1
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Long Y, Wendel JF, Zhang X, Wang M. Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants. TRENDS IN PLANT SCIENCE 2024; 29:638-649. [PMID: 38061928 DOI: 10.1016/j.tplants.2023.11.009] [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: 08/24/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 06/09/2024]
Abstract
Development of complex traits necessitates the functioning and coordination of intricate regulatory networks involving multiple genes. Understanding 3D chromatin structure can facilitate insight into the regulation of gene expression by regulatory elements. This potential, of visualizing the role of chromatin organization in the evolution and function of regulatory elements, remains largely unexplored. Here, we describe new perspectives that arise from the dual considerations of sequence variation of regulatory elements and chromatin structure, with a special focus on whole-genome doubling or polyploidy. We underscore the significance of hierarchical chromatin organization in gene regulation during evolution. In addition, we describe strategies for exploring chromatin organization in future investigations of regulatory evolution in plants, enabling insights into the evolutionary influence of regulatory elements on gene expression and, hence, phenotypes.
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Affiliation(s)
- Yuexuan Long
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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2
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Fleck K, Luria V, Garag N, Karger A, Hunter T, Marten D, Phu W, Nam KM, Sestan N, O’Donnell-Luria AH, Erceg J. Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585403. [PMID: 38559085 PMCID: PMC10980080 DOI: 10.1101/2024.03.17.585403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genome organization is intricately tied to regulating genes and associated cell fate decisions. In this study, we examine the positioning and functional significance of human genes, grouped by their evolutionary age, within the 3D organization of the genome. We reveal that genes of different evolutionary origin have distinct positioning relationships with both domains and loop anchors, and remarkably consistent relationships with boundaries across cell types. While the functional associations of each group of genes are primarily cell type-specific, such associations of conserved genes maintain greater stability across 3D genomic features and disease than recently evolved genes. Furthermore, the expression of these genes across various tissues follows an evolutionary progression, such that RNA levels increase from young genes to ancient genes. Thus, the distinct relationships of gene evolutionary age, function, and positioning within 3D genomic features contribute to tissue-specific gene regulation in development and disease.
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Affiliation(s)
- Katherine Fleck
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Nitanta Garag
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA 02115
| | - Trevor Hunter
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Daniel Marten
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - William Phu
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Kee-Myoung Nam
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06510
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510
| | - Anne H. O’Donnell-Luria
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Jelena Erceg
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030
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3
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Mañes-García J, Marco-Ferreres R, Beccari L. Shaping gene expression and its evolution by chromatin architecture and enhancer activity. Curr Top Dev Biol 2024; 159:406-437. [PMID: 38729683 DOI: 10.1016/bs.ctdb.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Transcriptional regulation plays a pivotal role in orchestrating the intricate genetic programs governing embryonic development. The expression of developmental genes relies on the combined activity of several cis-regulatory elements (CREs), such as enhancers and silencers, which can be located at long linear distances from the genes that they regulate and that interact with them through establishment of chromatin loops. Mutations affecting their activity or interaction with their target genes can lead to developmental disorders and are thought to have importantly contributed to the evolution of the animal body plan. The income of next-generation-sequencing approaches has allowed identifying over a million of sequences with putative regulatory potential in the human genome. Characterizing their function and establishing gene-CREs maps is essential to decode the logic governing developmental gene expression and is one of the major challenges of the post-genomic era. Chromatin 3D organization plays an essential role in determining how CREs specifically contact their target genes while avoiding deleterious off-target interactions. Our understanding of these aspects has greatly advanced with the income of chromatin conformation capture techniques and fluorescence microscopy approaches to visualize the organization of DNA elements in the nucleus. Here we will summarize relevant aspects of how the interplay between CRE activity and chromatin 3D organization regulates developmental gene expression and how it relates to pathological conditions and the evolution of animal body plan.
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Affiliation(s)
| | | | - Leonardo Beccari
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain.
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4
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Zintel TM, Pizzollo J, Claypool CG, Babbitt CC. Astrocytes Drive Divergent Metabolic Gene Expression in Humans and Chimpanzees. Genome Biol Evol 2024; 16:evad239. [PMID: 38159045 PMCID: PMC10829071 DOI: 10.1093/gbe/evad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 11/13/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024] Open
Abstract
The human brain utilizes ∼20% of all of the body's metabolic resources, while chimpanzee brains use <10%. Although previous work shows significant differences in metabolic gene expression between the brains of primates, we have yet to fully resolve the contribution of distinct brain cell types. To investigate cell type-specific interspecies differences in brain gene expression, we conducted RNA-seq on neural progenitor cells, neurons, and astrocytes generated from induced pluripotent stem cells from humans and chimpanzees. Interspecies differential expression analyses revealed that twice as many genes exhibit differential expression in astrocytes (12.2% of all genes expressed) than neurons (5.8%). Pathway enrichment analyses determined that astrocytes, rather than neurons, diverged in expression of glucose and lactate transmembrane transport, as well as pyruvate processing and oxidative phosphorylation. These findings suggest that astrocytes may have contributed significantly to the evolution of greater brain glucose metabolism with proximity to humans.
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Affiliation(s)
- Trisha M Zintel
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jason Pizzollo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Christopher G Claypool
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
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5
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Okhovat M, VanCampen J, Nevonen KA, Harshman L, Li W, Layman CE, Ward S, Herrera J, Wells J, Sheng RR, Mao Y, Ndjamen B, Lima AC, Vigh-Conrad KA, Stendahl AM, Yang R, Fedorov L, Matthews IR, Easow SA, Chan DK, Jan TA, Eichler EE, Rugonyi S, Conrad DF, Ahituv N, Carbone L. TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function. Nat Commun 2023; 14:8111. [PMID: 38062027 PMCID: PMC10703881 DOI: 10.1038/s41467-023-43841-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find 14% of all human TAD boundaries to be shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons compared to species-specific boundaries. CRISPR-Cas9 knockouts of an ultraconserved boundary in a mouse model lead to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in the upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations and showcases the functional importance of TAD evolution.
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Affiliation(s)
- Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA.
| | - Jake VanCampen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Lana Harshman
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Weiyu Li
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Cora E Layman
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Samantha Ward
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Jarod Herrera
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Jackson Wells
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Rory R Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Blaise Ndjamen
- Histology and Light Microscopy Core Facility, Gladstone Institutes, San Francisco, CA, USA
| | - Ana C Lima
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
| | | | - Alexandra M Stendahl
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Ran Yang
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Lev Fedorov
- OHSU Transgenic Mouse Models Core Lab, Oregon Health and Science University, Portland, OR, USA
| | - Ian R Matthews
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA
| | - Sarah A Easow
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA
| | - Dylan K Chan
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA
| | - Taha A Jan
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Sandra Rugonyi
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA.
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA.
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA.
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6
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Martín-Zamora FM, Davies BE, Donnellan RD, Guynes K, Martín-Durán JM. Functional genomics in Spiralia. Brief Funct Genomics 2023; 22:487-497. [PMID: 37981859 PMCID: PMC10658182 DOI: 10.1093/bfgp/elad036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.
