1
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Hung TC, Kingsley DM, Boettiger AN. Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. Nat Genet 2024; 56:306-314. [PMID: 38238628 DOI: 10.1038/s41588-023-01641-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/06/2023] [Indexed: 02/15/2024]
Abstract
Although promoters and their enhancers are frequently contained within a topologically associating domain (TAD), some developmentally important genes have their promoter and enhancers within different TADs. Hypotheses about molecular mechanisms enabling cross-TAD interactions remain to be assessed. To test these hypotheses, we used optical reconstruction of chromatin architecture to characterize the conformations of the Pitx1 locus on single chromosomes in developing mouse limbs. Our data support a model in which neighboring boundaries are stacked as a result of loop extrusion, bringing boundary-proximal cis-elements into contact. This stacking interaction also contributes to the appearance of architectural stripes in the population average maps. Through molecular dynamics simulations, we found that increasing boundary strengths facilitates the formation of the stacked boundary conformation, counter-intuitively facilitating border bypass. This work provides a revised view of the TAD borders' function, both facilitating and preventing cis-regulatory interactions, and introduces a framework to distinguish border-crossing from border-respecting enhancer-promoter pairs.
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Affiliation(s)
- Tzu-Chiao Hung
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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2
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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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3
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Rogers TF, Simakov O. Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians. Brief Funct Genomics 2023; 22:533-542. [PMID: 37815133 PMCID: PMC10658181 DOI: 10.1093/bfgp/elad043] [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: 04/29/2023] [Revised: 08/17/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023] Open
Abstract
Information on how 3D genome topology emerged in animal evolution, how stable it is during development, its role in the evolution of phenotypic novelties and how exactly it affects gene expression is highly debated. So far, data to address these questions are lacking with the exception of a few key model species. Several gene regulatory mechanisms have been proposed, including scenarios where genome topology has little to no impact on gene expression, and vice versa. The ancient and diverse clade of spiralians may provide a crucial testing ground for such mechanisms. Sprialians have followed distinct evolutionary trajectories, with some clades experiencing genome expansions and/or large-scale genome rearrangements, and others undergoing genome contraction, substantially impacting their size and organisation. These changes have been associated with many phenotypic innovations in this clade. In this review, we describe how emerging genome topology data, along with functional tools, allow for testing these scenarios and discuss their predicted outcomes.
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Affiliation(s)
- Thea F Rogers
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
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4
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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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5
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Zhu M, Wang Y, Guan L, Lu C, Sun R, Chen Y, Shi J, Zhu Y, Wang D. A novel chromosome 2q24.3-q32.1 microdeletion in a fetus with multiple malformations. J Clin Lab Anal 2022; 36:e24602. [PMID: 35819063 PMCID: PMC9396185 DOI: 10.1002/jcla.24602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Terminal or interstitial deletion of chromosome 2q is rarely reported but clinically significant, which can result in developmental malformations and psychomotor retardation in humans. In the present study, we analyzed this deletion to comprehensively clarify the relationship between phenotype and microdeletion region. METHODS We collected clinical records of the fetus and summarized patient symptoms. Subsequently, genomic DNA was extracted from fetal tissue or peripheral blood collected from parents. In addition, whole-exome sequencing (WES) and copy number variation sequencing (CNV-seq) were performed. RESULTS The fetus presented a previously unreported interstitial deletion of 2q24.3-q32.1. WES and CNV-seq revealed a de novo 18.46 Mb deletion at 2q24.3-q32.1, a region involving 94 protein-coding genes, including HOXD13, MAP3K20, DLX1, DLX2, SCN2A, and SCN1A. The fetus had upper and lower limb malformations, including camptodactyly and syndactyly, along with congenital cardiac defects. CONCLUSION Herein, we report a fetus with a novel microdeletion of chromosome 2q24.3-q32.1, likely a heterozygous pathogenic variant. Haploinsufficiency of HOXD13 might be related to limb deformity in the fetus.
