Jiang Y, Gao Y, Wang Y. GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes. Genome Res 2023; 33:1673-1689. [PMID: 37884342 PMCID: PMC10691551 DOI: 10.1101/gr.277784.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/23/2023] [Indexed: 10/28/2023]
Abstract
Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.
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Affiliation(s)
- Anguo Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Faculty of Mathematics and Natural Sciences, University of Cologne, and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, Cologne 50931, Germany
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xixi Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenliang Zhu
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuohui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yang
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fanxin Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weihuang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nange Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanpeng Gao
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
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Abstract
Human accelerated regions (HARs) are the fastest-evolving sequences in the human genome. When HARs were discovered in 2006, their function was mysterious due to scant annotation of the noncoding genome. Diverse technologies, from transgenic animals to machine learning, have consistently shown that HARs function as gene regulatory enhancers with significant enrichment in neurodevelopment. It is now possible to quantitatively measure the enhancer activity of thousands of HARs in parallel and model how each nucleotide contributes to gene expression. These strategies have revealed that many human HAR sequences function differently than their chimpanzee orthologs, though individual nucleotide changes in the same HAR may have opposite effects, consistent with compensatory substitutions. To fully evaluate the role of HARs in human evolution, it will be necessary to experimentally and computationally dissect them across more cell types and developmental stages.
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Affiliation(s)
- Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, San Francisco, California, USA; ,
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, California, USA; ,
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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Liu G, Zhang C, Wang Y, Dai G, Liu SQ, Wang W, Pan YH, Ding J, Li H. New exon and accelerated evolution of placental gene Nrk occurred in the ancestral lineage of placental mammals. Placenta 2021; 114:14-21. [PMID: 34418750 DOI: 10.1016/j.placenta.2021.08.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/20/2021] [Accepted: 08/12/2021] [Indexed: 11/18/2022]
Abstract
INTRODUCTION The chorioallantoic placenta is a specific organ for placental mammals. However, the adaptive events during its emergence are still poorly investigated. METHODS We scanned the chromosome X to detect the accelerated evolution in the ancestral lineage of placental mammals, and constructed 3D protein structure models of a candidate by homology modeling. RESULTS Eight branch-specific accelerated regions were identified. Five of these regions (P=5.61×10-11 ~ 9.03×10-8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Nrk belongs to the germinal center kinase-IV subfamily with the overall similar protein structure; however, a new exon emerged in ancestors of placental mammals and its sequence has been conserved since then. Structure modelling of NRK suggests that the accelerated exons and the placental-mammal-specific exon (as a new loop) could change the enzymatic activity and the structure of placental mammal NRK. DISCUSSION Since the new loop is surrounded by the accelerated protein regions, it is likely that the new loop occurred and shifted the function of NRK, and then the accelerated evolution of Nrk occurred to adapt the structure change caused by the new loop in the ancestral lineage of placental mammals. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection.
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Affiliation(s)
- Guopeng Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Chunxiao Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Yuting Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Guangyi Dai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China
| | - Wenshuai Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, 200062, China.
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Haipeng Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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Lee KS, Bang H, Choi JK, Kim K. Accelerated Evolution of the Regulatory Sequences of Brain Development in the Human Genome. Mol Cells 2020; 43:331-339. [PMID: 32235023 PMCID: PMC7191052 DOI: 10.14348/molcells.2020.2282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/03/2020] [Accepted: 03/08/2020] [Indexed: 12/14/2022] Open
Abstract
Genetic modifications in noncoding regulatory regions are likely critical to human evolution. Human-accelerated noncoding elements are highly conserved noncoding regions among vertebrates but have large differences across humans, which implies human-specific regulatory potential. In this study, we found that human-accelerated noncoding elements were frequently coupled with DNase I hypersensitive sites (DHSs), together with monomethylated and trimethylated histone H3 lysine 4, which are active regulatory markers. This coupling was particularly pronounced in fetal brains relative to adult brains, non-brain fetal tissues, and embryonic stem cells. However, fetal brain DHSs were also specifically enriched in deeply conserved sequences, implying coexistence of universal maintenance and human-specific fitness in human brain development. We assessed whether this coexisting pattern was a general one by quantitatively measuring evolutionary rates of DHSs. As a result, fetal brain DHSs showed a mixed but distinct signature of regional conservation and outlier point acceleration as compared to other DHSs. This finding suggests that brain developmental sequences are selectively constrained in general, whereas specific nucleotides are under positive selection or constraint relaxation simultaneously. Hence, we hypothesize that human- or primate-specific changes to universally conserved regulatory codes of brain development may drive the accelerated, and most likely adaptive, evolution of the regulatory network of the human brain.