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Affiliation(s)
- Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Rory D Donnellan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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7
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Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA. Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564272. [PMID: 37961120 PMCID: PMC10634871 DOI: 10.1101/2023.10.26.564272] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Phenotypic divergence between closely related species, including bonobos and chimpanzees (genus Pan), is largely driven by variation in gene regulation. The 3D structure of the genome mediates gene expression; however, genome folding differences in Pan are not well understood. Here, we apply machine learning to predict genome-wide 3D genome contact maps from DNA sequence for 56 bonobos and chimpanzees, encompassing all five extant lineages. We use a pairwise approach to estimate 3D divergence between individuals from the resulting contact maps in 4,420 1 Mb genomic windows. While most pairs were similar, ∼17% were predicted to be substantially divergent in genome folding. The most dissimilar maps were largely driven by single individuals with rare variants that produce unique 3D genome folding in a region. We also identified 89 genomic windows where bonobo and chimpanzee contact maps substantially diverged, including several windows harboring genes associated with traits implicated in Pan phenotypic divergence. We used in silico mutagenesis to identify 51 3D-modifying variants in these bonobo-chimpanzee divergent windows, finding that 34 or 66.67% induce genome folding changes via CTCF binding motif disruption. Our results reveal 3D genome variation at the population-level and identify genomic regions where changes in 3D folding may contribute to phenotypic differences in our closest living relatives.
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Affiliation(s)
- Colin M. Brand
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Shuzhen Kuang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
| | - Erin N. Gilbertson
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Biomedical Informatics Graduate Program, University of California San Francisco, San Francisco, CA
| | - Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN
| | - Katherine S. Pollard
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Biomedical Informatics Graduate Program, University of California San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| | | | - John A. Capra
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
- Biomedical Informatics Graduate Program, University of California San Francisco, San Francisco, CA
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8
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Barr KA, Rhodes KL, Gilad Y. The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees. Genome Biol 2023; 24:207. [PMID: 37697401 PMCID: PMC10496171 DOI: 10.1186/s13059-023-03019-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/21/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees. RESULTS We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes. CONCLUSIONS Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences.
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Affiliation(s)
- Kenneth A Barr
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | | | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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9
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Wang L, Wang X, Liu C, Xu W, Kuang W, Bu Q, Li H, Zhao Y, Jiang L, Chen Y, Qin F, Li S, Wei Q, Liu X, Liu B, Chen Y, Dai Y, Wang H, Tian J, Cao G, Zhao Y, Cen X. Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:551-572. [PMID: 37209997 PMCID: PMC10787020 DOI: 10.1016/j.gpb.2023.03.003] [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: 11/06/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/22/2023]
Abstract
The expression of linear DNA sequence is precisely regulated by the three-dimensional (3D) architecture of chromatin. Morphine-induced aberrant gene networks of neurons have been extensively investigated; however, how morphine impacts the 3D genomic architecture of neurons is still unknown. Here, we applied digestion-ligation-only high-throughput chromosome conformation capture (DLO Hi-C) technology to investigate the effects of morphine on the 3D chromatin architecture of primate cortical neurons. After receiving continuous morphine administration for 90 days on rhesus monkeys, we discovered that morphine re-arranged chromosome territories, with a total of 391 segmented compartments being switched. Morphine altered over half of the detected topologically associated domains (TADs), most of which exhibited a variety of shifts, followed by separating and fusing types. Analysis of the looping events at kilobase-scale resolution revealed that morphine increased not only the number but also the length of differential loops. Moreover, all identified differentially expressed genes from the RNA sequencing data were mapped to the specific TAD boundaries or differential loops, and were further validated for changed expression. Collectively, an altered 3D genomic architecture of cortical neurons may regulate the gene networks associated with morphine effects. Our finding provides critical hubs connecting chromosome spatial organization and gene networks associated with the morphine effects in humans.
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Affiliation(s)
- Liang Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaojie Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Chunqi Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Wei Xu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China; Shenzhen Key Laboratory of Drug Addiction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weihong Kuang
- Department of Psychiatry, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qian Bu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Hongchun Li
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Ying Zhao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Linhong Jiang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yaxing Chen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Feng Qin
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Shu Li
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qinfan Wei
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaocong Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Bin Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yuanyuan Chen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yanping Dai
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Hongbo Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Jingwei Tian
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yinglan Zhao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaobo Cen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China.
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10
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Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Nowakowski T, Ahituv N, Pollen A, Pollard KS. Three-dimensional genome rewiring in loci with human accelerated regions. Science 2023; 380:eabm1696. [PMID: 37104607 PMCID: PMC10999243 DOI: 10.1126/science.abm1696] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/01/2023] [Indexed: 04/29/2023]
Abstract
Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.
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Affiliation(s)
- Kathleen C Keough
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Tyler Fair
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marilyn Steyert
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Hane Ryu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Alex Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics and Bakar Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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11
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Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS. Comparing chromatin contact maps at scale: methods and insights. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535480. [PMID: 37066196 PMCID: PMC10104037 DOI: 10.1101/2023.04.04.535480] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Comparing chromatin contact maps is an essential step in quantifying how three-dimensional (3D) genome organization shapes development, evolution, and disease. However, no gold standard exists for comparing contact maps, and even simple methods often disagree. In this study, we propose novel comparison methods and evaluate them alongside existing approaches using genome-wide Hi-C data and 22,500 in silico predicted contact maps. We also quantify the robustness of methods to common sources of biological and technical variation, such as boundary size and noise. We find that simple difference-based methods such as mean squared error are suitable for initial screening, but biologically informed methods are necessary to identify why maps diverge and propose specific functional hypotheses. We provide a reference guide, codebase, and benchmark for rapidly comparing chromatin contact maps at scale to enable biological insights into the 3D organization of the genome.
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Affiliation(s)
- Laura M. Gunsalus
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - Evonne McArthur
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Ketrin Gjoni
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - Shuzhen Kuang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - Maureen Pittman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - John A. Capra
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
| | - Katherine S. Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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12
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Okhovat M, VanCampen J, Lima AC, Nevonen KA, Layman CE, Ward S, Herrera J, Stendahl AM, Yang R, Harshman L, Li W, Sheng RR, Mao Y, Fedorov L, Ndjamen B, Vigh-Conrad KA, Matthews IR, Easow SA, Chan DK, Jan TA, Eichler EE, Rugonyi S, Conrad DF, Ahituv N, Carbone L. TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531534. [PMID: 36945527 PMCID: PMC10028908 DOI: 10.1101/2023.03.07.531534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species, and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find that only 14% of all human TAD boundaries are shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons, compared to species-specific boundaries. CRISPR-Cas9 knockouts of two ultraconserved boundaries in mouse models leads to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations, and showcase the functional importance of TAD evolution.
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13
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Li Q, Perera D, Cao C, He J, Bian J, Chen X, Azeem F, Howe A, Au B, Wu J, Yan J, Long Q. Interaction-integrated linear mixed model reveals 3D-genetic basis underlying Autism. Genomics 2023; 115:110575. [PMID: 36758877 DOI: 10.1016/j.ygeno.2023.110575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Genetic interactions play critical roles in genotype-phenotype associations. We developed a novel interaction-integrated linear mixed model (ILMM) that integrates a priori knowledge into linear mixed models. ILMM enables statistical integration of genetic interactions upfront and overcomes the problems of searching for combinations. To demonstrate its utility, with 3D genomic interactions (assessed by Hi-C experiments) as a priori, we applied ILMM to whole-genome sequencing data for Autism Spectrum Disorders (ASD) and brain transcriptome data, revealing the 3D-genetic basis of ASD and 3D-expression quantitative loci (3D-eQTLs) for brain tissues. Notably, we reported a potential mechanism involving distal regulation between FOXP2 and DNMT3A, conferring the risk of ASD.
