1
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Chen Y, Zhou T, Liao Z, Gao W, Wu J, Zhang S, Li Y, Liu H, Zhou H, Xu C, Su P. Hnrnpk is essential for embryonic limb bud development as a transcription activator and a collaborator of insulator protein Ctcf. Cell Death Differ 2023; 30:2293-2308. [PMID: 37608075 PMCID: PMC10589297 DOI: 10.1038/s41418-023-01207-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Proper development of the limb bud relies on the concordance of various signals, but its molecular mechanisms have not yet been fully illustrated. Here we report that heterogeneous nuclear ribonucleoprotein K (hnRNPK) is essential for limb bud development. Its ablation in the limb bud results in limbless forelimbs and severe deformities of the hindlimbs. In terms of mechanism, hnRNPK functions as a transcription activator for the vital genes involved in the three regulatory axes of limb bud development. Simultaneously, for the first time we elucidate that hnRNPK binds to and coordinates with the insulator protein CCCTC binding factor (CTCF) to maintain a three-dimensional chromatin architecture. Ablation of hnRNPK weakens the binding strength of CTCF to topologically associating domain (TAD) boundaries, then leading to the loose TADs, and decreased interactions between promoters and enhancers, and further decreased transcription of developmental genes. Our study establishes a fundamental and novel role of hnRNPK in regulating limb bud development.
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Affiliation(s)
- Yuyu Chen
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Taifeng Zhou
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Zhiheng Liao
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Wenjie Gao
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
| | - Jinna Wu
- Department of Breast Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Shun Zhang
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Yongyong Li
- Precision Medicine Institute, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Hengyu Liu
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Hang Zhou
- Department of Orthopaedics, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
| | - Caixia Xu
- Research Center for Translational Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
| | - Peiqiang Su
- Department of Spine Surgery, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
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2
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Afzal Z, Lange JJ, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter BD, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023; 150:dev201259. [PMID: 37102683 PMCID: PMC10233718 DOI: 10.1242/dev.201259] [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: 09/01/2022] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in the specification of axial identity. Little is known about the properties of cis-regulatory elements and underlying transcriptional mechanisms that integrate graded signaling inputs to coordinately control Hox expression. Here, we optimized a single molecule fluorescent in situ hybridization (smFISH) technique with probes spanning introns to evaluate how three shared retinoic acid response element (RARE)-dependent enhancers in the Hoxb cluster regulate patterns of nascent transcription in vivo at the level of single cells in wild-type and mutant embryos. We predominately detect nascent transcription of only a single Hoxb gene in each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets of genes. Single and/or compound RARE mutations indicate that each enhancer differentially impacts global and local patterns of nascent transcription, suggesting that selectivity and competitive interactions between these enhancers is important to robustly maintain the proper levels and patterns of nascent Hoxb transcription. This implies that rapid and dynamic regulatory interactions potentiate transcription of genes through combined inputs from these enhancers in coordinating the retinoic acid response.
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Affiliation(s)
- Zainab Afzal
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
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3
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Shaping Hox gene activity to generate morphological diversity across vertebrate phylogeny. Essays Biochem 2022; 66:717-726. [PMID: 35924372 DOI: 10.1042/ebc20220050] [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] [Received: 05/27/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 02/07/2023]
Abstract
The importance of Hox genes for the development and evolution of the vertebrate axial skeleton and paired appendages has been recognized for already several decades. The steady growth of genomic sequence data from an increasing number of vertebrate species, together with the improvement of methods to analyze genomic structure and interactions, as well as to control gene activity in various species has refined our understanding of Hox gene activity in development and evolution. Here, I will review recent data addressing the influence of Hox regulatory processes in the evolution of the fins and the emergence of the tetrapod limb. In addition, I will discuss the involvement of posterior Hox genes in the control of vertebrate axial extension, focusing on an apparently divergent activity that Hox13 paralog group genes have on the regulation of tail bud development in mouse and zebrafish embryos.