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Affiliation(s)
- Kang Seon Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
| | - Hyoeun Bang
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
| | - Kwoneel Kim
- Department of Biology, Kyung Hee University, Seoul 0447, Korea
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Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Res 2015; 25:1245-55. [PMID: 26104583 PMCID: PMC4561485 DOI: 10.1101/gr.192591.115] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/15/2015] [Indexed: 01/19/2023]
Abstract
It has long been hypothesized that changes in gene regulation have played an important role in human evolution, but regulatory DNA has been much more difficult to study compared with protein-coding regions. Recent large-scale studies have created genome-scale catalogs of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To better define regulatory DNA that has been subject to human-specific adaptive evolution, we performed comprehensive evolutionary and population genetics analyses on over 18 million DHSs discovered in 130 cell types. We identified 524 DHSs that are conserved in nonhuman primates but accelerated in the human lineage (haDHS), and estimate that 70% of substitutions in haDHSs are attributable to positive selection. Through extensive computational and experimental analyses, we demonstrate that haDHSs are often active in brain or neuronal cell types; play an important role in regulating the expression of developmentally important genes, including many transcription factors such as SOX6, POU3F2, and HOX genes; and identify striking examples of adaptive regulatory evolution that may have contributed to human-specific phenotypes. More generally, our results reveal new insights into conserved and adaptive regulatory DNA in humans and refine the set of genomic substrates that distinguish humans from their closest living primate relatives.
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Affiliation(s)
- Rachel M Gittelman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Enna Hun
- Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jennifer Madeoy
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Len Pennacchio
- Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, California 94701, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - R David Hawkins
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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Necsulea A, Kaessmann H. Evolutionary dynamics of coding and non-coding transcriptomes. Nat Rev Genet 2014; 15:734-48. [PMID: 25297727 DOI: 10.1038/nrg3802] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive assessments of transcript sequences and expression levels. Here, we review the initial wave of the new generation of comparative transcriptomic studies in mammals and vertebrate outgroup species in the context of earlier work. Together with various large-scale genomic and epigenomic data, these studies have unveiled commonalities and differences in the dynamics of gene expression evolution for various types of coding and non-coding genes across mammalian lineages, organs, developmental stages, chromosomes and sexes. They have also provided intriguing new clues to the regulatory basis and phenotypic implications of evolutionary gene expression changes.
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Affiliation(s)
- Anamaria Necsulea
- Laboratory of Developmental Genomics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Henrik Kaessmann
- 1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Hubisz MJ, Pollard KS. Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution. Curr Opin Genet Dev 2014; 29:15-21. [PMID: 25156517 DOI: 10.1016/j.gde.2014.07.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 12/31/2022]
Abstract
Human accelerated regions (HARs) are DNA sequences that changed very little throughout mammalian evolution, but then experienced a burst of changes in humans since divergence from chimpanzees. This unexpected evolutionary signature is suggestive of deeply conserved function that was lost or changed on the human lineage. Since their discovery, the actual roles of HARs in human evolution have remained somewhat elusive, due to their being almost exclusively non-coding sequences with no annotation. Ongoing research is beginning to crack this problem by leveraging new genome sequences, functional genomics data, computational approaches, and genetic assays to reveal that many HARs are developmental gene regulatory elements and RNA genes, most of which evolved their uniquely human mutations through positive selection before divergence of archaic hominins and diversification of modern humans.
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Affiliation(s)
- Melissa J Hubisz
- Department of Biological Statistics and Computational Biology, Cornell University, 102D Weill Hall, Ithaca, NY 14853, USA
| | - Katherine S Pollard
- Gladstone Institutes, Division of Biostatistics & Institute for Human Genetics, University of California, 1650 Owens Street, San Francisco, CA 94158, USA.
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Gotea V, Elnitski L. Ascertaining regions affected by GC-biased gene conversion through weak-to-strong mutational hotspots. Genomics 2014; 103:349-56. [PMID: 24727706 DOI: 10.1016/j.ygeno.2014.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 03/31/2014] [Accepted: 04/04/2014] [Indexed: 12/24/2022]
Abstract
A major objective for evolutionary biology is to identify regions affected by positive selection. High dN/dS values for proteins and accelerated lineage-specific substitution rates for non-coding regions are considered classic signatures of positive selection. However, these could also be the result of non-adaptive phenomena, such as GC-biased gene conversion (gBGC), which favors the fixation of strong (C/G) over weak (A/T) nucleotides. Recent estimates indicate that gBGC affected up to 20% of regions with signatures of positive selection. Here we evaluate the impact of gBGC through its molecular signature of weak-to-strong mutational hotspots. We implemented specific modifications to the test proposed by Tang and Lewontin (1999) for identifying regions of differential variability and applied it to regions previously investigated for the influence of gBGC. While we found significant agreement with previous reports, our results suggest a smaller influence of gBGC than previously estimated, warranting further development of methods for its detection.