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Affiliation(s)
- Qing Li
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Deshan Perera
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Chen Cao
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Jingni He
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Jiayi Bian
- Department of Mathematics and Statistics, University of Calgary, Alberta T2N 1N4, Canada
| | - Xingyu Chen
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Feeha Azeem
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Aaron Howe
- Heritage Youth Researcher Summer Program, University of Calgary, Alberta T2N 1N4, Canada
| | - Billie Au
- Department of Medical Genetics, University of Calgary, Alberta T2N 1N4, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Alberta T2N 1N4, Canada
| | - Jingjing Wu
- Department of Mathematics and Statistics, University of Calgary, Alberta T2N 1N4, Canada
| | - Jun Yan
- Department of Physiology and Pharmacology, University of Calgary, Alberta T2N 1N4, Canada; Hotchkiss Brain Institute, University of Calgary, Alberta T2N 1N4, Canada.
| | - Quan Long
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada; Department of Medical Genetics, University of Calgary, Alberta T2N 1N4, Canada; Department of Mathematics and Statistics, University of Calgary, Alberta T2N 1N4, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Alberta T2N 1N4, Canada; Hotchkiss Brain Institute, University of Calgary, Alberta T2N 1N4, Canada.
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14
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Acemel RD, Lupiáñez DG. Evolution of 3D chromatin organization at different scales. Curr Opin Genet Dev 2023; 78:102019. [PMID: 36603519 DOI: 10.1016/j.gde.2022.102019] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 01/04/2023]
Abstract
Most animal genomes fold in 3D chromatin domains called topologically associated domains (TADs) that facilitate interactions between cis-regulatory elements (CREs) and promoters. Owing to their critical role in the control of developmental gene expression, we explore how TADs have shaped animal evolution. In the light of recent studies that profile TADs in disparate animal lineages, we discuss their phylogenetic distribution and the mechanisms that underlie their formation. We present evidence indicating that TADs are plastic entities composed of genomic strata of different ages: ancient cores are combined with newer regions and brought into extant TADs through genomic rearrangements. We highlight that newly incorporated TAD strata enable the establishment of new CRE-promoter interactions and in turn new expression patterns that can drive phenotypical innovation. We further highlight how subtle changes in chromatin folding may fine-tune the expression levels of developmental genes and hold a potential for evolutionary significance.
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15
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Current advances in primate genomics: novel approaches for understanding evolution and disease. Nat Rev Genet 2023; 24:314-331. [PMID: 36599936 DOI: 10.1038/s41576-022-00554-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 01/05/2023]
Abstract
Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.
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16
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Xia C, Huang L, Huang J, Zhang H, Huang Y, Benhamed M, Wang M, Chen X, Zhang M, Liu T, Chen W. Folding Features and Dynamics of 3D Genome Architecture in Plant Fungal Pathogens. Microbiol Spectr 2022; 10:e0260822. [PMID: 36250889 PMCID: PMC9769607 DOI: 10.1128/spectrum.02608-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/18/2022] [Indexed: 01/07/2023] Open
Abstract
The folding and dynamics of three-dimensional (3D) genome organization are fundamental for eukaryotes executing genome functions but have been largely unexplored in nonmodel fungi. Using high-throughput sequencing coupled with chromosome conformation capture (Hi-C) data, we generated two chromosome-level assemblies for Puccinia striiformis f. sp. tritici, a fungus causing stripe rust disease on wheat, for studying 3D genome architectures of plant pathogenic fungi. The chromatin organization of the fungus followed a combination of the fractal globule model and the equilibrium globule model. Surprisingly, chromosome compartmentalization was not detected. Dynamics of 3D genome organization during two developmental stages of P. striiformis f. sp. tritici indicated that regulation of gene activities might be independent of the changes of genome organization. In addition, chromatin conformation conservation was found to be independent of genome sequence synteny conservation among different fungi. These results highlighted the distinct folding principles of fungal 3D genomes. Our findings should be an important step toward a holistic understanding of the principles and functions of genome architecture across different eukaryotic kingdoms. IMPORTANCE Previously, our understanding of 3D genome architecture has mainly come from model mammals, insects, and plants. However, the organization and regulatory functions of 3D genomes in fungi are largely unknown. In this study, we comprehensively investigated P. striiformis f. sp. tritici, a plant fungal pathogen, and revealed distinct features of the 3D genome, comparing it with the universal folding feature of 3D genomes in higher eukaryotic organisms. We further suggested that there might be distinct regulatory mechanisms of gene expression that are independent of chromatin organization changes during the developmental stages of this rust fungus. Moreover, we showed that the evolutionary pattern of 3D genomes in this fungus is also different from the cases in mammalian genomes. In addition, the genome assembly pipeline and the generated two chromosome-level genomes will be valuable resources. These results highlighted the unexplored distinct features of 3D genome organization in fungi. Therefore, our study provided complementary knowledge to holistically understand the organization and functions of 3D genomes across different eukaryotes.
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Affiliation(s)
- Chongjing Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Liang Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
| | - Jie Huang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Huang
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Paris, France
| | - Moussa Benhamed
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Paris, France
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, Washington, USA
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
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17
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Can changes in 3D genome architecture create new regulatory landscapes that contribute to phenotypic evolution? Essays Biochem 2022; 66:745-752. [PMID: 36250960 DOI: 10.1042/ebc20220057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
Animal genomes are compartmentalized into insulated regulatory units named topology-associated domains (TADs). TADs insulate gene promoters from enhancers that occupy neighboring TADs. Chromosomal rearrangements that disrupt TAD structure can generate new regulatory interactions between enhancers and promoters that were once separated into different TADs, which might lead to new gene expression patterns. On the one hand, TAD rearrangements are known to cause deleterious phenotypes, but, on the other hand, rearrangements can also create novel expression patterns that may be selected during evolution because they generate advantageous phenotypes. Here, we review recent studies that explore the effects of chromosomal rearrangements and genetic perturbations on TAD structure and gene regulation in the context of development and evolution. We discuss the possible contribution of evolutionary breakpoints (EBRs) that affect TAD structure to the evolution of gene regulation and the phenotype.
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18
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A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships. Genome Biol 2022; 23:238. [PMID: 36352464 PMCID: PMC9647974 DOI: 10.1186/s13059-022-02790-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromatin contacts are essential for gene-expression regulation; however, obtaining a high-resolution genome-wide chromatin contact map is still prohibitively expensive owing to large genome sizes and the quadratic scale of pairwise data. Chromosome conformation capture (3C)-based methods such as Hi-C have been extensively used to obtain chromatin contacts. However, since the sparsity of these maps increases with an increase in genomic distance between contacts, long-range or trans-chromatin contacts are especially challenging to sample. RESULTS Here, we create a high-density reference genome-wide chromatin contact map using a meta-analytic approach. We integrate 3600 human, 6700 mouse, and 500 fly Hi-C experiments to create species-specific meta-Hi-C chromatin contact maps with 304 billion, 193 billion, and 19 billion contacts in respective species. We validate that meta-Hi-C contact maps are uniquely powered to capture functional chromatin contacts in both cis and trans. We find that while individual dataset Hi-C networks are largely unable to predict any long-range coexpression (median 0.54 AUC), meta-Hi-C networks perform comparably in both cis and trans (0.65 AUC vs 0.64 AUC). Similarly, for long-range expression quantitative trait loci (eQTL), meta-Hi-C contacts outperform all individual Hi-C experiments, providing an improvement over the conventionally used linear genomic distance-based association. Assessing between species, we find patterns of chromatin contact conservation in both cis and trans and strong associations with coexpression even in species for which Hi-C data is lacking. CONCLUSIONS We have generated an integrated chromatin interaction network which complements a large number of methodological and analytic approaches focused on improved specificity or interpretation. This high-depth "super-experiment" is surprisingly powerful in capturing long-range functional relationships of chromatin interactions, which are now able to predict coexpression, eQTLs, and cross-species relationships. The meta-Hi-C networks are available at https://labshare.cshl.edu/shares/gillislab/resource/HiC/ .