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4
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Transcriptional Regulation and Implications for Controlling Hox Gene Expression. J Dev Biol 2022; 10:jdb10010004. [PMID: 35076545 PMCID: PMC8788451 DOI: 10.3390/jdb10010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.
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5
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Roscito JG, Sameith K, Kirilenko BM, Hecker N, Winkler S, Dahl A, Rodrigues MT, Hiller M. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Rep 2022; 38:110280. [DOI: 10.1016/j.celrep.2021.110280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 01/02/2023] Open
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6
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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7
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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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8
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Razin SV, Ioudinkova ES, Kantidze OL, Iarovaia OV. Co-Regulated Genes and Gene Clusters. Genes (Basel) 2021; 12:907. [PMID: 34208174 PMCID: PMC8230824 DOI: 10.3390/genes12060907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/27/2022] Open
Abstract
There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.
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Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Elena S. Ioudinkova
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Omar L. Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Olga V. Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
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9
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Tissières V, Geier F, Kessler B, Wolf E, Zeller R, Lopez-Rios J. Gene Regulatory and Expression Differences between Mouse and Pig Limb Buds Provide Insights into the Evolutionary Emergence of Artiodactyl Traits. Cell Rep 2021; 31:107490. [PMID: 32268095 PMCID: PMC7166081 DOI: 10.1016/j.celrep.2020.03.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 08/19/2019] [Accepted: 03/16/2020] [Indexed: 10/28/2022] Open
Abstract
Digit loss/reductions are evolutionary adaptations in cursorial mammals such as pigs. To gain mechanistic insight into these processes, we performed a comparative molecular analysis of limb development in mouse and pig embryos, which revealed a loss of anterior-posterior polarity during distal progression of pig limb bud development. These alterations in pig limb buds are paralleled by changes in the mesenchymal response to Sonic hedgehog (SHH) signaling, which is altered upstream of the reduction and loss of Fgf8 expression in the ectoderm that overlaps the reduced and vestigial digit rudiments of the pig handplate, respectively. Furthermore, genome-wide open chromatin profiling using equivalent developmental stages of mouse and pig limb buds reveals the functional divergence of about one-third of the regulatory genome. This study uncovers widespread alterations in the regulatory landscapes of genes essential for limb development that likely contributed to the morphological diversion of artiodactyl limbs from the pentadactyl archetype of tetrapods.
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Affiliation(s)
- Virginie Tissières
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, 41013 Seville, Spain
| | - Florian Geier
- Bioinformatics Core Facility, Department of Biomedicine, University of Basel and University Hospital, 4053 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Barbara Kessler
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, 41013 Seville, Spain.
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10
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McKenna KZ, Wagner GP, Cooper KL. A developmental perspective of homology and evolutionary novelty. Curr Top Dev Biol 2021; 141:1-38. [PMID: 33602485 DOI: 10.1016/bs.ctdb.2020.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The development and evolution of multicellular body plans is complex. Many distinct organs and body parts must be reproduced at each generation, and those that are traceable over long time scales are considered homologous. Among the most pressing and least understood phenomena in evolutionary biology is the mode by which new homologs, or "novelties" are introduced to the body plan and whether the developmental changes associated with such evolution deserve special treatment. In this chapter, we address the concepts of homology and evolutionary novelty through the lens of development. We present a series of case studies, within insects and vertebrates, from which we propose a developmental model of multicellular organ identity. With this model in hand, we make predictions regarding the developmental evolution of body plans and highlight the need for more integrative analysis of developing systems.
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Affiliation(s)
- Kenneth Z McKenna
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.