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Affiliation(s)
- Valer Gotea
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Laura Elnitski
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Capra JA, Erwin GD, McKinsey G, Rubenstein JLR, Pollard KS. Many human accelerated regions are developmental enhancers. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130025. [PMID: 24218637 PMCID: PMC3826498 DOI: 10.1098/rstb.2013.0025] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The genetic changes underlying the dramatic differences in form and function between humans and other primates are largely unknown, although it is clear that gene regulatory changes play an important role. To identify regulatory sequences with potentially human-specific functions, we and others used comparative genomics to find non-coding regions conserved across mammals that have acquired many sequence changes in humans since divergence from chimpanzees. These regions are good candidates for performing human-specific regulatory functions. Here, we analysed the DNA sequence, evolutionary history, histone modifications, chromatin state and transcription factor (TF) binding sites of a combined set of 2649 non-coding human accelerated regions (ncHARs) and predicted that at least 30% of them function as developmental enhancers. We prioritized the predicted ncHAR enhancers using analysis of TF binding site gain and loss, along with the functional annotations and expression patterns of nearby genes. We then tested both the human and chimpanzee sequence for 29 ncHARs in transgenic mice, and found 24 novel developmental enhancers active in both species, 17 of which had very consistent patterns of activity in specific embryonic tissues. Of these ncHAR enhancers, five drove expression patterns suggestive of different activity for the human and chimpanzee sequence at embryonic day 11.5. The changes to human non-coding DNA in these ncHAR enhancers may modify the complex patterns of gene expression necessary for proper development in a human-specific manner and are thus promising candidates for understanding the genetic basis of human-specific biology.
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Affiliation(s)
- John A Capra
- Gladstone Institutes, University of California, , San Francisco, CA 94158, USA
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Pessia E, Popa A, Mousset S, Rezvoy C, Duret L, Marais GAB. Evidence for widespread GC-biased gene conversion in eukaryotes. Genome Biol Evol 2012; 4:675-82. [PMID: 22628461 PMCID: PMC5635611 DOI: 10.1093/gbe/evs052] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
GC-biased gene conversion (gBGC) is a process that tends to increase the GC content of recombining DNA over evolutionary time and is thought to explain the evolution of GC content in mammals and yeasts. Evidence for gBGC outside these two groups is growing but is still limited. Here, we analyzed 36 completely sequenced genomes representing four of the five major groups in eukaryotes (Unikonts, Excavates, Chromalveolates and Plantae). gBGC was investigated by directly comparing GC content and recombination rates in species where recombination data are available, that is, half of them. To study all species of our dataset, we used chromosome size as a proxy for recombination rate and compared it with GC content. Among the 17 species showing a significant relationship between GC content and chromosome size, 15 are consistent with the predictions of the gBGC model. Importantly, the species showing a pattern consistent with gBGC are found in all the four major groups of eukaryotes studied, which suggests that gBGC may be widespread in eukaryotes.