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19
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Torosin NS, Golla TR, Lawlor MA, Cao W, Ellison CE. Mode and Tempo of 3D Genome Evolution in Drosophila. Mol Biol Evol 2022; 39:6750036. [PMID: 36201625 PMCID: PMC9641997 DOI: 10.1093/molbev/msac216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Topologically associating domains (TADs) are thought to play an important role in preventing gene misexpression by spatially constraining enhancer-promoter contacts. The deleterious nature of gene misexpression implies that TADs should, therefore, be conserved among related species. Several early studies comparing chromosome conformation between species reported high levels of TAD conservation; however, more recent studies have questioned these results. Furthermore, recent work suggests that TAD reorganization is not associated with extensive changes in gene expression. Here, we investigate the evolutionary conservation of TADs among 11 species of Drosophila. We use Hi-C data to identify TADs in each species and employ a comparative phylogenetic approach to derive empirical estimates of the rate of TAD evolution. Surprisingly, we find that TADs evolve rapidly. However, we also find that the rate of evolution depends on the chromatin state of the TAD, with TADs enriched for developmentally regulated chromatin evolving significantly slower than TADs enriched for broadly expressed, active chromatin. We also find that, after controlling for differences in chromatin state, highly conserved TADs do not exhibit higher levels of gene expression constraint. These results suggest that, in general, most TADs evolve rapidly and their divergence is not associated with widespread changes in gene expression. However, higher levels of evolutionary conservation and gene expression constraints in TADs enriched for developmentally regulated chromatin suggest that these TAD subtypes may be more important for regulating gene expression, likely due to the larger number of long-distance enhancer-promoter contacts associated with developmental genes.
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Affiliation(s)
- Nicole S Torosin
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | - Tirupathi Rao Golla
- LifeCell, Kelambakkam Main Road, Keelakottaiyur, Chennai 600127, Tamil Nadu, India
| | - Matthew A Lawlor
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | - Weihuan Cao
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
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20
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Wright D, Schaeffer SW. The relevance of chromatin architecture to genome rearrangements in Drosophila. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210206. [PMID: 35694744 PMCID: PMC9189500 DOI: 10.1098/rstb.2021.0206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA within chromosomes in the nucleus is non-randomly organized into chromosome territories, compartments and topologically associated domains (TADs). Chromosomal rearrangements have the potential to alter chromatin organization and modify gene expression leading to selection against these structural variants. Drosophila pseudoobscura has a wealth of naturally occurring gene arrangements that were generated by overlapping inversion mutations caused by two chromosomal breaks that rejoin the central region in reverse order. Unlike humans, Drosophila inversion heterozygotes do not have negative effects associated with crossing over during meiosis because males use achiasmate mechanisms for proper segregation, and aberrant recombinant meiotic products generated in females are lost in polar bodies. As a result, Drosophila populations are found to harbour extensive inversion polymorphisms. It is not clear, however, whether chromatin architecture constrains which inversions breakpoints persist in populations. We mapped the breakpoints of seven inversions in D. pseudoobscura to the TAD map to determine if persisting inversion breakpoints are more likely to occur at boundaries between TADs. Our results show that breakpoints occur at TAD boundaries more than expected by chance. Some breakpoints may alter gene expression within TADs supporting the hypothesis that position effects contribute to inversion establishment. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Dynisty Wright
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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21
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The 3D architecture of the pepper genome and its relationship to function and evolution. Nat Commun 2022; 13:3479. [PMID: 35710823 PMCID: PMC9203530 DOI: 10.1038/s41467-022-31112-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/03/2022] [Indexed: 12/21/2022] Open
Abstract
The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper (Capsicum annuum) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints. The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression.
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22
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Hintermann A, Guerreiro I, Lopez-Delisle L, Bolt CC, Gitto S, Duboule D, Beccari L. Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken. Development 2022; 149:275867. [PMID: 35770682 PMCID: PMC9307994 DOI: 10.1242/dev.200594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022]
Abstract
Modifications in gene regulation are driving forces in the evolution of organisms. Part of these changes involve cis-regulatory elements (CREs), which contact their target genes through higher-order chromatin structures. However, how such architectures and variations in CREs contribute to transcriptional evolvability remains elusive. We use Hoxd genes as a paradigm for the emergence of regulatory innovations, as many relevant enhancers are located in a regulatory landscape highly conserved in amniotes. Here, we analysed their regulation in murine vibrissae and chicken feather primordia, two skin appendages expressing different Hoxd gene subsets, and compared the regulation of these genes in these appendages with that in the elongation of the posterior trunk. In the two former structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, probably as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the gene regulation that occurs in the mouse and chicken embryonic trunk partially relies on conserved CREs. A high proportion of these non-coding sequences active in the trunk have functionally diverged between species, suggesting that transcriptional robustness is maintained, despite considerable divergence in enhancer sequences. Summary: Analyses of the relationships between chromatin architecture and regulatory activities at the HoxD locus show that ancestral transcription patterns can be maintained while new regulations evolve.
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Affiliation(s)
- Aurélie Hintermann
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Isabel Guerreiro
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Lucille Lopez-Delisle
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Christopher Chase Bolt
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Sandra Gitto
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Denis Duboule
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
- Collège de France 3 , 11 Place Marcelin Berthelot, 75005 Paris , France
| | - Leonardo Beccari
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
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23
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Li D, He M, Tang Q, Tian S, Zhang J, Li Y, Wang D, Jin L, Ning C, Zhu W, Hu S, Long K, Ma J, Liu J, Zhang Z, Li M. Comparative 3D genome architecture in vertebrates. BMC Biol 2022; 20:99. [PMID: 35524220 PMCID: PMC9077971 DOI: 10.1186/s12915-022-01301-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Background The three-dimensional (3D) architecture of the genome has a highly ordered and hierarchical nature, which influences the regulation of essential nuclear processes at the basis of gene expression, such as gene transcription. While the hierarchical organization of heterochromatin and euchromatin can underlie differences in gene expression that determine evolutionary differences among species, the way 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. Results This analysis shows a correlation between genome size and chromosome length that affects chromosome territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through the evolution of vertebrates. Furthermore, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. Conclusions Our analysis uncovers organizational features that appear to determine the conservation and transcriptional regulation of functional genes across species. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01301-7.
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Affiliation(s)
- Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shilin Tian
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Novogene Bioinformatics Institute, Beijing, 100000, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Danyang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunyou Ning
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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24
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Abstract
We found the three-dimensional (3D) structure of chromatin at the chromosome level to be highly conserved for more than 50 million y of carnivore evolution. Intrachromosomal contacts were maintained even after chromosome rearrangements within carnivore lineages, demonstrating that the maintenance of 3D chromatin architecture is essential for conserved genome functions. These discoveries enabled the identification of orthologous chromosomal DNA segments among related species, a method we call 3D comparative scaffotyping. The method has application for putative chromosome assignment of chromosome-scale DNA sequence scaffolds produced by de novo genome sequencing. Broadly applied to biodiversity genome sequencing efforts, the approach can reduce costs associated with karyotyping and the physical mapping of DNA segments to chromosomes. High throughput chromatin conformation capture (Hi-C) of leukocyte DNA was used to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families: Felidae, Canidae, and Ursidae. Chromosome-scale scaffolds (C-scaffolds) of each species were initially used for whole-genome alignment to a reference genome within each family. This approach established putative orthologous relationships between C-scaffolds among the different species. Hi-C contact maps for all C-scaffolds were then visually compared and found to be distinct for a given reference chromosome or C-scaffold within a species and indistinguishable for orthologous C-scaffolds having a 1:1 relationship within a family. The visual patterns within families were strongly supported by eigenvectors from the Hi-C contact maps. Analysis of Hi-C contact maps and eigenvectors across the three carnivore families revealed that most cross-family orthologous subchromosomal fragments have a conserved three-dimensional (3D) chromatin structure and thus have been under strong evolutionary constraint for ∼54 My of carnivore evolution. The most pronounced differences in chromatin conformation were observed for the X chromosome and the red fox genome, whose chromosomes have undergone extensive rearrangements relative to other canids. We also demonstrate that Hi-C contact map pattern analysis can be used to accurately identify orthologous relationships between C-scaffolds and chromosomes, a method we termed “3D comparative scaffotyping.” This method provides a powerful means for estimating karyotypes in de novo sequenced species that have unknown karyotype and no physical mapping information.