| | - Kimberly L Cooper
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
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11
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HOX13-dependent chromatin accessibility underlies the transition towards the digit development program. Nat Commun 2020; 11:2491. [PMID: 32427842 PMCID: PMC7237422 DOI: 10.1038/s41467-020-16317-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/20/2020] [Indexed: 12/05/2022] Open
Abstract
Hox genes encode transcription factors (TFs) that establish morphological diversity in the developing embryo. The similar DNA-binding motifs of the various HOX TFs contrast with the wide-range of HOX-dependent genetic programs. The influence of the chromatin context on HOX binding specificity remains elusive. Here, we used the developing limb as a model system to compare the binding specificity of HOXA13 and HOXD13 (HOX13 hereafter), which are required for digit formation, and HOXA11, involved in forearm/leg development. We find that upon ectopic expression in distal limb buds, HOXA11 binds sites normally HOX13-specific. Importantly, these sites are loci whose chromatin accessibility relies on HOX13. Moreover, we show that chromatin accessibility specific to the distal limb requires HOX13 function. Based on these results, we propose that HOX13 TFs pioneer the distal limb-specific chromatin accessibility landscape for the proper implementation of the distal limb developmental program. Pioneer factors direct cell fate through switching inaccessible chromatin to an accessible state at specific target enhancers. Here the authors show that HOX13 transcription factors have a pioneer activity which is required for the proper implementation of the distal limb developmental program.
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12
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Amândio AR, Lopez-Delisle L, Bolt CC, Mascrez B, Duboule D. A complex regulatory landscape involved in the development of mammalian external genitals. eLife 2020; 9:e52962. [PMID: 32301703 PMCID: PMC7185996 DOI: 10.7554/elife.52962] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/17/2020] [Indexed: 02/04/2023] Open
Abstract
Developmental genes are often controlled by large regulatory landscapes matching topologically associating domains (TADs). In various contexts, the associated chromatin backbone is modified by specific enhancer-enhancer and enhancer-promoter interactions. We used a TAD flanking the mouse HoxD cluster to study how these regulatory architectures are formed and deconstructed once their function achieved. We describe this TAD as a functional unit, with several regulatory sequences acting together to elicit a transcriptional response. With one exception, deletion of these sequences didn't modify the transcriptional outcome, a result at odds with a conventional view of enhancer function. The deletion and inversion of a CTCF site located near these regulatory sequences did not affect transcription of the target gene. Slight modifications were nevertheless observed, in agreement with the loop extrusion model. We discuss these unexpected results considering both conventional and alternative explanations relying on the accumulation of poorly specific factors within the TAD backbone.
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Affiliation(s)
- Ana Rita Amândio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of GenevaGenevaSwitzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Department of Genetics and Evolution, University of GenevaGenevaSwitzerland
- Collège de FranceParisFrance
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13
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Abstract
Regulatory landscapes have been defined in vertebrates as large DNA segments containing diverse enhancer sequences that produce coherent gene transcription. These genomic platforms integrate multiple cellular signals and hence can trigger pleiotropic expression of developmental genes. Identifying and evaluating how these chromatin regions operate may be difficult as the underlying regulatory mechanisms can be as unique as the genes they control. In this brief article and accompanying poster, we discuss some of the ways in which regulatory landscapes operate, illustrating these mechanisms using genes important for vertebrate development as examples. We also highlight some of the techniques available to researchers for analysing regulatory landscapes.
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Affiliation(s)
- Christopher Chase Bolt
- Swiss Institute for Cancer Research (ISREC), School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
| | - Denis Duboule
- Swiss Institute for Cancer Research (ISREC), School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
- Collège de France, 75005 Paris, France
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14
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Le Caignec C, Pichon O, Briand A, de Courtivron B, Bonnard C, Lindenbaum P, Redon R, Schluth-Bolard C, Diguet F, Rollat-Farnier PA, Sanchez-Castro M, Vuillaume ML, Sanlaville D, Duboule D, Mégarbané A, Toutain A. Fryns type mesomelic dysplasia of the upper limbs caused by inverted duplications of the HOXD gene cluster. Eur J Hum Genet 2019; 28:324-332. [PMID: 31591517 DOI: 10.1038/s41431-019-0522-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 07/12/2019] [Accepted: 09/17/2019] [Indexed: 01/09/2023] Open
Abstract
The HoxD cluster is critical for vertebrate limb development. Enhancers located in both the telomeric and centromeric gene deserts flanking the cluster regulate the transcription of HoxD genes. In rare patients, duplications, balanced translocations or inversions misregulating HOXD genes are responsible for mesomelic dysplasia of the upper and lower limbs. By aCGH, whole-genome mate-pair sequencing, long-range PCR and fiber fluorescent in situ hybridization, we studied patients from two families displaying mesomelic dysplasia limited to the upper limbs. We identified microduplications including the HOXD cluster and showed that microduplications were in an inverted orientation and inserted between the HOXD cluster and the telomeric enhancers. Our results highlight the existence of an autosomal dominant condition consisting of isolated ulnar dysplasia caused by microduplications inserted between the HOXD cluster and the telomeric enhancers. The duplications likely disconnect the HOXD9 to HOXD11 genes from their regulatory sequences. This presumptive loss-of-function may have contributed to the phenotype. In both cases, however, these rearrangements brought HOXD13 closer to telomeric enhancers, suggesting that the alterations derive from the dominant-negative effect of this digit-specific protein when ectopically expressed during the early development of forearms, through the disruption of topologically associating domain structure at the HOXD locus.