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Affiliation(s)
- Eugénie Pessia
- Université Lyon 1, Centre National de la Recherche Scientifique, UMR5558, Laboratoire de Biométrie et Biologie évolutive, Villeurbanne, Cedex, France
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11
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Berná L, Chaurasia A, Angelini C, Federico C, Saccone S, D'Onofrio G. The footprint of metabolism in the organization of mammalian genomes. BMC Genomics 2012; 13:174. [PMID: 22568857 PMCID: PMC3384468 DOI: 10.1186/1471-2164-13-174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 05/08/2012] [Indexed: 01/02/2023] Open
Abstract
Background At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoints distribution, the thermal stability and the metabolic rate. Several studies carried out on bacteria and teleostean fish pointed towards the critical role played by the environment on the metabolic rate in shaping the base composition of genomes. In mammals the debate is still open, and evidences have been produced in favor of each evolutionary hypothesis. Human genes were assigned to three large functional categories (as well as to the corresponding functional classes) according to the KOG database: (i) information storage and processing, (ii) cellular processes and signaling, and (iii) metabolism. The classification was extended to the organisms so far analyzed performing a reciprocal Blastp and selecting the best reciprocal hit. The base composition was calculated for each sequence of the whole CDS dataset. Results The GC3 level of the above functional categories was increasing from (i) to (iii). This specific compositional pattern was found, as footprint, in all mammalian genomes, but not in frog and lizard ones. Comparative analysis of human versus both frog and lizard functional categories showed that genes involved in the metabolic processes underwent the highest GC3 increment. Analyzing the KOG functional classes of genes, again a well defined intra-genomic pattern was found in all mammals. Not only genes of metabolic pathways, but also genes involved in chromatin structure and dynamics, transcription, signal transduction mechanisms and cytoskeleton, showed an average GC3 level higher than that of the whole genome. In the case of the human genome, the genes of the aforementioned functional categories showed a high probability to be associated with the chromosomal bands. Conclusions In the light of different evolutionary hypotheses proposed so far, and contributing with different potential to the genome compositional heterogeneity of mammalian genomes, the one based on the metabolic rate seems to play not a minor role. Keeping in mind similar results reported in bacteria and in teleosts, the specific compositional patterns observed in mammals highlight metabolic rate as unifying factor that fits over a wide range of living organisms.
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Affiliation(s)
- Luisa Berná
- Genome Evolution and Organization - Department Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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Takahashi M, Saitou N. Identification and characterization of lineage-specific highly conserved noncoding sequences in Mammalian genomes. Genome Biol Evol 2012; 4:641-57. [PMID: 22505575 PMCID: PMC3381673 DOI: 10.1093/gbe/evs035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2012] [Indexed: 01/12/2023] Open
Abstract
Vertebrate genome comparisons revealed that there are highly conserved noncoding sequences (HCNSs) among a wide range of species and many of which contain regulatory elements. However, recently emerged sequences conserved in specific lineages have not been well studied. Toward this end, we identified 8,198 primate and 21,128 specific HCNSs as representative ones among mammals from human-marmoset and mouse-rat comparisons, respectively. Derived allele frequency analysis of primate-specific HCNSs showed that these HCNSs were under purifying selection, indicating that they may harbor important functions. We selected the top 1,000 largest HCNSs and compared the lineage-specific HCNS-flanking genes (LHF genes) with ultraconserved element (UCE)-flanking genes. Interestingly, the majority of LHF genes were different from UCE-flanking genes. This lineage-specific set of LHF genes was more enriched in protein-binding function. Conversely, the number of LHF genes that were also shared by UCEs was small but significantly larger than random expectation, and many of these genes were involved in anatomical development as transcriptional regulators, suggesting that certain groups of genes preferentially recruit new HCNSs in addition to old HCNSs that are conserved among vertebrates. This group of LHF genes might be involved in the various levels of lineage-specific evolution among vertebrates, mammals, primates, and rodents. If so, the emergence of HCNSs in and around these two groups of LHF genes developed lineage-specific characteristics. Our results provide new insight into lineage-specific evolution through interactions between HCNSs and their LHF genes.
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Affiliation(s)
- Mahoko Takahashi
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Japan
- Division of Population Genetics, National Institute of Genetics, Japan
- Present address: Department of Genetics, Stanford University
| | - Naruya Saitou
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Japan
- Division of Population Genetics, National Institute of Genetics, Japan
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Wittkopp PJ, Kalay G. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet 2011; 13:59-69. [DOI: 10.1038/nrg3095] [Citation(s) in RCA: 677] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Kostka D, Hubisz MJ, Siepel A, Pollard KS. The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol 2011; 29:1047-57. [PMID: 22075116 PMCID: PMC3278478 DOI: 10.1093/molbev/msr279] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
GC-biased gene conversion (gBGC) is a recombination-associated evolutionary process that accelerates the fixation of guanine or cytosine alleles, regardless of their effects on fitness. gBGC can increase the overall rate of substitutions, a hallmark of positive selection. Many fast-evolving genes and noncoding sequences in the human genome have GC-biased substitution patterns, suggesting that gBGC-in contrast to adaptive processes-may have driven the human changes in these sequences. To investigate this hypothesis, we developed a substitution model for DNA sequence evolution that quantifies the nonlinear interacting effects of selection and gBGC on substitution rates and patterns. Based on this model, we used a series of lineage-specific likelihood ratio tests to evaluate sequence alignments for evidence of changes in mode of selection, action of gBGC, or both. With a false positive rate of less than 5% for individual tests, we found that the majority (76%) of previously identified human accelerated regions are best explained without gBGC, whereas a substantial minority (19%) are best explained by the action of gBGC alone. Further, more than half (55%) have substitution rates that significantly exceed local estimates of the neutral rate, suggesting that these regions may have been shaped by positive selection rather than by relaxation of constraint. By distinguishing the effects of gBGC, relaxation of constraint, and positive selection we provide an integrated analysis of the evolutionary forces that shaped the fastest evolving regions of the human genome, which facilitates the design of targeted functional studies of adaptation in humans.