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Affiliation(s)
- Mianmian Zhu
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yihong Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lijie Guan
- Department of Ultrasound imaging, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chaosheng Lu
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rongyue Sun
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuan Chen
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jiamin Shi
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanying Zhu
- Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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6
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Razin SV, Zhegalova IV, Kantidze OL. Domain Model of Eukaryotic Genome Organization: From DNA Loops Fixed on the Nuclear Matrix to TADs. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:667-680. [PMID: 36154886 DOI: 10.1134/s0006297922070082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 06/16/2023]
Abstract
The article reviews the development of ideas on the domain organization of eukaryotic genome, with special attention on the studies of DNA loops anchored to the nuclear matrix and their role in the emergence of the modern model of eukaryotic genome spatial organization. Critical analysis of results demonstrating that topologically associated chromatin domains are structural-functional blocks of the genome supports the notion that these blocks are fundamentally different from domains whose existence was proposed by the domain hypothesis of eukaryotic genome organization formulated in the 1980s. Based on the discussed evidence, it is concluded that the model postulating that eukaryotic genome is built from uniformly organized structural-functional blocks has proven to be untenable.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Zhegalova
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Kharkevich Institute for Information Transmission Problems, Moscow, 127051, Russia
| | - Omar L Kantidze
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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7
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Context-dependent enhancer function revealed by targeted inter-TAD relocation. Nat Commun 2022; 13:3488. [PMID: 35715427 PMCID: PMC9205857 DOI: 10.1038/s41467-022-31241-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/09/2022] [Indexed: 11/08/2022] Open
Abstract
The expression of some genes depends on large, adjacent regions of the genome that contain multiple enhancers. These regulatory landscapes frequently align with Topologically Associating Domains (TADs), where they integrate the function of multiple similar enhancers to produce a global, TAD-specific regulation. We asked if an individual enhancer could overcome the influence of one of these landscapes, to drive gene transcription. To test this, we transferred an enhancer from its native location, into a nearby TAD with a related yet different functional specificity. We used the biphasic regulation of Hoxd genes during limb development as a paradigm. These genes are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced when the neighboring TAD activates its enhancers in distal limb cells. We transferred a distal limb enhancer into the proximal limb TAD and found that its new context suppresses its normal distal specificity, even though it is bound by HOX13 transcription factors, which are responsible for the distal activity. This activity can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the host chromatin context, which can exert a dominant control over its activity. Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new neighboring enhancers located in the recipient TAD.
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8
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Sood V, Misteli T. The stochastic nature of genome organization and function. Curr Opin Genet Dev 2022; 72:45-52. [PMID: 34808408 PMCID: PMC9014486 DOI: 10.1016/j.gde.2021.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/11/2021] [Accepted: 10/29/2021] [Indexed: 02/03/2023]
Abstract
Genomes have complex three-dimensional structures. High-resolution population-based biochemical studies over the last decade have painted a mostly static picture of the genome characterized by universal organizational features, such as chromatin domains and compartments. Yet, when analyzed at the single cell level, these architectural elements are highly variable. The heterogeneity in genome organization is in line with the inherent stochasticity of transcription that shows high variation between individual cells. We highlight recent findings on single-cell variability in genome organization and describe a framework for how the stochastic nature of chromatin organization may relate to transcription dynamics.
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Affiliation(s)
- Varun Sood
- National Cancer Institute, NIH, Bethesda, MD 20892, United States.
| | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD 20892, United States.