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Affiliation(s)
- Cédric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Nantes, France. .,Universite de Nantes, Nantes, France.
| | - Olivier Pichon
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Annaig Briand
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | | | - Christian Bonnard
- Service de Chirurgie Orthopédique Pédiatrique, CHRU de Tours, Tours, France.,Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France
| | - Pierre Lindenbaum
- INSERM, UMR_S1087, l'institut du thorax, Nantes, France.,CNRS, UMR 6291, Nantes, France
| | - Richard Redon
- INSERM, UMR_S1087, l'institut du thorax, Nantes, France.,CNRS, UMR 6291, Nantes, France
| | - Caroline Schluth-Bolard
- Department of Genetics, Lyon University Hospital, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Flavie Diguet
- Department of Genetics, Lyon University Hospital, Lyon, France
| | | | | | - Marie-Laure Vuillaume
- Service de Génétique, Hôpital Bretonneau, CHU, Tours, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Damien Sanlaville
- Department of Genetics, Lyon University Hospital, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Denis Duboule
- University of Geneva and Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | | | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, CHU, Tours, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
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15
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Gentile C, Berlivet S, Mayran A, Paquette D, Guerard-Millet F, Bajon E, Dostie J, Kmita M. PRC2-Associated Chromatin Contacts in the Developing Limb Reveal a Possible Mechanism for the Atypical Role of PRC2 in HoxA Gene Expression. Dev Cell 2019; 50:184-196.e4. [DOI: 10.1016/j.devcel.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/24/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
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16
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Roscito JG, Sameith K, Parra G, Langer BE, Petzold A, Moebius C, Bickle M, Rodrigues MT, Hiller M. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nat Commun 2018; 9:4737. [PMID: 30413698 PMCID: PMC6226452 DOI: 10.1038/s41467-018-07122-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023] Open
Abstract
Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits. Cis-regulatory elements are important factors for morphological changes. Here, the authors show widespread divergence of limb and eye regulatory elements in limb loss in snakes and eye degeneration in subterranean mammals respectively.
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Affiliation(s)
- Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany.,Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - Katrin Sameith
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Genis Parra
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Bjoern E Langer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Andreas Petzold
- Center for Regenerative Therapies TU Dresden, Dresden, 01307, Germany
| | - Claudia Moebius
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | | | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany. .,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany. .,Center for Systems Biology Dresden, Dresden, 01307, Germany.
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17
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Sheth R, Barozzi I, Langlais D, Osterwalder M, Nemec S, Carlson HL, Stadler HS, Visel A, Drouin J, Kmita M. Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13. Cell Rep 2017; 17:2913-2926. [PMID: 27974206 PMCID: PMC5697718 DOI: 10.1016/j.celrep.2016.11.039] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 01/12/2023] Open
Abstract
The combinatorial expression of Hox genes along the body axes is a major determinant of cell fate and plays a pivotal role in generating the animal body plan. Loss of HOXA13 and HOXD13 transcription factors (HOX13) leads to digit agenesis in mice, but how HOX13 proteins regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here, we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13−/−; Hoxd13−/−limbs. Our results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.
