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Lanciano S, Philippe C, Sarkar A, Pratella D, Domrane C, Doucet AJ, van Essen D, Saccani S, Ferry L, Defossez PA, Cristofari G. Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites. CELL GENOMICS 2024; 4:100498. [PMID: 38309261 PMCID: PMC10879037 DOI: 10.1016/j.xgen.2024.100498] [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: 06/02/2023] [Revised: 07/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and long-read sequencing to unveil L1 methylation heterogeneity across cell types, families, and individual loci and elucidate key principles involved. We find that the youngest primate L1 families are specifically hypomethylated in pluripotent stem cells and the placenta but not in most tumors. Locally, intronic L1 methylation is intimately associated with gene transcription. Conversely, the L1 methylation state can propagate to the proximal region up to 300 bp. This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is typically insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome.
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Affiliation(s)
- Sophie Lanciano
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Claude Philippe
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Arpita Sarkar
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - David Pratella
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Cécilia Domrane
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Aurélien J Doucet
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Dominic van Essen
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Simona Saccani
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Laure Ferry
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | | | - Gael Cristofari
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France.
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2
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Chuang NT, Gardner EJ, Terry DM, Crabtree J, Mahurkar AA, Rivell GL, Hong CC, Perry JA, Devine SE. Mutagenesis of human genomes by endogenous mobile elements on a population scale. Genome Res 2021; 31:2225-2235. [PMID: 34772701 PMCID: PMC8647825 DOI: 10.1101/gr.275323.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023]
Abstract
Several large-scale Illumina whole-genome sequencing (WGS) and whole-exome sequencing (WES) projects have emerged recently that have provided exceptional opportunities to discover mobile element insertions (MEIs) and study the impact of these MEIs on human genomes. However, these projects also have presented major challenges with respect to the scalability and computational costs associated with performing MEI discovery on tens or even hundreds of thousands of samples. To meet these challenges, we have developed a more efficient and scalable version of our mobile element locator tool (MELT) called CloudMELT. We then used MELT and CloudMELT to perform MEI discovery in 57,919 human genomes and exomes, leading to the discovery of 104,350 nonredundant MEIs. We leveraged this collection (1) to examine potentially active L1 source elements that drive the mobilization of new Alu, L1, and SVA MEIs in humans; (2) to examine the population distributions and subfamilies of these MEIs; and (3) to examine the mutagenesis of GENCODE genes, ENCODE-annotated features, and disease genes by these MEIs. Our study provides new insights on the L1 source elements that drive MEI mutagenesis and brings forth a better understanding of how this mutagenesis impacts human genomes.
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Affiliation(s)
- Nelson T Chuang
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Division of Gastroenterology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Eugene J Gardner
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Diane M Terry
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Anup A Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Guillermo L Rivell
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Scott E Devine
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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3
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Schwarz PM, Freisleben B. NOREC4DNA: using near-optimal rateless erasure codes for DNA storage. BMC Bioinformatics 2021; 22:406. [PMID: 34404355 PMCID: PMC8371904 DOI: 10.1186/s12859-021-04318-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/05/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND DNA is a promising storage medium for high-density long-term digital data storage. Since DNA synthesis and sequencing are still relatively expensive tasks, the coding methods used to store digital data in DNA should correct errors and avoid unstable or error-prone DNA sequences. Near-optimal rateless erasure codes, also called fountain codes, are particularly interesting codes to realize high-capacity and low-error DNA storage systems, as shown by Erlich and Zielinski in their approach based on the Luby transform (LT) code. Since LT is the most basic fountain code, there is a large untapped potential for improvement in using near-optimal erasure codes for DNA storage. RESULTS We present NOREC4DNA, a software framework to use, test, compare, and improve near-optimal rateless erasure codes (NORECs) for DNA storage systems. These codes can effectively be used to store digital information in DNA and cope with the restrictions of the DNA medium. Additionally, they can adapt to possible variable lengths of DNA strands and have nearly zero overhead. We describe the design and implementation of NOREC4DNA. Furthermore, we present experimental results demonstrating that NOREC4DNA can flexibly be used to evaluate the use of NORECs in DNA storage systems. In particular, we show that NORECs that apparently have not yet been used for DNA storage, such as Raptor and Online codes, can achieve significant improvements over LT codes that were used in previous work. NOREC4DNA is available on https://github.com/umr-ds/NOREC4DNA . CONCLUSION NOREC4DNA is a flexible and extensible software framework for using, evaluating, and comparing NORECs for DNA storage systems.
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Affiliation(s)
- Peter Michael Schwarz
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, 35032, Marburg, Germany.
| | - Bernd Freisleben
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, 35032, Marburg, Germany
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4
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Pichon F, Shen Y, Busato F, P Jochems S, Jacquelin B, Grand RL, Deleuze JF, Müller-Trutwin M, Tost J. Analysis and annotation of DNA methylation in two nonhuman primate species using the Infinium Human Methylation 450K and EPIC BeadChips. Epigenomics 2021; 13:169-186. [PMID: 33471557 DOI: 10.2217/epi-2020-0200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: Nonhuman primates are essential for research on many human diseases. The Infinium Human Methylation450/EPIC BeadChips are popular tools for the study of the methylation state across the human genome at affordable cost. Methods: We performed a precise evaluation and re-annotation of the BeadChip probes for the analysis of genome-wide DNA methylation patterns in rhesus macaques and African green monkeys through in silico analyses combined with functional validation by pyrosequencing. Results: Up to 165,847 of the 450K and 261,545 probes of the EPIC BeadChip can be reliably used. The annotation files are provided in a format compatible with a variety of standard bioinformatic pipelines. Conclusion: Our study will facilitate high-throughput DNA methylation analyses in Macaca mulatta and Chlorocebus sabaeus.
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Affiliation(s)
- Fabien Pichon
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Yimin Shen
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France.,Laboratory for Bioinformatics, Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Florence Busato
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Simon P Jochems
- Institut Pasteur, HIV Inflammation & Persistence Unit, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Leiden University Medical Center, Leiden, The Netherlands
| | | | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - Jean-Francois Deleuze
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France.,Laboratory for Bioinformatics, Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | | | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
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5
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Zhao Y, Dong L, Jiang C, Wang X, Xie J, Rashid MAR, Liu Y, Li M, Bu Z, Wang H, Ma X, Sun S, Wang X, Bo C, Zhou T, Kong L. Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization. BMC Biol 2020; 18:188. [PMID: 33267868 PMCID: PMC7713161 DOI: 10.1186/s12915-020-00917-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/05/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes. RESULTS Genome/subgenome-wide base-composition patterns were investigated by using the data of polymorphic site in 93 accessions from worldwide populations of bread wheat, its diploid and tetraploid progenitors, and their corresponding reference genome sequences. Individual-strand base equality rule and [AT]-increase pattern remain in recently formed hexaploid species bread wheat at the genome, subgenome, chromosome, and polymorphic site levels. However, D subgenome showed the fastest [AT]-increase across polymorphic site from Aegilops tauschii to bread wheat than that on A and B subgenomes from wild emmer to bread wheat. The fastest [AT]-increase could be detected almost all chromosome windows on D subgenome, suggesting different mechanisms between D and other two subgenomes. Interestingly, the [AT]-increase is mainly contributed by intergenic regions at non-selective sweeps, especially the fastest [AT]-increase of D subgenome. Further transition frequency and sequence context analysis indicated that three subgenomes shared same mutation type, but D subgenome owns the highest mutation rate on high-frequency mutation type. The highest mutation rate on D subgenome was further confirmed by using a bread-wheat-private SNP set. The exploration of loci/genes related to the [AT] value of D subgenome suggests the fastest [AT]-increase of D subgenome could be involved in DNA repair systems distributed on three subgenomes of bread wheat. CONCLUSIONS The highest mutation rate is detected on D subgenome of bread wheat during domestication after allopolyploidization, leading to the fastest [AT]-increase pattern of D subgenome. The phenomenon may come from the joint action of multiple repair systems inherited from its wild progenitors.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Luhao Dong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Conghui Jiang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xueqiang Wang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jianyin Xie
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, People's Republic of China
| | | | - Yanhe Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Mengyao Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Zhimu Bu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Hongwei Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xin Ma
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Silong Sun
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xiaoqian Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Cunyao Bo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Tingting Zhou
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
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6
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Furano AV, Jones CE, Periwal V, Callahan KE, Walser JC, Cook PR. Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p. PLoS Genet 2020; 16:e1008991. [PMID: 32797042 PMCID: PMC7449397 DOI: 10.1371/journal.pgen.1008991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/26/2020] [Accepted: 07/13/2020] [Indexed: 11/18/2022] Open
Abstract
Accounting for continual evolution of deleterious L1 retrotransposon families, which can contain hundreds to thousands of members remains a major issue in mammalian biology. L1 activity generated upwards of 40% of some mammalian genomes, including humans where they remain active, causing genetic defects and rearrangements. L1 encodes a coiled coil-containing protein that is essential for retrotransposition, and the emergence of novel primate L1 families has been correlated with episodes of extensive amino acid substitutions in the coiled coil. These results were interpreted as an adaptive response to maintain L1 activity, however its mechanism remained unknown. Although an adventitious mutation can inactivate coiled coil function, its effect could be buffered by epistatic interactions within the coiled coil, made more likely if the family contains a diverse set of coiled coil sequences-collectively referred to as the coiled coil sequence space. Amino acid substitutions that do not affect coiled coil function (i.e., its phenotype) could be "hidden" from (not subject to) purifying selection. The accumulation of such substitutions, often referred to as cryptic genetic variation, has been documented in various proteins. Here we report that this phenomenon was in effect during the latest episode of primate coiled coil evolution, which occurred 30-10 MYA during the emergence of primate L1Pa7-L1Pa3 families. First, we experimentally demonstrated that while coiled coil function (measured by retrotransposition) can be eliminated by single epistatic mutations, it nonetheless can also withstand extensive amino acid substitutions. Second, principal component and cluster analysis showed that the coiled coil sequence space of each of the L1Pa7-3 families was notably increased by the presence of distinct, coexisting coiled coil sequences. Thus, sampling related networks of functional sequences rather than traversing discrete adaptive states characterized the persistence L1 activity during this evolutionary event.