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9
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Li J, Glover JD, Zhang H, Peng M, Tan J, Mallick CB, Hou D, Yang Y, Wu S, Liu Y, Peng Q, Zheng SC, Crosse EI, Medvinsky A, Anderson RA, Brown H, Yuan Z, Zhou S, Xu Y, Kemp JP, Ho YYW, Loesch DZ, Wang L, Li Y, Tang S, Wu X, Walters RG, Lin K, Meng R, Lv J, Chernus JM, Neiswanger K, Feingold E, Evans DM, Medland SE, Martin NG, Weinberg SM, Marazita ML, Chen G, Chen Z, Zhou Y, Cheeseman M, Wang L, Jin L, Headon DJ, Wang S. Limb development genes underlie variation in human fingerprint patterns. Cell 2022; 185:95-112.e18. [PMID: 34995520 PMCID: PMC8740935 DOI: 10.1016/j.cell.2021.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022]
Abstract
Fingerprints are of long-standing practical and cultural interest, but little is known about the mechanisms that underlie their variation. Using genome-wide scans in Han Chinese cohorts, we identified 18 loci associated with fingerprint type across the digits, including a genetic basis for the long-recognized “pattern-block” correlations among the middle three digits. In particular, we identified a variant near EVI1 that alters regulatory activity and established a role for EVI1 in dermatoglyph patterning in mice. Dynamic EVI1 expression during human development supports its role in shaping the limbs and digits, rather than influencing skin patterning directly. Trans-ethnic meta-analysis identified 43 fingerprint-associated loci, with nearby genes being strongly enriched for general limb development pathways. We also found that fingerprint patterns were genetically correlated with hand proportions. Taken together, these findings support the key role of limb development genes in influencing the outcome of fingerprint patterning. GWAS identifies variants associated with fingerprint type across all digits Fingerprint-associated genes are strongly enriched for limb development functions Evi1 alters dermatoglyphs in mice by modulating limb rather than skin development Fingerprint patterns are genetically correlated with hand and finger proportions
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Affiliation(s)
- Jinxi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - James D Glover
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Haiguo Zhang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Meifang Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Chandana Basu Mallick
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK; Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Dan Hou
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Sijie Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yu Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Edie I Crosse
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu 225326, PRC
| | - Shen Zhou
- Shanghai Foreign Language School, Shanghai 200083, PRC
| | - Yanqing Xu
- Forest Ridge School of the Sacred Heart, Bellevue, WA 98006, USA
| | - John P Kemp
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia
| | - Yvonne Y W Ho
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | - Danuta Z Loesch
- Psychology Department, La Trobe University, Melbourne, VIC, Australia
| | | | | | | | - Xiaoli Wu
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kuang Lin
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ruogu Meng
- Center for Data Science in Health and Medicine, Peking University, Beijing 100191, PRC
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, PRC
| | - Jonathan M Chernus
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Katherine Neiswanger
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David M Evans
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | | | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mary L Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Clinical and Translational Science, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Gang Chen
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Yong Zhou
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PRC
| | - Michael Cheeseman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Lan Wang
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai 200438, PRC.
| | - Denis J Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, PRC.
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10
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Freire-Pritchett P, Ray-Jones H, Della Rosa M, Eijsbouts CQ, Orchard WR, Wingett SW, Wallace C, Cairns J, Spivakov M, Malysheva V. Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools. Nat Protoc 2021; 16:4144-4176. [PMID: 34373652 PMCID: PMC7612634 DOI: 10.1038/s41596-021-00567-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 04/28/2021] [Indexed: 11/10/2022]
Abstract
Capture Hi-C is widely used to obtain high-resolution profiles of chromosomal interactions involving, at least on one end, regions of interest such as gene promoters. Signal detection in Capture Hi-C data is challenging and cannot be adequately accomplished with tools developed for other chromosome conformation capture methods, including standard Hi-C. Capture Hi-C Analysis of Genomic Organization (CHiCAGO) is a computational pipeline developed specifically for Capture Hi-C analysis. It implements a statistical model accounting for biological and technical background components, as well as bespoke normalization and multiple testing procedures for this data type. Here we provide a step-by-step guide to the CHiCAGO workflow that is aimed at users with basic experience of the command line and R. We also describe more advanced strategies for tuning the key parameters for custom experiments and provide guidance on data preprocessing and downstream analysis using companion tools. In a typical experiment, CHiCAGO takes ~2-3 h to run, although pre- and postprocessing steps may take much longer.