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25
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Laverre A, Tannier E, Necsulea A. Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness. Genome Res 2021; 32:280-296. [PMID: 34930799 PMCID: PMC8805723 DOI: 10.1101/gr.275901.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022]
Abstract
Gene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements are rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Here, we address these questions by comparing genome-wide maps of promoter-centered chromatin contacts in mouse and human. We show that there is significant evolutionary conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter–enhancer contacts, illustrating how the structure of regulatory landscapes constrains large-scale genome evolution. We show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny, or contacts with target genes, is significantly associated with gene expression evolution.
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Affiliation(s)
- Alexandre Laverre
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive
| | - Eric Tannier
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Centre de recherche Inria de Lyon
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26
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Chiliński M, Sengupta K, Plewczynski D. From DNA human sequence to the chromatin higher order organisation and its biological meaning: Using biomolecular interaction networks to understand the influence of structural variation on spatial genome organisation and its functional effect. Semin Cell Dev Biol 2021; 121:171-185. [PMID: 34429265 DOI: 10.1016/j.semcdb.2021.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022]
Abstract
The three-dimensional structure of the human genome has been proven to have a significant functional impact on gene expression. The high-order spatial chromatin is organised first by looping mediated by multiple protein factors, and then it is further formed into larger structures of topologically associated domains (TADs) or chromatin contact domains (CCDs), followed by A/B compartments and finally the chromosomal territories (CTs). The genetic variation observed in human population influences the multi-scale structures, posing a question regarding the functional impact of structural variants reflected by the variability of the genes expression patterns. The current methods of evaluating the functional effect include eQTLs analysis which uses statistical testing of influence of variants on spatially close genes. Rarely, non-coding DNA sequence changes are evaluated by their impact on the biomolecular interaction network (BIN) reflecting the cellular interactome that can be analysed by the classical graph-theoretic algorithms. Therefore, in the second part of the review, we introduce the concept of BIN, i.e. a meta-network model of the complete molecular interactome developed by integrating various biological networks. The BIN meta-network model includes DNA-protein binding by the plethora of protein factors as well as chromatin interactions, therefore allowing connection of genomics with the downstream biomolecular processes present in a cell. As an illustration, we scrutinise the chromatin interactions mediated by the CTCF protein detected in a ChIA-PET experiment in the human lymphoblastoid cell line GM12878. In the corresponding BIN meta-network the DNA spatial proximity is represented as a graph model, combined with the Proteins-Interaction Network (PIN) of human proteome using the Gene Association Network (GAN). Furthermore, we enriched the BIN with the signalling and metabolic pathways and Gene Ontology (GO) terms to assert its functional context. Finally, we mapped the Single Nucleotide Polymorphisms (SNPs) from the GWAS studies and identified the chromatin mutational hot-spots associated with a significant enrichment of SNPs related to autoimmune diseases. Afterwards, we mapped Structural Variants (SVs) from healthy individuals of 1000 Genomes Project and identified an interesting example of the missing protein complex associated with protein Q6GYQ0 due to a deletion on chromosome 14. Such an analysis using the meta-network BIN model is therefore helpful in evaluating the influence of genetic variation on spatial organisation of the genome and its functional effect in a cell.
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Affiliation(s)
- Mateusz Chiliński
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland; Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Kaustav Sengupta
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland; Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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27
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Tena JJ, Santos-Pereira JM. Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease. Front Cell Dev Biol 2021; 9:702787. [PMID: 34295901 PMCID: PMC8290416 DOI: 10.3389/fcell.2021.702787] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 01/02/2023] Open
Abstract
Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as structural scaffolds for the establishment of regulatory landscapes (RLs). In this review, we discuss recent advances in the connection between TADs and gene regulation, their relationship with gene RLs and their dynamics during development and differentiation. Moreover, we describe how restructuring TADs may lead to pathological conditions, which explains their high evolutionary conservation, but at the same time it provides a substrate for the emergence of evolutionary innovations that lay at the origin of vertebrates and other phylogenetic clades.
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Affiliation(s)
- Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - José M. Santos-Pereira
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
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28
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Abstract
In eukaryotes, the genome is hierarchically packed inside the nucleus, which facilitates physical contact between cis-regulatory elements (CREs), such as enhancers and promoters. Accumulating evidence highlights the critical role of higher-order chromatin structure in precise regulation of spatiotemporal gene expression under diverse biological contexts including lineage commitment and cell activation by external stimulus. Genomics and imaging-based technologies, such as Hi-C and DNA fluorescence in situ hybridization (FISH), have revealed the key principles of genome folding, while newly developed tools focus on improvement in resolution, throughput and modality at single-cell and population levels, and challenge the knowledge obtained through conventional approaches. In this review, we discuss recent advances in our understanding of principles of higher-order chromosome conformation and technologies to investigate 4D chromatin interactions.
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Affiliation(s)
- Namyoung Jung
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Tae-Kyung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Yonsei University, Seoul 03722, Korea
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29
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Lee DI, Roy S. GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization. Genome Biol 2021; 22:164. [PMID: 34034791 PMCID: PMC8152090 DOI: 10.1186/s13059-021-02378-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior performance against seven TAD-calling methods and three smoothing methods. GRiNCH is applicable to multiple platforms including SPRITE and HiChIP and can predict novel boundary factors with potential roles in genome organization.
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Affiliation(s)
- Da-Inn Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, 53715, USA
| | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, 53715, USA. .,Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, 53715, USA.
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30
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Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures. Nat Commun 2021; 12:3116. [PMID: 34035253 PMCID: PMC8149829 DOI: 10.1038/s41467-021-23397-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
Changes in the epigenetic regulation of gene expression have a central role in evolution. Here, we extensively profiled a panel of human, chimpanzee, gorilla, orangutan, and macaque lymphoblastoid cell lines (LCLs), using ChIP-seq for five histone marks, ATAC-seq and RNA-seq, further complemented with whole genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS). We annotated regulatory elements (RE) and integrated chromatin contact maps to define gene regulatory architectures, creating the largest catalog of RE in primates to date. We report that epigenetic conservation and its correlation with sequence conservation in primates depends on the activity state of the regulatory element. Our gene regulatory architectures reveal the coordination of different types of components and highlight the role of promoters and intragenic enhancers (gE) in the regulation of gene expression. We observe that most regulatory changes occur in weakly active gE. Remarkably, novel human-specific gE with weak activities are enriched in human-specific nucleotide changes. These elements appear in genes with signals of positive selection and human acceleration, tissue-specific expression, and particular functional enrichments, suggesting that the regulatory evolution of these genes may have contributed to human adaptation.
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31
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Dannemann M, Gallego Romero I. Harnessing pluripotent stem cells as models to decipher human evolution. FEBS J 2021; 289:2992-3010. [PMID: 33876573 DOI: 10.1111/febs.15885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
The study of human evolution, long constrained by a lack of experimental model systems, has been transformed by the emergence of the induced pluripotent stem cell (iPSC) field. iPSCs can be readily established from noninvasive tissue sources, from both humans and other primates; they can be maintained in the laboratory indefinitely, and they can be differentiated into other tissue types. These qualities mean that iPSCs are rapidly becoming established as viable and powerful model systems with which it is possible to address questions in human evolution that were until now logistically and ethically intractable, especially in the quest to understand humans' place among the great apes, and the genetic basis of human uniqueness. In this review, we discuss the key lessons and takeaways of this nascent field; from the types of research, iPSCs make possible to lingering challenges and likely future directions. We provide a comprehensive overview of how the seemingly unlikely combination of iPSCs and explicit evolutionary frameworks is transforming what is possible in our understanding of humanity's past and present.