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Affiliation(s)
- Anthony V. Furano
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Charlie E. Jones
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Vipul Periwal
- Laboratory of Biological Modeling, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kathryn E. Callahan
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jean-Claude Walser
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Pamela R. Cook
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
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7
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Ruggiero RP, Boissinot S. Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons. Mob DNA 2020; 11:14. [PMID: 32280379 PMCID: PMC7140322 DOI: 10.1186/s13100-020-00209-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/24/2020] [Indexed: 12/03/2022] Open
Abstract
Background Non-LTR retrotransposons often exhibit base composition that is markedly different from the nucleotide content of their host’s gene. For instance, the mammalian L1 element is AT-rich with a strong A bias on the positive strand, which results in a reduced transcription. It is plausible that the A-richness of mammalian L1 is a self-regulatory mechanism reflecting a trade-off between transposition efficiency and the deleterious effect of L1 on its host. We examined if the A-richness of L1 is a general feature of non-LTR retrotransposons or if different clades of elements have evolved different nucleotide content. We also investigated if elements belonging to the same clade evolved towards different base composition in different genomes or if elements from different clades evolved towards similar base composition in the same genome. Results We found that non-LTR retrotransposons differ in base composition among clades within the same host but also that elements belonging to the same clade differ in base composition among hosts. We showed that nucleotide content remains constant within the same host over extended period of evolutionary time, despite mutational patterns that should drive nucleotide content away from the observed base composition. Conclusions Our results suggest that base composition is evolving under selection and may be reflective of the long-term co-evolution between non-LTR retrotransposons and their host. Finally, the coexistence of elements with drastically different base composition suggests that these elements may be using different strategies to persist and multiply in the genome of their host.
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Affiliation(s)
- Robert P Ruggiero
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates PO 129188
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates PO 129188
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8
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Bruijnesteijn J, de Groot N, van der Wiel MKH, Otting N, de Vos-Rouweler AJM, de Groot NG, Bontrop RE. Unparalleled Rapid Evolution of KIR Genes in Rhesus and Cynomolgus Macaque Populations. THE JOURNAL OF IMMUNOLOGY 2020; 204:1770-1786. [PMID: 32111732 DOI: 10.4049/jimmunol.1901140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/21/2020] [Indexed: 12/19/2022]
Abstract
The killer cell Ig-like receptors (KIR) modulate immune responses through interactions with MHC class I molecules. The KIR region in large cohorts of rhesus and cynomolgus macaque populations were characterized, and the experimental design enabled the definition of a considerable number of alleles (n = 576) and haplotypes, which are highly variable with regard to architecture. Although high levels of polymorphism were recorded, only a few alleles are shared between species and populations. The rapid evolution of allelic polymorphism, accumulated by point mutations, was further confirmed by the emergence of a novel KIR allele in a rhesus macaque family. In addition to allelic variation, abundant orthologous and species-specific KIR genes were identified, the latter of which are frequently generated by fusion events. The concerted action of both genetic mechanisms, in combination with differential selective pressures at the population level, resulted in the unparalleled rapid evolution of the KIR gene region in two closely related macaque species. The variation of the KIR gene repertoire at the species and population level might have an impact on the outcome of preclinical studies with macaque models.
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Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Marit K H van der Wiel
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and .,Theoretical Biology and Bioinformatics Group, Utrecht University, 3527 Utrecht, the Netherlands
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9
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Wang J, Li X, Do Kim K, Scanlon MJ, Jackson SA, Springer NM, Yu J. Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean. Genome Biol 2019; 20:74. [PMID: 31018867 PMCID: PMC6482504 DOI: 10.1186/s13059-019-1683-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/28/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Interestingly, domesticated accessions have significantly higher [A] and [T] values across genome-wide polymorphic sites than accessions sampled from the corresponding progenitor species. However, the relative contributions of different genomic regions to this genome divergence pattern and underlying mechanisms have not been well characterized. RESULTS Here, we investigate the genome-wide base-composition patterns by analyzing millions of SNPs segregating among 100 accessions from a teosinte-maize comparison set and among 302 accessions from a wild-domesticated soybean comparison set. We show that non-genic part of the genome has a greater contribution than genic SNPs to the [AT]-increase observed between wild and domesticated accessions in maize and soybean. The separation between wild and domesticated accessions in [AT] values is significantly enlarged in non-genic and pericentromeric regions. Motif frequency and sequence context analyses show the motifs (PyCG) related to solar-UV signature are enriched in these regions, particularly when they are methylated. Additional analysis using population-private SNPs also implicates the role of these motifs in relatively recent mutations. With base-composition across polymorphic sites as a genome phenotype, genome scans identify a set of putative candidate genes involved in UV damage repair pathways. CONCLUSIONS The [AT]-increase is more pronounced in genomic regions that are non-genic, pericentromeric, transposable elements; methylated; and with low recombination. Our findings establish important links among UV radiation, mutation, DNA repair, methylation, and genome evolution.
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Affiliation(s)
- Jinyu Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - Michael J. Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108 USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
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10
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Chen J, Jian X, Deng S, Ma Z, Shou X, Shen Y, Zhang Q, Song Z, Li Z, Peng H, Peng C, Chen M, Luo C, Zhao D, Ye Z, Shen M, Zhang Y, Zhou J, Fahira A, Wang Y, Li S, Zhang Z, Ye H, Li Y, Shen J, Chen H, Tang F, Yao Z, Shi Z, Chen C, Xie L, Wang Y, Fu C, Mao Y, Zhou L, Gao D, Yan H, Zhao Y, Huang C, Shi Y. Identification of recurrent USP48 and BRAF mutations in Cushing's disease. Nat Commun 2018; 9:3171. [PMID: 30093687 PMCID: PMC6085354 DOI: 10.1038/s41467-018-05275-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 06/13/2018] [Indexed: 12/15/2022] Open
Abstract
Cushing's disease results from corticotroph adenomas of the pituitary that hypersecrete adrenocorticotropin (ACTH), leading to excess glucocorticoid and hypercortisolism. Mutations of the deubiquitinase gene USP8 occur in 35-62% of corticotroph adenomas. However, the major driver mutations in USP8 wild-type tumors remain elusive. Here, we report recurrent mutations in the deubiquitinase gene USP48 (predominantly encoding p.M415I or p.M415V; 21/91 subjects) and BRAF (encoding p.V600E; 15/91 subjects) in corticotroph adenomas with wild-type USP8. Similar to USP8 mutants, both USP48 and BRAF mutants enhance the promoter activity and transcription of the gene encoding proopiomelanocortin (POMC), which is the precursor of ACTH, providing a potential mechanism for ACTH overproduction in corticotroph adenomas. Moreover, primary corticotroph tumor cells harboring BRAF V600E are sensitive to the BRAF inhibitor vemurafenib. Our study thus contributes to the understanding of the molecular mechanism of the pathogenesis of corticotroph adenoma and informs therapeutic targets for this disease.