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Affiliation(s)
| | - Helen Ray-Jones
- Functional Gene Control Group, Epigenetics Section, MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Monica Della Rosa
- Functional Gene Control Group, Epigenetics Section, MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Chris Q Eijsbouts
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Steven W Wingett
- Bioinformatics, The Babraham Institute, Cambridge, UK.,Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Chris Wallace
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.,MRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge, UK
| | | | - Mikhail Spivakov
- Functional Gene Control Group, Epigenetics Section, MRC London Institute of Medical Sciences, London, UK. .,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
| | - Valeriya Malysheva
- Functional Gene Control Group, Epigenetics Section, MRC London Institute of Medical Sciences, London, UK. .,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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11
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Sears KE, Gros J, Davey M. Limb development, evolution, and regeneration & repair: Part 1. Dev Dyn 2021; 250:1218-1219. [PMID: 34402127 DOI: 10.1002/dvdy.411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Karen E Sears
- Departments of Ecology and Evolutionary Biology and Molecular, Cell, and Developmental Biology, UCLA, California, Los Angeles, USA
| | - Jerome Gros
- Department of Developmental and Stem Biology, Institute Pasteur, Paris, France
| | - Megan Davey
- Functional Genetics and Development, The Roslin Institute, The University of Edinburgh, Midlothian, Scotland, UK
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12
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Bolt CC, Lopez-Delisle L, Mascrez B, Duboule D. Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations. Nat Commun 2021; 12:5013. [PMID: 34408147 PMCID: PMC8373931 DOI: 10.1038/s41467-021-25330-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Human families with chromosomal rearrangements at 2q31, where the human HOXD locus maps, display mesomelic dysplasia, a severe shortening and bending of the limb. In mice, the dominant Ulnaless inversion of the HoxD cluster produces a similar phenotype suggesting the same origin for these malformations in humans and mice. Here we engineer 1 Mb inversion including the HoxD gene cluster, which positioned Hoxd13 close to proximal limb enhancers. Using this model, we show that these enhancers contact and activate Hoxd13 in proximal cells, inducing the formation of mesomelic dysplasia. We show that a secondary Hoxd13 null mutation in-cis with the inversion completely rescues the alterations, demonstrating that ectopic HOXD13 is directly responsible for this bone anomaly. Single-cell expression analysis and evaluation of HOXD13 binding sites suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.
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MESH Headings
- Abnormalities, Multiple/embryology
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Animals
- Bone Diseases, Developmental/embryology
- Bone Diseases, Developmental/genetics
- Bone Diseases, Developmental/metabolism
- Disease Models, Animal
- Female
- Gene Deletion
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Limb Deformities, Congenital/embryology
- Limb Deformities, Congenital/genetics
- Limb Deformities, Congenital/metabolism
- Loss of Function Mutation
- Male
- Mice, Inbred C57BL
- Multigene Family
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Mice
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Affiliation(s)
- Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
- Collège de France, Paris, France.
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13
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Beccari L, Jaquier G, Lopez-Delisle L, Rodriguez-Carballo E, Mascrez B, Gitto S, Woltering J, Duboule D. Dbx2 regulation in limbs suggests interTAD sharing of enhancers. Dev Dyn 2021; 250:1280-1299. [PMID: 33497014 PMCID: PMC8451760 DOI: 10.1002/dvdy.303] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND During tetrapod limb development, the HOXA13 and HOXD13 transcription factors are critical for the emergence and organization of the autopod, the most distal aspect where digits will develop. Since previous work had suggested that the Dbx2 gene is a target of these factors, we set up to analyze in detail this potential regulatory interaction. RESULTS We show that HOX13 proteins bind to mammalian-specific sequences at the vicinity of the Dbx2 locus that have enhancer activity in developing digits. However, the functional inactivation of the DBX2 protein did not elicit any particular phenotype related to Hox genes inactivation in digits, suggesting either redundant or compensatory mechanisms. We report that the neighboring Nell2 and Ano6 genes are also expressed in distal limb buds and are in part controlled by the same Dbx2 enhancers despite being localized into two different topologically associating domains (TADs) flanking the Dbx2 locus. CONCLUSIONS We conclude that Hoxa13 and Hoxd genes cooperatively activate Dbx2 expression in developing digits through binding to mammalian specific regulatory sequences in the Dbx2 neighborhood. Furthermore, these enhancers can overcome TAD boundaries in either direction to co-regulate a set of genes located in distinct chromatin domains.
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Affiliation(s)
- Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, University Claude Bernard Lyon1, Lyon, France
| | - Gabriel Jaquier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Eddie Rodriguez-Carballo
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Joost Woltering
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,School of Life Sciences, Federal School of Technology (EPFL), Lausanne, Switzerland.,Collège de France, Paris, France
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