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Affiliation(s)
| | - Irene Gallego Romero
- Institute of Genomics, University of Tartu, Estonia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Australia.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Centre for Stem Cell Systems, The University of Melbourne, Parkville, Australia
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32
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Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution. Nat Genet 2021; 53:467-476. [PMID: 33731941 PMCID: PMC8038968 DOI: 10.1038/s41588-021-00804-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/26/2021] [Indexed: 01/06/2023]
Abstract
Gene regulatory divergence is thought to play a central role in determining human-specific traits. However, our ability to link divergent regulation to divergent phenotypes is limited. Here, we utilized human-chimpanzee hybrid induced pluripotent stem cells to study gene expression separating these species. The tetraploid hybrid cells allowed us to separate cis- from trans-regulatory effects, and to control for non-genetic confounding factors. We differentiated these cells into cranial neural crest cells (CNCCs), the primary cell type giving rise to the face. We discovered evidence of lineage-specific selection on the hedgehog signaling pathway, including a human-specific 6-fold down-regulation of EVC2 (LIMBIN), a key hedgehog gene. Inducing a similar down-regulation of EVC2 substantially reduced hedgehog signaling output. Mice and humans lacking functional EVC2 show striking phenotypic parallels to human-chimpanzee craniofacial differences, suggesting that the regulatory divergence of hedgehog signaling may have contributed to the unique craniofacial morphology of humans.
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33
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Yuan X, Scott IC, Wilson MD. Heart Enhancers: Development and Disease Control at a Distance. Front Genet 2021; 12:642975. [PMID: 33777110 PMCID: PMC7987942 DOI: 10.3389/fgene.2021.642975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bound by lineage-determining transcription factors and signaling effectors, enhancers play essential roles in controlling spatiotemporal gene expression profiles during development, homeostasis and disease. Recent synergistic advances in functional genomic technologies, combined with the developmental biology toolbox, have resulted in unprecedented genome-wide annotation of heart enhancers and their target genes. Starting with early studies of vertebrate heart enhancers and ending with state-of-the-art genome-wide enhancer discovery and testing, we will review how studying heart enhancers in metazoan species has helped inform our understanding of cardiac development and disease.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian C. Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D. Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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34
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Zhang L, Zhao J, Bi H, Yang X, Zhang Z, Su Y, Li Z, Zhang L, Sanderson BJ, Liu J, Ma T. Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication. HORTICULTURE RESEARCH 2021; 8:62. [PMID: 33750794 PMCID: PMC7943600 DOI: 10.1038/s41438-021-00494-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/07/2020] [Accepted: 01/03/2021] [Indexed: 05/20/2023]
Abstract
The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.
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Affiliation(s)
- Le Zhang
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 310024, Hangzhou, China.
| | - Jingtian Zhao
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Hao Bi
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Xiangyu Yang
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Zhiyang Zhang
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Yutao Su
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Zhenghao Li
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Lei Zhang
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Jianquan Liu
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, 730000, Lanzhou, China
| | - Tao Ma
- College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065, Chengdu, China.
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35
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Mittleman BE, Pott S, Warland S, Barr K, Cuevas C, Gilad Y. Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees. eLife 2021; 10:e62548. [PMID: 33595436 PMCID: PMC7954529 DOI: 10.7554/elife.62548] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
While comparative functional genomic studies have shown that inter-species differences in gene expression can be explained by corresponding inter-species differences in genetic and epigenetic regulatory mechanisms, co-transcriptional mechanisms, such as alternative polyadenylation (APA), have received little attention. We characterized APA in lymphoblastoid cell lines from six humans and six chimpanzees by identifying and estimating the usage for 44,432 polyadenylation sites (PAS) in 9518 genes. Although APA is largely conserved, 1705 genes showed significantly different PAS usage (FDR 0.05) between species. Genes with divergent APA also tend to be differentially expressed, are enriched among genes showing differences in protein translation, and can explain a subset of observed inter-species protein expression differences that do not differ at the transcript level. Finally, we found that genes with a dominant PAS, which is used more often than other PAS, are particularly enriched for differentially expressed genes.
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Affiliation(s)
- Briana E Mittleman
- Genetics, Genomics and Systems Biology, University of ChicagoChicagoUnited States
| | - Sebastian Pott
- Department of Human Genetics, University of ChicagoChicagoUnited States
| | - Shane Warland
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
| | - Kenneth Barr
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
| | - Claudia Cuevas
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
| | - Yoav Gilad
- Department of Human Genetics, University of ChicagoChicagoUnited States
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
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36
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Liao Y, Zhang X, Chakraborty M, Emerson JJ. Topologically associating domains and their role in the evolution of genome structure and function in Drosophila. Genome Res 2021; 31:397-410. [PMID: 33563719 PMCID: PMC7919452 DOI: 10.1101/gr.266130.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022]
Abstract
Topologically associating domains (TADs) were recently identified as fundamental units of three-dimensional eukaryotic genomic organization, although our knowledge of the influence of TADs on genome evolution remains preliminary. To study the molecular evolution of TADs in Drosophila species, we constructed a new reference-grade genome assembly and accompanying high-resolution TAD map for D. pseudoobscura Comparison of D. pseudoobscura and D. melanogaster, which are separated by ∼49 million years of divergence, showed that ∼30%-40% of their genomes retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower expression divergence than those located in nonconserved TADs. Furthermore, we found that a substantial proportion of long genes (>50 kbp) in D. melanogaster (42%) and D. pseudoobscura (26%) constitute their own TADs, implying transcript structure may be one of the deterministic factors for TAD formation. By using structural variants (SVs) identified from 14 D. melanogaster strains, its three closest sibling species from the D. simulans species complex, and two obscura clade species, we uncovered evidence of selection acting on SVs at TAD boundaries, but with the nature of selection differing between SV types. Deletions are depleted at TAD boundaries in both divergent and polymorphic SVs, suggesting purifying selection, whereas divergent tandem duplications are enriched at TAD boundaries relative to polymorphism, suggesting they are adaptive. Our findings highlight how important TADs are in shaping the acquisition and retention of structural mutations that fundamentally alter genome organization.
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Affiliation(s)
- Yi Liao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - Xinwen Zhang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA.,Center for Complex Biological Systems, University of California, Irvine, California 92697, USA
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Zhuo X, Du AY, Pehrsson EC, Li D, Wang T. Epigenomic differences in the human and chimpanzee genomes are associated with structural variation. Genome Res 2021; 31:279-290. [PMID: 33303495 PMCID: PMC7849402 DOI: 10.1101/gr.263491.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022]
Abstract
Structural variation (SV), including insertions and deletions (indels), is a primary mechanism of genome evolution. However, the mechanism by which SV contributes to epigenome evolution is poorly understood. In this study, we characterized the association between lineage-specific indels and epigenome differences between human and chimpanzee to investigate how SVs might have shaped the epigenetic landscape. By intersecting medium-to-large human-chimpanzee indels (20 bp-50 kb) with putative promoters and enhancers in cranial neural crest cells (CNCCs) and repressed regions in induced pluripotent cells (iPSCs), we found that 12% of indels overlap putative regulatory and repressed regions (RRRs), and 15% of these indels are associated with lineage-biased RRRs. Indel-associated putative enhancer and repressive regions are approximately 1.3 times and approximately three times as likely to be lineage-biased, respectively, as those not associated with indels. We found a twofold enrichment of medium-sized indels (20-50 bp) in CpG island (CGI)-containing promoters than expected by chance. Lastly, from human-specific transposable element insertions, we identified putative regulatory elements, including NR2F1-bound putative CNCC enhancers derived from SVAs and putative iPSC promoters derived from LTR5s. Our results show that different types of indels are associated with specific epigenomic diversity between human and chimpanzee.