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Affiliation(s)
- Rushikesh Sheth
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, QC H2W1R7, Canada.
| | - Iros Barozzi
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Langlais
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, H3G0B1 QC, Canada
| | | | - Stephen Nemec
- Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, H2W1R7 QC, Canada
| | - Hanqian L Carlson
- Department of Skeletal Biology, Shriners Hospital for Children, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - H Scott Stadler
- Department of Skeletal Biology, Shriners Hospital for Children, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95340, USA
| | - Jacques Drouin
- Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, H2W1R7 QC, Canada; Department of Medicine, Université de Montréal, Montréal, H3T1J4 QC, Canada
| | - Marie Kmita
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, QC H2W1R7, Canada; Department of Medicine, Université de Montréal, Montréal, H3T1J4 QC, Canada.
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18
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Rodríguez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev 2017; 31:2264-2281. [PMID: 29273679 PMCID: PMC5769770 DOI: 10.1101/gad.307769.117] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context.
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Affiliation(s)
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Pierre J Fabre
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Imane El-Idrissi
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Thi Hanh Nguyen Huynh
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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19
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Paço A, Freitas R. Hox D genes and the fin-to-limb
transition: Insights from fish studies. Genesis 2017; 56. [DOI: 10.1002/dvg.23069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/14/2017] [Accepted: 09/08/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Ana Paço
- IBMC - Instituto de Biologia Celular e Molecular; Porto Portugal
- I3S - Instituto de Investigação e Inovação em Saúde; Porto Portugal
- Universidade do Porto; Porto Portugal
| | - Renata Freitas
- IBMC - Instituto de Biologia Celular e Molecular; Porto Portugal
- I3S - Instituto de Investigação e Inovação em Saúde; Porto Portugal
- Universidade do Porto; Porto Portugal
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20
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Darbellay F, Duboule D. Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci. Curr Top Dev Biol 2017; 116:299-314. [PMID: 26970625 DOI: 10.1016/bs.ctdb.2015.11.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hox gene clusters of jaw vertebrates display a tight genomic organization, which has no equivalent in any other bilateria genomes sequenced thus far. It was previously argued that such a topological consolidation toward a condensed, metagenic structure was due to the accumulation of long-range regulations flanking Hox loci, a phenomenon made possible by the successive genome duplications that occurred at the root of the vertebrate lineage, similar to gene neofunctionalization but applied to a coordinated multigenic system. Here, we propose that the emergence of such large vertebrate regulatory landscapes containing a range of global enhancers was greatly facilitated by the presence of topologically associating domains (TADs). These chromatin domains, mostly constitutive, may have been used as genomic niches where novel regulations could evolve due to both the preexistence of a structural backbone poised to integrate novel regulatory inputs, and a highly adaptive transcriptional readout. We propose a scenario for the coevolution of such TADs and the emergence of pleiotropy at ancestral vertebrate Hox loci.
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Affiliation(s)
- Fabrice Darbellay
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland
| | - Denis Duboule
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland; Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
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21
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Tanaka M. Alterations in anterior-posterior patterning and its accompanying changes along the proximal-distal axis during the fin-to-limb transition. Genesis 2017; 56. [PMID: 28834131 DOI: 10.1002/dvg.23053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 11/07/2022]
Abstract
The evolution from fins to limbs was one of the most successful innovations for vertebrates, allowing them to vastly expand their behaviors and habitats. Fossil records suggest that morphological changes occurred not only along the proximal-distal axis included appearance of the autopod, but also occurred along the anterior-posterior axis included reductions in the size and number of basal bones and digits. This review focuses on recent progress in developmental and genetic studies aimed at elucidating the mechanisms underlying alteration of anterior-posterior patterning and its accompanying changes along the proximal-distal axis during the fin-to-limb transition.