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Affiliation(s)
- Jianhua Chen
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
- Department of Otolaryngology Head and Neck Surgery & Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Xuemin Jian
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
- Department of Otolaryngology Head and Neck Surgery & Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Siyu Deng
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zengyi Ma
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Xuefei Shou
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Yue Shen
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Qilin Zhang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Zhijian Song
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
- Department of Otolaryngology Head and Neck Surgery & Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Zhiqiang Li
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
- Department of Otolaryngology Head and Neck Surgery & Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Hong Peng
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Cheng Peng
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Min Chen
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Dan Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhao Ye
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Ming Shen
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Yichao Zhang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Juan Zhou
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
- Department of Otolaryngology Head and Neck Surgery & Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Aamir Fahira
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
- Department of Otolaryngology Head and Neck Surgery & Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Yongfei Wang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Shiqi Li
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Zhaoyun Zhang
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Hongying Ye
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Yiming Li
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jiawei Shen
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
- Department of Otolaryngology Head and Neck Surgery & Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Hong Chen
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Department of Pathology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Feng Tang
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Department of Pathology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zhenwei Yao
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Department of Radiology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zhifeng Shi
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Chunjui Chen
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology (SCBIT), Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Ye Wang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Chaowei Fu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
- State Key Laboratory of Medical Neurobiology, Institute of Neurosurgery, Shanghai Medical College, Fudan University, 200040, Shanghai, China
| | - Liangfu Zhou
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China
| | - Daming Gao
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hai Yan
- Department of Pathology, Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yao Zhao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
- Shanghai Pituitary Tumor Center, Shanghai, 200040, China.
- Institute of Neurosurgery, Fudan University, Shanghai, 200040, China.
- State Key Laboratory of Medical Neurobiology, Institute of Neurosurgery, Shanghai Medical College, Fudan University, 200040, Shanghai, China.
| | - Chuanxin Huang
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yongyong Shi
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China.
- Department of Otolaryngology Head and Neck Surgery & Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
- Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.
- Department of Psychiatry, First Teaching Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China.
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, Shandong, 266003, China.
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11
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Wippermann A, Noll T. DNA methylation in CHO cells. J Biotechnol 2017; 258:206-210. [DOI: 10.1016/j.jbiotec.2017.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 01/22/2023]
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12
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Yang B, Li X, Lei L, Chen J. APOBEC: From mutator to editor. J Genet Genomics 2017; 44:423-437. [PMID: 28964683 DOI: 10.1016/j.jgg.2017.04.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/04/2017] [Accepted: 04/10/2017] [Indexed: 12/21/2022]
Abstract
APOBECs (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) are a family of cytidine deaminases that prefer single-stranded nucleic acids as substrates. Besides their physiological functions, APOBEC family members have been found to cause hypermutations of cancer genomes, which could be correlated with cancer development and poor prognosis. Recently, APOBEC family members have been combined with the versatile CRISPR/Cas9 system to perform targeted base editing or induce hypermutagenesis. This combination improved the CRISPR/Cas9-mediated gene editing at single-base precision, greatly enhancing its usefulness. Here, we review the physiological functions and structural characteristics of APOBEC family members and their roles as endogenous mutators that contribute to hypermutations during carcinogenesis. We also review the various iterations of the APOBEC-CRISPR/Cas9 gene-editing tools, pointing out their features and limitations as well as the possibilities for future developments.
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Affiliation(s)
- Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Xiaosa Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Liqun Lei
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jia Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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13
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Di Gioia SA, Connors S, Matsunami N, Cannavino J, Rose MF, Gilette NM, Artoni P, de Macena Sobreira NL, Chan WM, Webb BD, Robson CD, Cheng L, Van Ryzin C, Ramirez-Martinez A, Mohassel P, Leppert M, Scholand MB, Grunseich C, Ferreira CR, Hartman T, Hayes IM, Morgan T, Markie DM, Fagiolini M, Swift A, Chines PS, Speck-Martins CE, Collins FS, Jabs EW, Bönnemann CG, Olson EN, Carey JC, Robertson SP, Manoli I, Engle EC. A defect in myoblast fusion underlies Carey-Fineman-Ziter syndrome. Nat Commun 2017; 8:16077. [PMID: 28681861 PMCID: PMC5504296 DOI: 10.1038/ncomms16077] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 05/25/2017] [Indexed: 01/12/2023] Open
Abstract
Multinucleate cellular syncytial formation is a hallmark of skeletal muscle differentiation. Myomaker, encoded by Mymk (Tmem8c), is a well-conserved plasma membrane protein required for myoblast fusion to form multinucleated myotubes in mouse, chick, and zebrafish. Here, we report that autosomal recessive mutations in MYMK (OMIM 615345) cause Carey-Fineman-Ziter syndrome in humans (CFZS; OMIM 254940) by reducing but not eliminating MYMK function. We characterize MYMK-CFZS as a congenital myopathy with marked facial weakness and additional clinical and pathologic features that distinguish it from other congenital neuromuscular syndromes. We show that a heterologous cell fusion assay in vitro and allelic complementation experiments in mymk knockdown and mymkinsT/insT zebrafish in vivo can differentiate between MYMK wild type, hypomorphic and null alleles. Collectively, these data establish that MYMK activity is necessary for normal muscle development and maintenance in humans, and expand the spectrum of congenital myopathies to include cell-cell fusion deficits.
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Affiliation(s)
- Silvio Alessandro Di Gioia
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Samantha Connors
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Norisada Matsunami
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Jessica Cannavino
- Department of Molecular Biology and Neuroscience, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Matthew F. Rose
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Medical Genetics Training Program, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nicole M. Gilette
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
| | - Pietro Artoni
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nara Lygia de Macena Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Wai-Man Chan
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Bryn D. Webb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Caroline D. Robson
- Department of Radiology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Long Cheng
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Carol Van Ryzin
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
| | - Andres Ramirez-Martinez
- Department of Molecular Biology and Neuroscience, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
| | - Mark Leppert
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Mary Beth Scholand
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
| | - Carlos R. Ferreira
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
| | - Tyler Hartman
- Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine, Hanover, New Hampshire 03755-1404, USA
| | - Ian M. Hayes
- Genetic Health Services New Zealand, Auckland City Hospital, Auckland 1142, New Zealand
| | - Tim Morgan
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - David M. Markie
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Michela Fagiolini
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Amy Swift
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
| | - Peter S. Chines
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
| | | | - Francis S. Collins
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
- Office of the Director, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
| | - Ethylin Wang Jabs
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Carsten G. Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
| | - Eric N. Olson
- Department of Molecular Biology and Neuroscience, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - John C. Carey
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Stephen P. Robertson
- Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Irini Manoli
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-1477, USA
| | - Elizabeth C. Engle
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Medical Genetics Training Program, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
- Department Ophthalmology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02115, USA
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14
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Lim B, Mun J, Kim SY. Intrinsic Molecular Processes: Impact on Mutagenesis. Trends Cancer 2017; 3:357-371. [PMID: 28718413 DOI: 10.1016/j.trecan.2017.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/23/2017] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
Mutations provide resources for genome evolution by generating genetic variability. In addition, mutations act as a driving force leading to disease pathogenesis, and thus have important implications for disease diagnosis, prognosis, and treatment. Understanding the mechanisms underlying how mutations occur is therefore of prime importance for elucidating evolutionary and pathogenic processes. Recent genomics studies have revealed that mutations occur non-randomly across the human genome. In particular, the distribution of mutations is highly associated with intrinsic molecular processes including transcription, chromatin organization, DNA replication timing, and DNA repair. Interplay between intrinsic processes and extrinsic mutagenic exposure may thus imprint a characteristic mutational landscape on tumors. We discuss the impact of intrinsic molecular processes on mutation acquisition in cancer.