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Affiliation(s)
- Xiaoyu Zhuo
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Alan Y Du
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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38
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Ali S, Arif I, Iqbal A, Hussain I, Abrar M, Khan MR, Shubin N, Abbasi AA. Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Dev Dyn 2021; 250:669-683. [PMID: 33381902 PMCID: PMC9292287 DOI: 10.1002/dvdy.291] [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: 04/21/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/03/2022] Open
Abstract
Background The zinc finger‐containing transcription factor Gli2, is a key mediator of Hedgehog (Hh) signaling and participates in embryonic patterning of various organs including the central nervous system (CNS) and limbs. Abnormal expression of Gli2 can impede the transcription of Hh target genes through disruption of proper balance between Gli2 and Gli3 functions. Therefore, delineation of enhancers that are required for complementary roles of Glis would allow the interrogation of those pathogenic variants that cause gene dysregulation, and a corresponding abnormal phenotype. Previously, we reported tissue‐specific enhancers for Gli family including Gli2 through direct tetrapod‐teleost comparisons. Results Here, we employed the sequence alignments of slowly evolving spotted gar and elephant shark and have identified six novel conserved noncoding elements in human GLI2 containing locus. Zebrafish‐based transgenic assays revealed that combined action of these autonomous CNEs reflects many aspects of Gli2 specific endogenous transcriptional activity, including CNS and pectoral fins. Conclusion Taken together with our previous findings, this study suggests that Hh‐signaling controlled deployment of Gli2 activity in embryonic patterning arose in the common ancestor of gnathostomes. These GLI2 specific cis‐regulatory modules will help to identify DNA variants that probably reside outside of coding intervals and are associated with congenital anomalies. We performed a phylogenetic footprint analyses of human GLI2 containing locus by incorporating relatively slowly evolving gar and elephant shark genomes and have identified multiple novel conserved non‐coding elements (CNEs) that were not predicted by direct human‐teleostcomparisons. Comparative analyses suggest that majority of the GLI2 associated CNEs identified in the present data and reported previously arose in the common ancestor of gnathostomes but lost in teleosts, presumably because of fast teleost sequence evolution. Functional testing of GLI2 associated CNEs by employing zebrafish based transgenic reporter assays revealed their tissue specific cis‐regulatory potential that corresponds with the results based on whole‐mount in situ hybridization analysis of gli2 mRNA in zebrafish. The delineated set of GLI2 associated enhancers can be further interrogated to determine their role in canonical Hh signaling, gene dysregulation, and a corresponding congenital anomaly.
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Affiliation(s)
- Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irum Arif
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Ayesha Iqbal
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Islamabad, Pakistan
| | - Neil Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
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39
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Torosin NS, Anand A, Golla TR, Cao W, Ellison CE. 3D genome evolution and reorganization in the Drosophila melanogaster species group. PLoS Genet 2020; 16:e1009229. [PMID: 33284803 PMCID: PMC7746282 DOI: 10.1371/journal.pgen.1009229] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 12/17/2020] [Accepted: 10/27/2020] [Indexed: 01/17/2023] Open
Abstract
Topologically associating domains, or TADs, are functional units that organize chromosomes into 3D structures of interacting chromatin. TADs play an important role in regulating gene expression by constraining enhancer-promoter contacts and there is evidence that deletion of TAD boundaries leads to aberrant expression of neighboring genes. While the mechanisms of TAD formation have been well-studied, current knowledge on the patterns of TAD evolution across species is limited. Due to the integral role TADs play in gene regulation, their structure and organization is expected to be conserved during evolution. However, more recent research suggests that TAD structures diverge relatively rapidly. We use Hi-C chromosome conformation capture to measure evolutionary conservation of whole TADs and TAD boundary elements between D. melanogaster and D. triauraria, two early-branching species from the melanogaster species group which diverged ∼15 million years ago. We find that the majority of TADs have been reorganized since the common ancestor of D. melanogaster and D. triauraria, via a combination of chromosomal rearrangements and gain/loss of TAD boundaries. TAD reorganization between these two species is associated with a localized effect on gene expression, near the site of disruption. By separating TADs into subtypes based on their chromatin state, we find that different subtypes are evolving under different evolutionary forces. TADs enriched for broadly expressed, transcriptionally active genes are evolving rapidly, potentially due to positive selection, whereas TADs enriched for developmentally-regulated genes remain conserved, presumably due to their importance in restricting gene-regulatory element interactions. These results provide novel insight into the evolutionary dynamics of TADs and help to reconcile contradictory reports related to the evolutionary conservation of TADs and whether changes in TAD structure affect gene expression. Chromosomes are organized inside the three-dimensional nucleus in a hierarchical fashion, from the wrapping of DNA around nucleosomes to the presence of compartments of active and inactive chromatin. Here, we focus on domains of interacting chromatin known as topologically associating domains, or TADs. TADs are dozens to hundreds of kilobases in size and tend to contain genes with similar epigenetic states. While much research has been done on the mechanisms of TAD formation, less is known about the role of TADs in genome evolution. The research that does exist is contradictory, with some studies claiming that TADs are highly conserved and others reporting that TADs diverge rapidly. We compared the TAD locations between two Drosophila species and found that the majority have been reorganized. We also identified TAD subtypes that differ in terms of their evolutionary conservation: TADs that contain developmental genes are less likely to be reorganized while TADs that contain broadly expressed genes evolve rapidly. We found that TAD reorganization has an effect on gene expression, but only for genes located near the site of disruption. These results provide new insight into the evolution of 3D genome organization and help to reconcile previous contradictions in the literature.
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Affiliation(s)
- Nicole S. Torosin
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States
| | - Aparna Anand
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States
| | - Tirupathi Rao Golla
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States
| | - Christopher E. Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States
- * E-mail:
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40
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Eres IE, Gilad Y. A TAD Skeptic: Is 3D Genome Topology Conserved? Trends Genet 2020; 37:216-223. [PMID: 33203573 DOI: 10.1016/j.tig.2020.10.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/17/2020] [Accepted: 10/20/2020] [Indexed: 01/08/2023]
Abstract
The notion that topologically associating domains (TADs) are highly conserved across species is prevalent in the field of 3D genomics. However, what exactly is meant by 'highly conserved' and what are the actual comparative data that support this notion? To address these questions, we performed a historical review of the relevant literature and retraced numerous citation chains to reveal the primary data that were used as the basis for the widely accepted conclusion that TADs are highly conserved across evolution. A thorough review of the available evidence suggests the answer may be more complex than what is commonly presented.
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Affiliation(s)
- Ittai E Eres
- Department of Human Genetics, University of Chicago, Cummings Life Science Center, 928 E. 58th St., Chicago, IL 60637, USA
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Cummings Life Science Center, 928 E. 58th St., Chicago, IL 60637, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., N417, MC6091, Chicago, IL 60637, USA.
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41
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Galan S, Machnik N, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nat Genet 2020; 52:1247-1255. [PMID: 33077914 PMCID: PMC7610641 DOI: 10.1038/s41588-020-00712-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.
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Affiliation(s)
- Silvia Galan
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- National Centre for Genomic Analysis, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nick Machnik
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Kai Kruse
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Marc A Marti-Renom
- National Centre for Genomic Analysis, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Pompeu Fabra University, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.