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Affiliation(s)
- Dennis Kostka
- Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, USA.
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15
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Suzuki Y. Statistical methods for detecting natural selection from genomic data. Genes Genet Syst 2011; 85:359-76. [PMID: 21415566 DOI: 10.1266/ggs.85.359] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the study of molecular and phenotypic evolution, understanding the relative importance of random genetic drift and positive selection as the mechanisms for driving divergences between populations and maintaining polymorphisms within populations has been a central issue. A variety of statistical methods has been developed for detecting natural selection operating at the amino acid and nucleotide sequence levels. These methods may be largely classified into those aimed at detecting recurrent and/or recent/ongoing natural selection by utilizing the divergence and/or polymorphism data. Using these methods, pervasive positive selection has been identified for protein-coding and non-coding sequences in the genomic analysis of some organisms. However, many of these methods have been criticized by using computer simulation and real data analysis to produce excessive false-positives and to be sensitive to various disturbing factors. Importantly, some of these methods have been invalidated experimentally. These facts indicate that many of the statistical methods for detecting natural selection are unreliable. In addition, the signals that have been believed as the evidence for fixations of advantageous mutations due to positive selection may also be interpreted as the evidence for fixations of deleterious mutations due to random genetic drift. The genomic diversity data are rapidly accumulating in various organisms, and detection of natural selection may play a critical role for clarifying the relative role of random genetic drift and positive selection in molecular and phenotypic evolution. It is therefore important to develop reliable statistical methods that are unbiased as well as robust against various disturbing factors, for inferring natural selection.
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Affiliation(s)
- Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, Japan.
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16
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Katzman S, Capra JA, Haussler D, Pollard KS. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol 2011; 3:614-26. [PMID: 21697099 PMCID: PMC3157837 DOI: 10.1093/gbe/evr058] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Fast evolving regions of many metazoan genomes show a bias toward substitutions that change weak (A,T) into strong (G,C) base pairs. Single-nucleotide polymorphisms (SNPs) do not share this pattern, suggesting that it results from biased fixation rather than biased mutation. Supporting this hypothesis, analyses of polymorphism in specific regions of the human genome have identified a positive correlation between weak to strong (W→S) SNPs and derived allele frequency (DAF), suggesting that SNPs become increasingly GC biased over time, especially in regions of high recombination. Using polymorphism data generated by the 1000 Genomes Project from 179 individuals from 4 human populations, we evaluated the extent and distribution of ongoing GC-biased evolution in the human genome. We quantified GC fixation bias by comparing the DAFs of W→S mutations and S→W mutations using a Mann-Whitney U test. Genome-wide, W→S SNPs have significantly higher DAFs than S→W SNPs. This pattern is widespread across the human genome but varies in magnitude along the chromosomes. We found extreme GC-biased evolution in neighborhoods of recombination hot spots, a significant correlation between GC bias and recombination rate, and an inverse correlation between GC bias and chromosome arm length. These findings demonstrate the presence of ongoing fixation bias favoring G and C alleles throughout the human genome and suggest that the bias is caused by a recombination-associated process, such as GC-biased gene conversion.
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Affiliation(s)
- Sol Katzman
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, USA
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17
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Necşulea A, Popa A, Cooper DN, Stenson PD, Mouchiroud D, Gautier C, Duret L. Meiotic recombination favors the spreading of deleterious mutations in human populations. Hum Mutat 2011; 32:198-206. [PMID: 21120948 DOI: 10.1002/humu.21407] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 10/28/2010] [Indexed: 11/09/2022]
Abstract
Although mutations that are detrimental to the fitness of organisms are expected to be rapidly purged from populations by natural selection, some disease-causing mutations are present at high frequencies in human populations. Several nonexclusive hypotheses have been proposed to account for this apparent paradox (high new mutation rate, genetic drift, overdominance, or recent changes in selective pressure). However, the factors ultimately responsible for the presence at high frequency of disease-causing mutations are still contentious. Here we establish the existence of an additional process that contributes to the spreading of deleterious mutations: GC-biased gene conversion (gBGC), a process associated with recombination that tends to favor the transmission of GC-alleles over AT-alleles. We show that the spectrum of amino acid-altering polymorphisms in human populations exhibits the footprints of gBGC. This pattern cannot be explained in terms of selection and is evident with all nonsynonymous mutations, including those predicted to be detrimental to protein structure and function, and those implicated in human genetic disease. We present simulations to illustrate the conditions under which gBGC can extend the persistence time of deleterious mutations in a finite population. These results indicate that gBGC meiotic drive contributes to the spreading of deleterious mutations in human populations.