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Affiliation(s)
- Byungho Lim
- Research Center for Drug Discovery Technology, Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, Daejeon, Korea
| | - Jihyeob Mun
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Functional Genomics, University of Science and Technology, Daejeon, Korea.
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15
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Simplification, Innateness, and the Absorption of Meaning from Context: How Novelty Arises from Gradual Network Evolution. Evol Biol 2017; 44:145-189. [PMID: 28572690 PMCID: PMC5429377 DOI: 10.1007/s11692-017-9407-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 01/06/2017] [Indexed: 02/07/2023]
Abstract
How does new genetic information arise? Traditional thinking holds that mutation happens by accident and then spreads in the population by either natural selection or random genetic drift. There have been at least two fundamental conceptual problems with imagining an alternative. First, it seemed that the only alternative is a mutation that responds "smartly" to the immediate environment; but in complex multicellulars, it is hard to imagine how this could be implemented. Second, if there were mechanisms of mutation that "knew" what genetic changes would be favored in a given environment, this would have only begged the question of how they acquired that particular knowledge to begin with. This paper offers an alternative that avoids these problems. It holds that mutational mechanisms act on information that is in the genome, based on considerations of simplicity, parsimony, elegance, etc. (which are different than fitness considerations). This simplification process, under the performance pressure exerted by selection, not only leads to the improvement of adaptations but also creates elements that have the capacity to serve in new contexts they were not originally selected for. Novelty, then, arises at the system level from emergent interactions between such elements. Thus, mechanistically driven mutation neither requires Lamarckian transmission nor closes the door on novelty, because the changes it implements interact with one another globally in surprising and beneficial ways. Finally, I argue, for example, that genes used together are fused together; that simplification leads to complexity; and that evolution and learning are conceptually linked.
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16
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Sahakyan AB, Balasubramanian S. Single genome retrieval of context-dependent variability in mutation rates for human germline. BMC Genomics 2017; 18:81. [PMID: 28086752 PMCID: PMC5237266 DOI: 10.1186/s12864-016-3440-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 12/19/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. RESULTS The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database. Due to the nature of the method design and the imposed stringency criteria, we expect our rate constants to be good estimates for the rates of spontaneous mutations. Benefiting from such data, we study the short-range nucleotide (up to 7-mer) organisation and the germline basal substitution propensity (BSP) profile of the human genome; characterise novel, CpG-independent, substitution prone and resistant motifs; confirm a decreased tendency of moieties with low BSP to undergo somatic mutations in a number of cancer types; and, produce a Trek-based estimate of the overall mutation rate in human. CONCLUSIONS The extended set of rate constants we report may enrich our resources and help advance our understanding of genome dynamics and evolution, with possible implications for the role of spontaneous mutations in the emergence of pathological genotypes and neutral evolution of proteomes.
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Affiliation(s)
- Aleksandr B Sahakyan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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17
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Halloran JW, Zhu D, Qian DC, Byun J, Gorlova OY, Amos CI, Gorlov IP. Prediction of the gene expression in normal lung tissue by the gene expression in blood. BMC Med Genomics 2015; 8:77. [PMID: 26576671 PMCID: PMC4650316 DOI: 10.1186/s12920-015-0152-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/10/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Comparative analysis of gene expression in human tissues is important for understanding the molecular mechanisms underlying tissue-specific control of gene expression. It can also open an avenue for using gene expression in blood (which is the most easily accessible human tissue) to predict gene expression in other (less accessible) tissues, which would facilitate the development of novel gene expression based models for assessing disease risk and progression. Until recently, direct comparative analysis across different tissues was not possible due to the scarcity of paired tissue samples from the same individuals. METHODS In this study we used paired whole blood/lung gene expression data from the Genotype-Tissue Expression (GTEx) project. We built a generalized linear regression model for each gene using gene expression in lung as the outcome and gene expression in blood, age and gender as predictors. RESULTS For ~18 % of the genes, gene expression in blood was a significant predictor of gene expression in lung. We found that the number of single nucleotide polymorphisms (SNPs) influencing expression of a given gene in either blood or lung, also known as the number of quantitative trait loci (eQTLs), was positively associated with efficacy of blood-based prediction of that gene's expression in lung. This association was strongest for shared eQTLs: those influencing gene expression in both blood and lung. CONCLUSIONS In conclusion, for a considerable number of human genes, their expression levels in lung can be predicted using observable gene expression in blood. An abundance of shared eQTLs may explain the strong blood/lung correlations in the gene expression.
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Affiliation(s)
- Justin W Halloran
- Department of Biological Sciences, Dartmouth College, 78 College St., Hanover, NH, 03755, USA.
| | - Dakai Zhu
- Department of Biomedical Data Science, The Geisel School of Medicine, Dartmouth College, HB7937, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
| | - David C Qian
- Department of Biomedical Data Science, The Geisel School of Medicine, Dartmouth College, HB7937, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
| | - Jinyoung Byun
- Department of Biomedical Data Science, The Geisel School of Medicine, Dartmouth College, HB7937, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
| | - Olga Y Gorlova
- Department of Biomedical Data Science, The Geisel School of Medicine, Dartmouth College, HB7937, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
| | - Christopher I Amos
- Department of Biomedical Data Science, The Geisel School of Medicine, Dartmouth College, HB7937, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
| | - Ivan P Gorlov
- Department of Biomedical Data Science, The Geisel School of Medicine, Dartmouth College, HB7937, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
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18
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Gkountela S, Zhang KX, Shafiq TA, Liao WW, Hargan-Calvopiña J, Chen PY, Clark AT. DNA Demethylation Dynamics in the Human Prenatal Germline. Cell 2015; 161:1425-36. [PMID: 26004067 DOI: 10.1016/j.cell.2015.05.012] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/13/2015] [Accepted: 03/25/2015] [Indexed: 12/11/2022]
Abstract
Global DNA demethylation in humans is a fundamental process that occurs in pre-implantation embryos and reversion to naive ground state pluripotent stem cells (PSCs). However, the extent of DNA methylation reprogramming in human germline cells is unknown. Here, we performed whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq) of human prenatal germline cells from 53 to 137 days of development. We discovered that the transcriptome and methylome of human germline is distinct from both human PSCs and the inner cell mass (ICM) of human blastocysts. Using this resource to monitor the outcome of global DNA demethylation with reversion of primed PSCs to the naive ground state, we uncovered hotspots of ultralow methylation at transposons that are protected from demethylation in the germline and ICM. Taken together, the human germline serves as a valuable in vivo tool for monitoring the epigenome of cells that have emerged from a global DNA demethylation event.
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Affiliation(s)
- Sofia Gkountela
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kelvin X Zhang
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tiasha A Shafiq
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wen-Wei Liao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Joseph Hargan-Calvopiña
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan.
| | - Amander T Clark
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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19
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Clifford RL, Patel JK, John AE, Tatler AL, Mazengarb L, Brightling CE, Knox AJ. CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: regulation by BET. Am J Physiol Lung Cell Mol Physiol 2015; 308:L962-72. [PMID: 25713319 PMCID: PMC4421784 DOI: 10.1152/ajplung.00021.2015] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 02/13/2015] [Indexed: 01/03/2023] Open
Abstract
Asthma is characterized by airway inflammation and remodeling and CXCL8 is a CXC chemokine that drives steroid-resistant neutrophilic airway inflammation. We have shown that airway smooth muscle (ASM) cells isolated from asthmatic individuals secrete more CXCL8 than cells from nonasthmatic individuals. Here we investigated chromatin modifications at the CXCL8 promoter in ASM cells from nonasthmatic and asthmatic donors to further understand how CXCL8 is dysregulated in asthma. ASM cells from asthmatic donors had increased histone H3 acetylation, specifically histone H3K18 acetylation, and increased binding of histone acetyltransferase p300 compared with nonasthmatic donors but no differences in CXCL8 DNA methylation. The acetylation reader proteins Brd3 and Brd4 were bound to the CXCL8 promoter and Brd inhibitors inhibited CXCL8 secretion from ASM cells by disrupting Brd4 and RNA polymerase II binding to the CXCL8 promoter. Our results show a novel dysregulation of CXCL8 transcriptional regulation in asthma characterized by a promoter complex that is abnormal in ASM cells isolated from asthmatic donors and can be modulated by Brd inhibitors. Brd inhibitors may provide a new therapeutic strategy for steroid-resistant inflammation.