- Medical Research Council London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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Abstract
The male-specific Y chromosome harbors genes important for sperm production. Because Y is repetitive, its DNA sequence was deciphered for only a few species, and its evolution remains elusive. Here we compared the Y chromosomes of great apes (human, chimpanzee, bonobo, gorilla, and orangutan) and found that many of their repetitive sequences and multicopy genes were likely already present in their common ancestor. Y repeats had increased intrachromosomal contacts, which might facilitate preservation of genes and gene regulatory elements. Chimpanzee and bonobo, experiencing high sperm competition, underwent many DNA changes and gene losses on the Y. Our research is significant for understanding the role of the Y chromosome in reproduction of nonhuman great apes, all of which are endangered. The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee share a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys from short and long sequencing reads and aligned them with the publicly available human, chimpanzee, and gorilla Y assemblies. Analyzing this dataset, we found that the genus Pan, which includes chimpanzee and bonobo, experienced accelerated substitution rates. Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan. Furthermore, we inferred that the great ape common ancestor already possessed multicopy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Our results highlight the dynamic mode of Y chromosome evolution and open avenues for studies of male-specific dispersal in endangered great ape species.
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43
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Housman G, Gilad Y. Prime time for primate functional genomics. Curr Opin Genet Dev 2020; 62:1-7. [PMID: 32544775 DOI: 10.1016/j.gde.2020.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Functional genomics research is continually improving our understanding of genotype-phenotype relationships in humans, and comparative genomics perspectives can provide additional insight into the evolutionary histories of such relationships. To specifically identify conservation or species-specific divergence in humans, we must look to our closest extant evolutionary relatives. Primate functional genomics research has been steadily advancing and expanding, in spite of several limitations and challenges that this field faces. New technologies and cheaper sequencing provide a unique opportunity to enhance and expand primate comparative studies, and we outline possible paths going forward. The potential human-specific insights that can be gained from primate functional genomics research are substantial, and we propose that now is a prime time to expand such endeavors.
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Affiliation(s)
- Genevieve Housman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., N417, MC6091, Chicago, IL 60637 USA.
| | - Yoav Gilad
- Section of Genetic Medicine, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., N417, MC6091, Chicago, IL 60637 USA; Department of Human Genetics, University of Chicago, Cummings Life Science Center, 928 E. 58th St., Chicago, IL 60637 USA
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44
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Branching out: what omics can tell us about primate evolution. Curr Opin Genet Dev 2020; 62:65-71. [DOI: 10.1016/j.gde.2020.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/25/2022]
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45
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Diehl AG, Ouyang N, Boyle AP. Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. Nat Commun 2020; 11:1796. [PMID: 32286261 PMCID: PMC7156512 DOI: 10.1038/s41467-020-15520-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/14/2020] [Indexed: 01/12/2023] Open
Abstract
Chromatin looping is important for gene regulation, and studies of 3D chromatin structure across species and cell types have improved our understanding of the principles governing chromatin looping. However, 3D genome evolution and its relationship with natural selection remains largely unexplored. In mammals, the CTCF protein defines the boundaries of most chromatin loops, and variations in CTCF occupancy are associated with looping divergence. While many CTCF binding sites fall within transposable elements (TEs), their contribution to 3D chromatin structural evolution is unknown. Here we report the relative contributions of TE-driven CTCF binding site expansions to conserved and divergent chromatin looping in human and mouse. We demonstrate that TE-derived CTCF binding divergence may explain a large fraction of variable loops. These variable loops contribute significantly to corresponding gene expression variability across cells and species, possibly by refining sub-TAD-scale loop contacts responsible for cell-type-specific enhancer-promoter interactions.
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Affiliation(s)
- Adam G Diehl
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Ningxin Ouyang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Alan P Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
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46
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Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing. Genes (Basel) 2020; 11:genes11030276. [PMID: 32143403 PMCID: PMC7140787 DOI: 10.3390/genes11030276] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/29/2020] [Accepted: 02/29/2020] [Indexed: 12/19/2022] Open
Abstract
Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits. Structural variants (SVs), including deletions and inversions, comprise a larger proportion of genetic differences between and within species, making them an important yet understudied source of trait divergence. Here, we used a combination of long-read and -range sequencing approaches to characterize the structural variant landscape of two additional Pan troglodytes verus individuals, one of whom carries 13% admixture from Pan troglodytes troglodytes. We performed optical mapping of both individuals followed by nanopore sequencing of one individual. Filtering for larger variants (>10 kbp) and combined with genotyping of SVs using short-read data from the Great Ape Genome Project, we identified 425 deletions and 59 inversions, of which 88 and 36, respectively, were novel. Compared with gene expression in humans, we found a significant enrichment of chimpanzee genes with differential expression in lymphoblastoid cell lines and induced pluripotent stem cells, both within deletions and near inversion breakpoints. We examined chromatin-conformation maps from human and chimpanzee using these same cell types and observed alterations in genomic interactions at SV breakpoints. Finally, we focused on 56 genes impacted by SVs in >90% of chimpanzees and absent in humans and gorillas, which may contribute to chimpanzee-specific features. Sequencing a greater set of individuals from diverse subspecies will be critical to establish the complete landscape of genetic variation in chimpanzees.
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47
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Sundaram V, Wysocka J. Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190347. [PMID: 32075564 PMCID: PMC7061989 DOI: 10.1098/rstb.2019.0347] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic gene regulation is mediated by cis-regulatory elements, which are embedded within the vast non-coding genomic space and recognized by the transcription factors in a sequence- and context-dependent manner. A large proportion of eukaryotic genomes, including at least half of the human genome, are composed of transposable elements (TEs), which in their ancestral form carried their own cis-regulatory sequences able to exploit the host trans environment to promote TE transcription and facilitate transposition. Although not all present-day TE copies have retained this regulatory function, the preexisting regulatory potential of TEs can provide a rich source of cis-regulatory innovation for the host. Here, we review recent evidence documenting diverse contributions of TE sequences to gene regulation by functioning as enhancers, promoters, silencers and boundary elements. We discuss how TE-derived enhancer sequences can rapidly facilitate changes in existing gene regulatory networks and mediate species- and cell-type-specific regulatory innovations, and we postulate a unique contribution of TEs to species-specific gene expression divergence in pluripotency and early embryogenesis. With advances in genome-wide technologies and analyses, systematic investigation of TEs' cis-regulatory potential is now possible and our understanding of the biological impact of genomic TEs is increasing. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Vasavi Sundaram
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, USA
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Hernández-Lemus E, Reyes-Gopar H, Espinal-Enríquez J, Ochoa S. The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. Genes (Basel) 2019; 10:E865. [PMID: 31671657 PMCID: PMC6896122 DOI: 10.3390/genes10110865] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex disease at many different levels. The molecular phenomenology of cancer is also quite rich. The mutational and genomic origins of cancer and their downstream effects on processes such as the reprogramming of the gene regulatory control and the molecular pathways depending on such control have been recognized as central to the characterization of the disease. More important though is the understanding of their causes, prognosis, and therapeutics. There is a multitude of factors associated with anomalous control of gene expression in cancer. Many of these factors are now amenable to be studied comprehensively by means of experiments based on diverse omic technologies. However, characterizing each dimension of the phenomenon individually has proven to fall short in presenting a clear picture of expression regulation as a whole. In this review article, we discuss some of the more relevant factors affecting gene expression control both, under normal conditions and in tumor settings. We describe the different omic approaches that we can use as well as the computational genomic analysis needed to track down these factors. Then we present theoretical and computational frameworks developed to integrate the amount of diverse information provided by such single-omic analyses. We contextualize this within a systems biology-based multi-omic regulation setting, aimed at better understanding the complex interplay of gene expression deregulation in cancer.
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Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Helena Reyes-Gopar
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
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