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Affiliation(s)
- Anamaria Necşulea
- Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
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18
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Ratnakumar A, Mousset S, Glémin S, Berglund J, Galtier N, Duret L, Webster MT. Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc Lond B Biol Sci 2010; 365:2571-80. [PMID: 20643747 DOI: 10.1098/rstb.2010.0007] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The identification of loci influenced by positive selection is a major goal of evolutionary genetics. A popular approach is to perform scans of alignments on a genome-wide scale in order to find regions evolving at accelerated rates on a particular branch of a phylogenetic tree. However, positive selection is not the only process that can lead to accelerated evolution. Notably, GC-biased gene conversion (gBGC) is a recombination-associated process that results in the biased fixation of G and C nucleotides. This process can potentially generate bursts of nucleotide substitutions within hotspots of meiotic recombination. Here, we analyse the results of a scan for positive selection on genes on branches across the primate phylogeny. We show that genes identified as targets of positive selection have a significant tendency to exhibit the genomic signature of gBGC. Using a maximum-likelihood framework, we estimate that more than 20 per cent of cases of significantly elevated non-synonymous to synonymous substitution rates ratio (d(N)/d(S)), particularly in shorter branches, could be due to gBGC. We demonstrate that in some cases, gBGC can lead to very high d(N)/d(S) (more than 2). Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection.
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Affiliation(s)
- Abhirami Ratnakumar
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
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19
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Hünemeier T, Ruiz-Linares A, Silveira Á, Paixão-Côrtes VR, Salzano FM, Bortolini MC. Brief communication: Population data support the adaptive nature of HACNS1 sapiens/neandertal-chimpanzee differences in a limb expression domain. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 143:478-81. [DOI: 10.1002/ajpa.21378] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. GC-biased evolution near human accelerated regions. PLoS Genet 2010; 6:e1000960. [PMID: 20502635 PMCID: PMC2873926 DOI: 10.1371/journal.pgen.1000960] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 04/20/2010] [Indexed: 12/30/2022] Open
Abstract
Regions of the genome that have been the target of positive selection specifically along the human lineage are of special importance in human biology. We used high throughput sequencing combined with methods to enrich human genomic samples for particular targets to obtain the sequence of 22 chromosomal samples at high depth in 40 kb neighborhoods of 49 previously identified 100–400 bp elements that show evidence for human accelerated evolution. In addition to selection, the pattern of nucleotide substitutions in several of these elements suggested an historical bias favoring the conversion of weak (A or T) alleles into strong (G or C) alleles. Here we found strong evidence in the derived allele frequency spectra of many of these 40 kb regions for ongoing weak-to-strong fixation bias. Comparison of the nucleotide composition at polymorphic loci to the composition at sites of fixed substitutions additionally reveals the signature of historical weak-to-strong fixation bias in a subset of these regions. Most of the regions with evidence for historical bias do not also have signatures of ongoing bias, suggesting that the evolutionary forces generating weak-to-strong bias are not constant over time. To investigate the role of selection in shaping these regions, we analyzed the spatial pattern of polymorphism in our samples. We found no significant evidence for selective sweeps, possibly because the signal of such sweeps has decayed beyond the power of our tests to detect them. Together, these results do not rule out functional roles for the observed changes in these regions—indeed there is good evidence that the first two are functional elements in humans—but they suggest that a fixation process (such as biased gene conversion) that is biased at the nucleotide level, but is otherwise selectively neutral, could be an important evolutionary force at play in them, both historically and at present. The search for functional regions in the human genome, beyond the protein-coding portion, often relies on signals of conservation across species. The Human Accelerated Regions (HARs) are strongly conserved elements, ranging in size from 100–400 bp, that show an unexpected number of human-specific changes. This pattern suggests that HARs may be functional elements that have significantly changed during human evolution. To analyze the evolutionary forces that led these changes, we studied 40 kb neighborhoods of the top 49 HARs. We took advantage of recently developed DNA sequencing technology, coupled with methods to isolate genomic DNA for our target regions only, to determine the genotypes in 22 chromosomal samples. This polymorphism data showed no significant evidence for adaptive selective sweeps in HAR regions. By contrast, we found strong evidence for a nucleotide bias in the fixation of mutations from A or T to G or C basepairs. Our work reveals that this bias in the HAR neighborhoods is not just an historic phenomenon, but is ongoing in the present day human population. This finding adds credence to the possibility that non-selective forces, such as biased gene conversion, could have contributed to the evolution of several of these regions.