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Affiliation(s)
- Rachel L Clifford
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Jamie K Patel
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Alison E John
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Amanda L Tatler
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Lisa Mazengarb
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
| | - Christopher E Brightling
- Institute for Lung Health, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Alan J Knox
- Department of Respiratory Medicine and Nottingham Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom; and
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20
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Abstract
Species survival depends on the faithful replication of genetic information, which is continually monitored and maintained by DNA repair pathways that correct replication errors and the thousands of lesions that arise daily from the inherent chemical lability of DNA and the effects of genotoxic agents. Nonetheless, neutrally evolving DNA (not under purifying selection) accumulates base substitutions with time (the neutral mutation rate). Thus, repair processes are not 100% efficient. The neutral mutation rate varies both between and within chromosomes. For example it is 10-50 fold higher at CpGs than at non-CpG positions. Interestingly, the neutral mutation rate at non-CpG sites is positively correlated with CpG content. Although the basis of this correlation was not immediately apparent, some bioinformatic results were consistent with the induction of non-CpG mutations by DNA repair at flanking CpG sites. Recent studies with a model system showed that in vivo repair of preformed lesions (mismatches, abasic sites, single stranded nicks) can in fact induce mutations in flanking DNA. Mismatch repair (MMR) is an essential component for repair-induced mutations, which can occur as distant as 5 kb from the introduced lesions. Most, but not all, mutations involved the C of TpCpN (G of NpGpA) which is the target sequence of the C-preferring single-stranded DNA specific APOBEC deaminases. APOBEC-mediated mutations are not limited to our model system: Recent studies by others showed that some tumors harbor mutations with the same signature, as can intermediates in RNA-guided endonuclease-mediated genome editing. APOBEC deaminases participate in normal physiological functions such as generating mutations that inactivate viruses or endogenous retrotransposons, or that enhance immunoglobulin diversity in B cells. The recruitment of normally physiological error-prone processes during DNA repair would have important implications for disease, aging and evolution. This perspective briefly reviews both the bioinformatic and biochemical literature relevant to repair-induced mutagenesis and discusses future directions required to understand the mechanistic basis of this process.
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Affiliation(s)
- Jia Chen
- School of Life Science and Technology, ShanghaiTech University, Building 8, 319 Yueyang Road, Shanghai 200031, China
| | - Anthony V Furano
- Section on Genomic Structure and Function, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8, Room 203, 8 Center Drive, MSC 0830, Bethesda, MD 20892-0830, USA.
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21
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Lee J, Kim YJ, Mun S, Kim HS, Han K. Identification of human-specific AluS elements through comparative genomics. Gene 2014; 555:208-16. [PMID: 25447892 DOI: 10.1016/j.gene.2014.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 11/03/2014] [Accepted: 11/05/2014] [Indexed: 01/08/2023]
Abstract
Mobile elements are responsible for ~45% of the human genome. Among them is the Alu element, accounting for 10% of the human genome (>1.1million copies). Several studies of Alu elements have reported that they are frequently involved in human genetic diseases and genomic rearrangements. In this study, we investigated the AluS subfamily, which is a relatively old Alu subfamily and has the highest copy number in primate genomes. Previously, a set of 263 human-specific AluS insertions was identified in the human genome. To validate these, we compared each of the human-specific AluS loci with its pre-insertion site in other primate genomes, including chimpanzee, gorilla, and orangutan. We obtained 24 putative human-specific AluS candidates via the in silico analysis and manual inspection, and then tried to verify them using PCR amplification and DNA sequencing. Through the PCR product sequencing, we were able to detect two instances of near-parallel Alu insertions in nearby sites that led to computational false negatives. Finally, we computationally and experimentally verified 23 human-specific AluS elements. We reported three alternative Alu insertion events, which are accompanied by filler DNA and/or Alu retrotransposition mediated-deletion. Bisulfite sequencing was carried out to examine DNA methylation levels of human-specific AluS elements. The results showed that fixed AluS elements are hypermethylated compared with polymorphic elements, indicating a possible relation between DNA methylation and Alu fixation in the human genome.
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Affiliation(s)
- Jae Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea
| | - Yun-Ji Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea.
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22
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Hanson MA, Gluckman PD. Early developmental conditioning of later health and disease: physiology or pathophysiology? Physiol Rev 2014; 94:1027-76. [PMID: 25287859 PMCID: PMC4187033 DOI: 10.1152/physrev.00029.2013] [Citation(s) in RCA: 722] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Extensive experimental animal studies and epidemiological observations have shown that environmental influences during early development affect the risk of later pathophysiological processes associated with chronic, especially noncommunicable, disease (NCD). This field is recognized as the developmental origins of health and disease (DOHaD). We discuss the extent to which DOHaD represents the result of the physiological processes of developmental plasticity, which may have potential adverse consequences in terms of NCD risk later, or whether it is the manifestation of pathophysiological processes acting in early life but only becoming apparent as disease later. We argue that the evidence suggests the former, through the operation of conditioning processes induced across the normal range of developmental environments, and we summarize current knowledge of the physiological processes involved. The adaptive pathway to later risk accords with current concepts in evolutionary developmental biology, especially those concerning parental effects. Outside the normal range, effects on development can result in nonadaptive processes, and we review their underlying mechanisms and consequences. New concepts concerning the underlying epigenetic and other mechanisms involved in both disruptive and nondisruptive pathways to disease are reviewed, including the evidence for transgenerational passage of risk from both maternal and paternal lines. These concepts have wider implications for understanding the causes and possible prevention of NCDs such as type 2 diabetes and cardiovascular disease, for broader social policy and for the increasing attention paid in public health to the lifecourse approach to NCD prevention.
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Affiliation(s)
- M A Hanson
- Academic Unit of Human Development and Health, University of Southampton, and NIHR Nutrition Biomedical Research Centre, University Hospital, Southampton, United Kingdom; and Liggins Institute and Gravida (National Centre for Growth and Development), University of Auckland, Auckland, New Zealand
| | - P D Gluckman
- Academic Unit of Human Development and Health, University of Southampton, and NIHR Nutrition Biomedical Research Centre, University Hospital, Southampton, United Kingdom; and Liggins Institute and Gravida (National Centre for Growth and Development), University of Auckland, Auckland, New Zealand
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23
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Livnat A. Interaction-based evolution: how natural selection and nonrandom mutation work together. Biol Direct 2013; 8:24. [PMID: 24139515 PMCID: PMC4231362 DOI: 10.1186/1745-6150-8-24] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/26/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. PRESENTATION OF THE HYPOTHESIS Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation-while not Lamarckian, or "directed" to increase fitness-is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination's fitness. TESTING AND IMPLICATIONS OF THE HYPOTHESIS This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional theory can actually experience selection on interactions and thus has a much greater adaptive potential than previously considered. Empirical evidence for the proposed mechanism from both molecular evolution and evolution at the organismal level is discussed, and multiple predictions are offered by which it may be tested. REVIEWERS This article was reviewed by Nigel Goldenfeld (nominated by Eugene V. Koonin), Jürgen Brosius and W. Ford Doolittle.
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Affiliation(s)
- Adi Livnat
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061,
USA
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24
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Comparative analysis of context-dependent mutagenesis using human and mouse models. BIOMED RESEARCH INTERNATIONAL 2013; 2013:989410. [PMID: 24058920 PMCID: PMC3766559 DOI: 10.1155/2013/989410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/19/2013] [Indexed: 11/17/2022]
Abstract
Substitution rates strongly depend on their nucleotide context. One of the most studied examples is the excess of C > T mutations in the CG context in various groups of organisms, including vertebrates. Studies on the molecular mechanisms underlying this mutation regularity have provided insights into evolution, mutagenesis, and cancer development. Recently several other hypermutable motifs were identified in the human genome. There is an increased frequency of T > C mutations in the second position of the words ATTG and ATAG and an increased frequency of A > C mutations in the first position of the word ACAA. For a better understanding of evolution, it is of interest whether these mutation regularities are human specific or present in other vertebrates, as their presence might affect the validity of currently used substitution models and molecular clocks. A comprehensive analysis of mutagenesis in 4 bp mutation contexts requires a vast amount of mutation data. Such data may be derived from the comparisons of individual genomes or from single nucleotide polymorphism (SNP) databases. Using this approach, we performed a systematical comparison of mutation regularities within 2-4 bp contexts in Mus musculus and Homo sapiens and uncovered that even closely related organisms may have notable differences in context-dependent mutation regularities.