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Affiliation(s)
- Sol Katzman
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Andrew D. Kern
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Katherine S. Pollard
- Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America
| | - Sofie R. Salama
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - David Haussler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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21
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Haygood R, Babbitt CC, Fedrigo O, Wray GA. Contrasts between adaptive coding and noncoding changes during human evolution. Proc Natl Acad Sci U S A 2010; 107:7853-7. [PMID: 20385805 PMCID: PMC2867918 DOI: 10.1073/pnas.0911249107] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Changes in non-protein-coding regulatory DNA sequences have been proposed to play distinctive roles in adaptive evolution. We analyzed correlations between gene functions and evidence for positive selection in a common statistical framework across several large surveys of coding and noncoding sequences throughout the human genome. Strong correlations with both classifications in gene ontologies and measurements of gene expression indicate that neural development and function have adapted mainly through noncoding changes. In contrast, adaptation via coding changes is dominated by immunity, olfaction, and male reproduction. Genes with highly tissue-specific expression have undergone more adaptive coding changes, suggesting that pleiotropic constraints inhibit such changes in broadly expressed genes. In contrast, adaptive noncoding changes do not exhibit this pattern. Our findings underscore the probable importance of noncoding changes in the evolution of human traits, particularly cognitive traits.
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Affiliation(s)
- Ralph Haygood
- Biology Department and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA.
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22
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Surprising fitness consequences of GC-biased gene conversion: I. Mutation load and inbreeding depression. Genetics 2010; 185:939-59. [PMID: 20421602 DOI: 10.1534/genetics.110.116368] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
GC-biased gene conversion (gBGC) is a recombination-associated process mimicking selection in favor of G and C alleles. It is increasingly recognized as a widespread force in shaping the genomic nucleotide landscape. In recombination hotspots, gBGC can lead to bursts of fixation of GC nucleotides and to accelerated nucleotide substitution rates. It was recently shown that these episodes of strong gBGC could give spurious signatures of adaptation and/or relaxed selection. There is also evidence that gBGC could drive the fixation of deleterious amino acid mutations in some primate genes. This raises the question of the potential fitness effects of gBGC. While gBGC has been metaphorically termed the "Achilles' heel" of our genome, we do not know whether interference between gBGC and selection merely has practical consequences for the analysis of sequence data or whether it has broader fundamental implications for individuals and populations. I developed a population genetics model to predict the consequences of gBGC on the mutation load and inbreeding depression. I also used estimates available for humans to quantitatively evaluate the fitness impact of gBGC. Surprising features emerged from this model: (i) Contrary to classical mutation load models, gBGC generates a fixation load independent of population size and could contribute to a significant part of the load; (ii) gBGC can maintain recessive deleterious mutations for a long time at intermediate frequency, in a similar way to overdominance, and these mutations generate high inbreeding depression, even if they are slightly deleterious; (iii) since mating systems affect both the selection efficacy and gBGC intensity, gBGC challenges classical predictions concerning the interaction between mating systems and deleterious mutations, and gBGC could constitute an additional cost of outcrossing; and (iv) if mutations are biased toward A and T alleles, very low gBGC levels can reduce the load. A robust prediction is that the gBGC level minimizing the load depends only on the mutational bias and population size. These surprising results suggest that gBGC may have nonnegligible fitness consequences and could play a significant role in the evolution of genetic systems. They also shed light on the evolution of gBGC itself.
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23
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Sholtis SJ, Noonan JP. Gene regulation and the origins of human biological uniqueness. Trends Genet 2010; 26:110-8. [PMID: 20106546 DOI: 10.1016/j.tig.2009.12.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Revised: 12/23/2009] [Accepted: 12/23/2009] [Indexed: 02/01/2023]
Abstract
What makes us human? It is likely that changes in gene expression and regulation, in addition to those in protein-coding genes, drove the evolution of uniquely human biological traits. In this review, we discuss how efforts to annotate regulatory functions in the human genome are being combined with maps of human-specific sequence acceleration to identify cis-regulatory elements with human-specific activity. Although the evolutionary interpretation of these events is a subject of considerable debate, the technical and analytical means are now at hand to identify the set of evolutionary genetic events that shaped our species.
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Affiliation(s)
- Samuel J Sholtis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
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24
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Noonan JP. Regulatory DNAs and the evolution of human development. Curr Opin Genet Dev 2009; 19:557-64. [PMID: 19913404 DOI: 10.1016/j.gde.2009.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Revised: 10/06/2009] [Accepted: 10/07/2009] [Indexed: 10/20/2022]
Abstract
Changes in gene regulation have long been thought to underlie biological differences between humans and other primates. Recent advances have facilitated the study of human-specific sequence changes in regulatory DNAs in the context of human development. Comparative genomic analyses coupled with genome-wide in vivo developmental enhancer screens have identified thousands of known and likely regulatory elements in the genome. These have provided the substrate for statistical and experimental identification of regulatory sequences with human-specific developmental activities. On the basis of these early results, the outlines of an integrated strategy have emerged that combines gene expression atlases of human development, in vivo reverse genetic studies of regulatory DNAs, and maps of human-specific sequence change to reveal the genetic basis of unique human biology.
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Affiliation(s)
- James P Noonan
- Department of Genetics and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA.
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25
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Chen CH, Chuang TJ, Liao BY, Chen FC. Scanning for the signatures of positive selection for human-specific insertions and deletions. Genome Biol Evol 2009; 1:415-9. [PMID: 20333210 PMCID: PMC2817433 DOI: 10.1093/gbe/evp041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2009] [Indexed: 12/03/2022] Open
Abstract
Human-specific small insertions and deletions (HS indels, with lengths <100 bp) are reported to be ubiquitous in the human genome. However, whether these indels contribute to human-specific traits remains unclear. Here we employ a modified McDonald–Kreitman (MK) test and a combinatorial population genetics approach to infer, respectively, the occurrence of positive selection and recent selective sweep events associated with HS indels. We first extract 625,890 HS indels from the human–chimpanzee–macaque–mouse multiple alignments and classify them into nonpolymorphic (41%) and polymorphic (59%) indels with reference to the human indel polymorphism data. The modified MK test is then applied to 100-kb partially overlapped sliding windows across the human genome to scan for the signs of positive selection. After excluding the possibility of biased gene conversion and controlling for false discovery rate, we show that HS indels are potentially positively selected in about 10 Mb of the human genome. Furthermore, the indel-associated positively selected regions overlap with genes more often than expected. However, our result suggests that the potential targets of positive selection are located in noncoding regions. Meanwhile, we also demonstrate that the genomic regions surrounding HS indels are more frequently involved in recent selective sweep than the other regions. In addition, HS indels are associated with distinct recent selective sweep events in different human subpopulations. Our results suggest that HS indels may have been associated with human adaptive changes at both the species level and the subpopulation level.
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26
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Duret L, Galtier N. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet 2009; 10:285-311. [PMID: 19630562 DOI: 10.1146/annurev-genom-082908-150001] [Citation(s) in RCA: 468] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recombination is typically thought of as a symmetrical process resulting in large-scale reciprocal genetic exchanges between homologous chromosomes. Recombination events, however, are also accompanied by short-scale, unidirectional exchanges known as gene conversion in the neighborhood of the initiating double-strand break. A large body of evidence suggests that gene conversion is GC-biased in many eukaryotes, including mammals and human. AT/GC heterozygotes produce more GC- than AT-gametes, thus conferring a population advantage to GC-alleles in high-recombining regions. This apparently unimportant feature of our molecular machinery has major evolutionary consequences. Structurally, GC-biased gene conversion explains the spatial distribution of GC-content in mammalian genomes-the so-called isochore structure. Functionally, GC-biased gene conversion promotes the segregation and fixation of deleterious AT --> GC mutations, thus increasing our genomic mutation load. Here we review the recent evidence for a GC-biased gene conversion process in mammals, and its consequences for genomic landscapes, molecular evolution, and human functional genomics.
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Affiliation(s)
- Laurent Duret
- Université de Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France.
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27
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Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, FitzPatrick DR, Afzal V, Pennacchio LA, Rubin EM, Noonan JP. Response to Comment on "Human-Specific Gain of Function in a Developmental Enhancer". Science 2009. [DOI: 10.1126/science.1166571] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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