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25
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Segmenting the human genome based on states of neutral genetic divergence. Proc Natl Acad Sci U S A 2013; 110:14699-704. [PMID: 23959903 DOI: 10.1073/pnas.1221792110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.
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26
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Clifford RL, Singer CA, John AE. Epigenetics and miRNA emerge as key regulators of smooth muscle cell phenotype and function. Pulm Pharmacol Ther 2013; 26:75-85. [PMID: 22800879 PMCID: PMC4076625 DOI: 10.1016/j.pupt.2012.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 07/02/2012] [Accepted: 07/04/2012] [Indexed: 10/28/2022]
Abstract
Regulation of phenotypic plasticity in smooth muscle requires an understanding of the mechanisms regulating phenotype-specific genes and the processes dysregulated during pathogenesis. Decades of study in airway smooth muscle has provided extensive knowledge of the gene expression patterns and signaling pathways necessary to maintain and alter smooth muscle cell phenotype. With this solid foundation, the importance and complexity of inheritable epigenetic modifications and mechanisms silencing gene expression have now emerged as fundamental components regulating aspects of inflammation, proliferation and remodeling.
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Affiliation(s)
- Rachel L. Clifford
- University of Nottingham Division of Respiratory Medicine and Nottingham Respiratory Research Unit Clinical Sciences Building, City Hospital Hucknall Road, Nottingham NG5 1PB, England, UK
| | - Cherie A. Singer
- University of Nevada School of Medicine Center for Molecular Medicine 573 Department of Pharmacology, Reno, NV 89557, USA
| | - Alison E. John
- Corresponding Author University of Nottingham Division of Respiratory Medicine and Nottingham Respiratory Research Unit Clinical Sciences Building, City Hospital Hucknall Road, Nottingham NG5 1PB, England, UK Tel:+44 115 8231106 Fax: +44 115 8231946
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27
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van Dyk E, Pretorius PJ. Point mutation instability (PIN) mutator phenotype as model for true back mutations seen in hereditary tyrosinemia type 1 - a hypothesis. J Inherit Metab Dis 2012; 35:407-11. [PMID: 22002443 DOI: 10.1007/s10545-011-9401-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/12/2011] [Accepted: 09/15/2011] [Indexed: 12/12/2022]
Abstract
Hereditary tyrosinemia type 1 (HT1) is an autosomal recessive disorder affecting fumarylacetoacetate hydrolase (FAH), the last enzyme in the tyrosine catabolism pathway. The liver mosaicism observed in HT1 patients is due to the reversion to the wild type of one allele of the original point mutation in fah. It is generally accepted that these reversions are true back mutations; however, the mechanism is still unresolved. Previous reports excluded intragenic recombination, mitotic recombination, or homologous recombination with a pseudogene as possible mechanisms of mutation reversion in HT1. Sequence analysis did not reveal DNA motifs, tandem repeats or other sequence peculiarities that may be involved in mutation reversion. We propose the hypothesis that a point mutation instability mutator (PIN) phenotype brought about by the sustained stress environment created by the accumulating metabolites in the cell is the driver of the true back mutations in HT1. The metabolites accumulating in HT1 create a sustained stress environment by activating the extracellular signal-regulated kinase (ERK) and AKT survival pathways, inducing aberrant mitosis and development of death resistant cells, depleting glutathione, and impairing DNA ligase IV and possibly DNA polymerases δ and ε. This continual production of proliferative and stress-related survival signals in the cellular environment coupled with the mutagenicity of FAA, may instigate a mutator phenotype and could end in tumorigenesis and/or mutation reversion. The establishment of a PIN-mutator phenotype therefore not only seems to be a possible mechanism underlying the true back mutations, but also contributes to explaining the clinical heterogeneity seen in hereditary tyrosinemia type 1.
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Affiliation(s)
- Etresia van Dyk
- Centre for Human Metabonomics, School for Physical and Chemical Sciences, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa.
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28
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The impact of the organism on its descendants. GENETICS RESEARCH INTERNATIONAL 2011; 2012:640612. [PMID: 22567396 PMCID: PMC3335618 DOI: 10.1155/2012/640612] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/30/2011] [Accepted: 10/24/2011] [Indexed: 11/18/2022]
Abstract
Historically, evolutionary biologists have taken the view that an understanding of development is irrelevant to theories of evolution. However, the integration of several disciplines in recent years suggests that this position is wrong. The capacity of the organism to adapt to challenges from the environment can set up conditions that affect the subsequent evolution of its descendants. Moreover, molecular events arising from epigenetic processes can be transmitted from one generation to the next and influence genetic mutation. This in turn can facilitate evolution in the conditions in which epigenetic change was first initiated.
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Abstract
It has been known for many years that the mutation rate varies across the genome. However, only with the advent of large genomic data sets is the full extent of this variation becoming apparent. The mutation rate varies over many different scales, from adjacent sites to whole chromosomes, with the strongest variation seen at the smallest scales. Some of these patterns have clear mechanistic bases, but much of the rate variation remains unexplained, and some of it is deeply perplexing. Variation in the mutation rate has important implications in evolutionary biology and underexplored implications for our understanding of hereditary disease and cancer.
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30
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Cooper DN, Bacolla A, Férec C, Vasquez KM, Kehrer-Sawatzki H, Chen JM. On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum Mutat 2011; 32:1075-99. [PMID: 21853507 PMCID: PMC3177966 DOI: 10.1002/humu.21557] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 06/17/2011] [Indexed: 12/21/2022]
Abstract
Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher order features of the genomic architecture. The human genome is now recognized to contain "pervasive architectural flaws" in that certain DNA sequences are inherently mutation prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here, we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of noncanonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair and may serve to increase mutation frequencies in generalized fashion (i.e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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31
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Cohen CJ, Rebollo R, Babovic S, Dai EL, Robinson WP, Mager DL. Placenta-specific expression of the interleukin-2 (IL-2) receptor β subunit from an endogenous retroviral promoter. J Biol Chem 2011; 286:35543-35552. [PMID: 21865161 DOI: 10.1074/jbc.m111.227637] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The long terminal repeat (LTR) sequences of endogenous retroviruses and retroelements contain promoter elements and are known to form chimeric transcripts with nearby cellular genes. Here we show that an LTR of the THE1D retroelement family has been domesticated as an alternative promoter of human IL2RB, the gene encoding the β subunit of the IL-2 receptor. The LTR promoter confers expression specifically in the placental trophoblast as opposed to its native transcription in the hematopoietic system. Rather than sequence-specific determinants, DNA methylation was found to regulate transcription initiation and splicing efficiency in a tissue-specific manner. Furthermore, we detected the cytoplasmic signaling domain of the IL-2Rβ protein in the placenta, suggesting that IL-2Rβ undergoes preferential proteolytic cleavage in this tissue. These findings implicate novel functions for this cytokine receptor subunit in the villous trophoblast and reveal an intriguing example of ancient LTR exaptation to drive tissue-specific gene expression.
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Affiliation(s)
- Carla J Cohen
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3
| | - Rita Rebollo
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3
| | - Sonja Babovic
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3
| | - Elizabeth L Dai
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3
| | - Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, British Columbia V6T 1Z4; Child and Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Dixie L Mager
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3; Department of Medical Genetics, University of British Columbia, British Columbia V6T 1Z4.
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Misawa K. A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes. BMC Genomics 2011; 12:397. [PMID: 21819607 PMCID: PMC3169530 DOI: 10.1186/1471-2164-12-397] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 08/06/2011] [Indexed: 11/16/2022] Open
Abstract
Background Developing a model for codon substitutions is essential for the analyses of protein sequences. Recent studies on the mutation rates in the non-coding regions have shown that CpG mutation rates in the human genome are negatively correlated to the local GC content and to the densities of functional elements. This study aimed at understanding the effect of genomic features, namely, GC content, gene density, and frequency of CpG islands, on the rates of codon substitution in human chromosomes. Results Codon substitution rates of CpG to TpG mutations, TpG to CpG mutations, and non-CpG transitions and transversions in humans were estimated by comparing the coding regions of thousands of human and chimpanzee genes and inferring their ancestral sequences by using macaque genes as the outgroup. Since the genomic features are depending on each other, partial regression coefficients of these features were obtained. Conclusion The substitution rates of codons depend on gene densities of the chromosomes. Transcription-associated mutation is one such pressure. On the basis of these results, a model of codon substitutions that incorporates the effect of genomic features on codon substitution in human chromosomes was developed.
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Affiliation(s)
- Kazuharu Misawa
- Research Program for Computational Science, Research and Development Group for Next-Generation Integrated Living Matter Simulation, Fusion of Data and Analysis Research and Development Team, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan.
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Clément Y, Arndt PF. Substitution patterns are under different influences in primates and rodents. Genome Biol Evol 2011; 3:236-45. [PMID: 21339508 PMCID: PMC3068003 DOI: 10.1093/gbe/evr011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There are large-scale variations of the GC-content along mammalian chromosomes that have been called isochore structures. Primates and rodents have different isochore structures, which suggests that these lineages exhibit different modes of GC-content evolution. It has been shown that, in the human lineage, GC-biased gene conversion (gBGC), a neutral process associated with meiotic recombination, acts on GC-content evolution by influencing A or T to G or C substitution rates. We computed genome-wide substitution patterns in the mouse lineage from multiple alignments and compared them with substitution patterns in the human lineage. We found that in the mouse lineage, gBGC is active but weaker than in the human lineage and that male-specific recombination better predicts GC-content evolution than female-specific recombination. Furthermore, we were able to show that G or C to A or T substitution rates are predicted by a combination of different factors in both lineages. A or T to G or C substitution rates are most strongly predicted by meiotic recombination in the human lineage but by CpG odds ratio (the observed CpG frequency normalized by the expected CpG frequency) in the mouse lineage, suggesting that substitution patterns are under different influences in primates and rodents.
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Affiliation(s)
- Yves Clément
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Misawa K, Kikuno RF. Relationship between amino acid composition and gene expression in the mouse genome. BMC Res Notes 2011; 4:20. [PMID: 21272306 PMCID: PMC3038927 DOI: 10.1186/1756-0500-4-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 01/27/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Codon bias is a phenomenon that refers to the differences in the frequencies of synonymous codons among different genes. In many organisms, natural selection is considered to be a cause of codon bias because codon usage in highly expressed genes is biased toward optimal codons. Methods have previously been developed to predict the expression level of genes from their nucleotide sequences, which is based on the observation that synonymous codon usage shows an overall bias toward a few codons called major codons. However, the relationship between codon bias and gene expression level, as proposed by the translation-selection model, is less evident in mammals. FINDINGS We investigated the correlations between the expression levels of 1,182 mouse genes and amino acid composition, as well as between gene expression and codon preference. We found that a weak but significant correlation exists between gene expression levels and amino acid composition in mouse. In total, less than 10% of variation of expression levels is explained by amino acid components. We found the effect of codon preference on gene expression was weaker than the effect of amino acid composition, because no significant correlations were observed with respect to codon preference. CONCLUSION These results suggest that it is difficult to predict expression level from amino acid components or from codon bias in mouse.
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Affiliation(s)
- Kazuharu Misawa
- Research Program for Computational Science, Research and Development Group for Next-Generation Integrated Living Matter Simulation, Fusion of Data and Analysis Research and Development Team, RIKEN, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.
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Bell CG, Finer S, Lindgren CM, Wilson GA, Rakyan VK, Teschendorff AE, Akan P, Stupka E, Down TA, Prokopenko I, Morison IM, Mill J, Pidsley R, Deloukas P, Frayling TM, Hattersley AT, McCarthy MI, Beck S, Hitman GA. Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus. PLoS One 2010; 5:e14040. [PMID: 21124985 PMCID: PMC2987816 DOI: 10.1371/journal.pone.0014040] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 10/27/2010] [Indexed: 01/04/2023] Open
Abstract
Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D), focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip) and absolute methylation values were estimated using a Bayesian algorithm (BATMAN). Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p = 9.40×10−4, permutation p = 1.0×10−3). Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p = 1.13×10−7). Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM), encapsulates a Highly Conserved Non-Coding Element (HCNE) that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA) SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases.
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Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom.
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Yuan Z, Sun X, Jiang D, Ding Y, Lu Z, Gong L, Liu H, Xie J. Origin and evolution of a placental-specific microRNA family in the human genome. BMC Evol Biol 2010; 10:346. [PMID: 21067568 PMCID: PMC2996404 DOI: 10.1186/1471-2148-10-346] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 11/10/2010] [Indexed: 12/13/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a class of short regulatory RNAs encoded in the genome of DNA viruses, some single cell organisms, plants and animals. With the rapid development of technology, more and more miRNAs are being discovered. However, the origin and evolution of most miRNAs remain obscure. Here we report the origin and evolution dynamics of a human miRNA family. Results We have shown that all members of the miR-1302 family are derived from MER53 elements. Although the conservation scores of the MER53-derived pre-miRNA sequences are low, we have identified 36 potential paralogs of MER53-derived miR-1302 genes in the human genome and 58 potential orthologs of the human miR-1302 family in placental mammals. We suggest that in placental species, this miRNA family has evolved following the birth-and-death model of evolution. Three possible mechanisms that can mediate miRNA duplication in evolutionary history have been proposed: the transposition of the MER53 element, segmental duplications and Alu-mediated recombination. Finally, we have found that the target genes of miR-1302 are over-represented in transportation, localization, and system development processes and in the positive regulation of cellular processes. Many of them are predicted to function in binding and transcription regulation. Conclusions The members of miR-1302 family that are derived from MER53 elements are placental-specific miRNAs. They emerged at the early stage of the recent 180 million years since eutherian mammals diverged from marsupials. Under the birth-and-death model, the miR-1302 genes have experienced a complex expansion with some members evolving by segmental duplications and some by Alu-mediated recombination events.
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Affiliation(s)
- Zhidong Yuan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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Paquet Y, Anderson A. Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features. Nucleic Acids Res 2010; 38:4907-16. [PMID: 20392819 PMCID: PMC2926601 DOI: 10.1093/nar/gkq234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Transposable elements derived from the 7SL RNA gene, such as Alu elements in primates, have had remarkable success in several mammalian lineages. The results presented here show a broad spectrum of functions for genomic segments that display sequence composition similarities with the 7SL RNA gene. Using thoroughly documented loci, we report that DNaseI-hypersensitive sites can be singled out in large genomic sequences by an assessment of sequence composition similarities with the 7SL RNA gene. We apply a root word frequency approach to illustrate a distinctive relationship between the sequence of the 7SL RNA gene and several classes of functional genomic features that are not presumed to be of transposable origin. Transposable elements that show noticeable similarities with the 7SL sequence include Alu sequences, as expected, but also long terminal repeats and the 5′-untranslated regions of long interspersed repetitive elements. In sequences masked for repeated elements, we find, when using the 7SL RNA gene as query sequence, distinctive similarities with promoters, exons and distal gene regulatory regions. The latter being the most notoriously difficult to detect, this approach may be useful for finding genomic segments that have regulatory functions and that may have escaped detection by existing methods.
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Affiliation(s)
- Yanick Paquet
- Centre de recherche en cancérologie de l’Université Laval, L’Hôtel-Dieu de Québec, Centre hospitalier universitaire de Québec, Québec G1R 2J6 and Département de biologie, Université Laval, Québec G1K 7P4, Canada
| | - Alan Anderson
- Centre de recherche en cancérologie de l’Université Laval, L’Hôtel-Dieu de Québec, Centre hospitalier universitaire de Québec, Québec G1R 2J6 and Département de biologie, Université Laval, Québec G1K 7P4, Canada
- *To whom correspondence should be addressed. Tel: + 418 691 5281; Fax: +418 691 5439;
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Cooper DN, Ball EV, Mort M. Chromosomal distribution of disease genes in the human genome. Genet Test Mol Biomarkers 2010; 14:441-6. [PMID: 20642358 DOI: 10.1089/gtmb.2010.0081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genes are nonrandomly distributed in the human genome, both within and between chromosomes. Thus, genes of similar function and common evolutionary origin are often clustered, as are genes with similar expression profiles. We now report that the >2400 genes known to underlie human monogenic inherited disease are non-randomly distributed in the genome over and above the general nonrandomness evident in the distribution of human genes. Further, a subset of 315 inherited disease genes subject to gross deletion was found to exhibit a degree of clustering that was twice that manifested by disease genes in general. The clustering of human disease genes is likely to have important implications for understanding the genotype-phenotype relationship in contiguous gene syndromes as well as those conditions characterized by multigene deletions or complex chromosomal rearrangements.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom.
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39
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Lee SH, Cho SY, Shannon MF, Fan J, Rangasamy D. The impact of CpG island on defining transcriptional activation of the mouse L1 retrotransposable elements. PLoS One 2010; 5:e11353. [PMID: 20613872 PMCID: PMC2894050 DOI: 10.1371/journal.pone.0011353] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 05/20/2010] [Indexed: 12/31/2022] Open
Abstract
Background L1 retrotransposable elements are potent insertional mutagens responsible for the generation of genomic variation and diversification of mammalian genomes, but reliable estimates of the numbers of actively transposing L1 elements are mostly nonexistent. While the human and mouse genomes contain comparable numbers of L1 elements, several phylogenetic and L1Xplore analyses in the mouse genome suggest that 1,500–3,000 active L1 elements currently exist and that they are still expanding in the genome. Conversely, the human genome contains only 150 active L1 elements. In addition, there is a discrepancy among the nature and number of mouse L1 elements in L1Xplore and the mouse genome browser at the UCSC and in the literature. To date, the reason why a high copy number of active L1 elements exist in the mouse genome but not in the human genome is unknown, as are the potential mechanisms that are responsible for transcriptional activation of mouse L1 elements. Methodology/Principal Findings We analyzed the promoter sequences of the 1,501 potentially active mouse L1 elements retrieved from the GenBank and L1Xplore databases and evaluated their transcription factors binding sites and CpG content. To this end, we found that a substantial number of mouse L1 elements contain altered transcription factor YY1 binding sites on their promoter sequences that are required for transcriptional initiation, suggesting that only a half of L1 elements are capable of being transcriptionally active. Furthermore, we present experimental evidence that previously unreported CpG islands exist in the promoters of the most active TF family of mouse L1 elements. The presence of sequence variations and polymorphisms in CpG islands of L1 promoters that arise from transition mutations indicates that CpG methylation could play a significant role in determining the activity of L1 elements in the mouse genome. Conclusions A comprehensive analysis of mouse L1 promoters suggests that the number of transcriptionally active elements is significantly lower than the total number of full-length copies from the three active mouse L1 families. Like human L1 elements, the CpG islands and potentially the transcription factor YY1 binding sites are likely to be required for transcriptional initiation of mouse L1 elements.
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Affiliation(s)
- Sung-Hun Lee
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Soo-Young Cho
- Division of Molecular and Life Sciences, Hanyang University, Ansan, Republic of Korea
| | - M. Frances Shannon
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Jun Fan
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Danny Rangasamy
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
- * E-mail:
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Abstract
The accumulation of base substitutions (mutations) not subject to natural selection is the neutral mutation rate. Because this rate reflects the in vivo processes involved in maintaining the integrity of genetic information, the factors that affect the neutral mutation rate are of considerable interest. Mammals exhibit two dramatically different neutral mutation rates: the CpG mutation rate, wherein the C of most CpGs (i.e., methyl-CpG) mutate at 10-50 times that of C in any other context or of any other base. The latter mutations constitute the non-CpG rate. The high CpG rate results from the spontaneous deamination of methyl-C to T and incomplete restoration of the ensuing T:G mismatches to C:Gs. Here, we determined the neutral non-CpG mutation rate as a function of CpG content by comparing sequence divergence of thousands of pairs of neutrally evolving chimpanzee and human orthologs that differ primarily in CpG content. Both the mutation rate and the mutational spectrum (transition/transversion ratio) of non-CpG residues change in parallel as sigmoidal (logistic) functions of CpG content. As different mechanisms generate transitions and transversions, these results indicate that both mutation rate and mutational processes are contingent on the local CpG content. We consider several possible mechanisms that might explain how CpG exerts these effects.
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Affiliation(s)
- Jean-Claude Walser
- Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA
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Kvikstad EM, Makova KD. The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res 2010; 20:600-13. [PMID: 20219940 DOI: 10.1101/gr.099044.109] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the sex chromosomes. Here, using a multiple regression framework, we investigate primate Alu and L1 densities shaped by regional genome features and location on a particular chromosome type. As a result of our analysis, first, we build statistical models explaining up to 79% and 44% of variation in Alu and L1 element density, respectively. Second, we analyze sex chromosome versus autosome TE densities corrected for regional genomic effects. We discover that sex-chromosome bias in Alu and L1 distributions not only persists after accounting for these effects, but even presents differences in patterns, confirming preferential Alu integration in the male germline, yet likely integration of L1s in both male and female germlines or in early embryogenesis. Additionally, our models reveal that local base composition (measured by GC content and density of L1 target sites) and natural selection (inferred via density of most conserved elements) are significant to predicting densities of L1s. Interestingly, measurements of local double-stranded breaks (a 13-mer associated with genome instability) strongly correlate with densities of Alu elements; little evidence was found for the role of recombination-driven deletion in driving TE distributions over evolutionary time. Thus, Alu and L1 densities have been influenced by the combination of distinct local genome landscapes and the unique evolutionary dynamics of sex chromosomes.
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Affiliation(s)
- Erika M Kvikstad
- Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.
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42
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Wu W, Shen X, Tao S. Characteristics of the CArG-SRF binding context in mammalian genomes. Mamm Genome 2009; 21:104-13. [PMID: 19953255 DOI: 10.1007/s00335-009-9238-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 11/11/2009] [Indexed: 11/28/2022]
Abstract
Serum response factor (SRF), a member of the MADS family, binds a 10-bp cis element known as the CArG box. However, despite our extensive knowledge of SRF and the CArG box, limited information is available on the CArG-SRF binding context or how CArG flanking sequences are defined. We used statistical tests and computer simulation to find characteristics of the CArG-SRF binding context. Based on the combination of published literature and a search of DBTSS, 150 and 136 functional CArG boxes together with 10 bp flanking on each side were found in mouse and human genomes, respectively. By statistical analysis of the 30 positions we found some new conserved positions of interest (P < 0.005) such as -15, -8, and +8, in addition to the ten highly conserved positions of the CArG box. Intriguingly, studies comparing the flanking positions between consensus CArG boxes and CArG-like boxes showed that there are more conserved positions in the latter. Moreover, CpG content within the CArG-SRF binding context is much higher than that within introns. Collectively, these results suggest that there are some special pre-existing features in the flanking sequences of functional CArG boxes probably contributing to SRF selectively recognizing and binding to the functional CArG from millions of functionless CArG boxes in mammalian genomes. This is a significant step toward understanding the mechanism of transcriptional regulation of SRF-dependent genes.
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Affiliation(s)
- Wenwu Wu
- College of Life Science, Northwest A&F University, 712100, Yangling, Shaanxi, China
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43
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Diamonds and rust: how transposable elements influence mammalian genomes. Conference on Mobile Elements in Mammalian Genomes. EMBO Rep 2009; 10:1306-10. [PMID: 19949412 DOI: 10.1038/embor.2009.248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 10/20/2009] [Indexed: 11/08/2022] Open
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Understanding what determines the frequency and pattern of human germline mutations. Nat Rev Genet 2009; 10:478-88. [PMID: 19488047 DOI: 10.1038/nrg2529] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Surprising findings about human germline mutation have come from applying new technologies to detect rare mutations in germline DNA, from analysing DNA sequence divergence between humans and closely related species, and from investigating human polymorphic variation. In this Review we discuss how these approaches affect our current understanding of the roles of sex, age, mutation hot spots, germline selection and genomic factors in determining human nucleotide substitution mutation patterns and frequencies. To enhance our understanding of mutation and disease, more extensive molecular data on the human germ line with regard to mutation origin, DNA repair, epigenetic status and the effect of newly arisen mutations on gamete development are needed.
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Abstract
Why are some genomic positions more mutable than others? The identification of cryptic mutation hotspots in the human genome indicates that the determinants of mutation rates are more complex than anticipated.
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Affiliation(s)
- Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, France.
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