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Affiliation(s)
- Mikiko Tanaka
- Department of Life Science and Technology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
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22
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Saxena A, Towers M, Cooper KL. The origins, scaling and loss of tetrapod digits. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0482. [PMID: 27994123 PMCID: PMC5182414 DOI: 10.1098/rstb.2015.0482] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/19/2022] Open
Abstract
Many of the great morphologists of the nineteenth century marvelled at similarities between the limbs of diverse species, and Charles Darwin noted these homologies as significant supporting evidence for descent with modification from a common ancestor. Sir Richard Owen also took great care to highlight each of the elements of the forelimb and hindlimb in a multitude of species with focused attention on the homology between the hoof of the horse and the middle digit of man. The ensuing decades brought about a convergence of palaeontology, experimental embryology and molecular biology to lend further support to the homologies of tetrapod limbs and their developmental origins. However, for all that we now understand about the conserved mechanisms of limb development and the development of gross morphological disturbances, little of what is presented in the experimental or medical literature reflects the remarkable diversity resulting from the 450 million year experiment of natural selection. An understanding of conserved and divergent limb morphologies in this new age of genomics and genome engineering promises to reveal more of the developmental potential residing in all limbs and to unravel the mechanisms of evolutionary variation in limb size and shape. In this review, we present the current state of our rapidly advancing understanding of the evolutionary origin of hands and feet and highlight what is known about the mechanisms that shape diverse limbs.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Aditya Saxena
- Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Matthew Towers
- Bateson Centre, Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Kimberly L. Cooper
- Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,e-mail:
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23
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Guerreiro I, Gitto S, Novoa A, Codourey J, Nguyen Huynh TH, Gonzalez F, Milinkovitch MC, Mallo M, Duboule D. Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan. eLife 2016; 5. [PMID: 27476854 PMCID: PMC4969037 DOI: 10.7554/elife.16087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/10/2016] [Indexed: 12/15/2022] Open
Abstract
Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated with changes in the function or regulation of Hox genes. Here, we use an interspecies comparative approach to investigate different regulatory aspects at the snake HoxD locus. We report that, unlike in other vertebrates, snake mesoderm-specific enhancers are mostly located within the HoxD cluster itself rather than outside. In addition, despite both the absence of limbs and an altered Hoxd gene regulation in external genitalia, the limb-associated bimodal HoxD chromatin structure is maintained at the snake locus. Finally, we show that snake and mouse orthologous enhancer sequences can display distinct expression specificities. These results show that vertebrate morphological evolution likely involved extensive reorganisation at Hox loci, yet within a generally conserved regulatory framework.
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Affiliation(s)
- Isabel Guerreiro
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Ana Novoa
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Julien Codourey
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Federico Gonzalez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Moises Mallo
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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24
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Tanaka M. Fins into limbs: Autopod acquisition and anterior elements reduction by modifying gene networks involving 5’Hox , Gli3 , and Shh. Dev Biol 2016; 413:1-7. [DOI: 10.1016/j.ydbio.2016.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 11/25/2022]
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25
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HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution. Sci Rep 2016; 6:22720. [PMID: 26940624 PMCID: PMC4778128 DOI: 10.1038/srep22720] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 02/18/2016] [Indexed: 11/24/2022] Open
Abstract
The role of Homeobox transcription factors during fin and limb development have been the focus of recent work investigating the evolutionary origin of limb-specific morphologies. Here we characterize the expression of HoxD genes, as well as the cluster-associated genes Evx2 and LNP, in the paddlefish Polyodon spathula, a basal ray-finned fish. Our results demonstrate a collinear pattern of nesting in early fin buds that includes HoxD14, a gene previously thought to be isolated from global Hox regulation. We also show that in both Polyodon and the catshark Scyliorhinus canicula (a representative chondrichthyan) late phase HoxD transcripts are present in cells of the fin-fold and co-localize with And1, a component of the dermal skeleton. These new data support an ancestral role for HoxD genes in patterning the fin-folds of jawed vertebrates, and fuel new hypotheses about the evolution of cluster regulation and the potential downstream differentiation outcomes of distinct HoxD-regulated compartments.
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26
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Acemel RD, Tena JJ, Irastorza-Azcarate I, Marlétaz F, Gómez-Marín C, de la Calle-Mustienes E, Bertrand S, Diaz SG, Aldea D, Aury JM, Mangenot S, Holland PWH, Devos DP, Maeso I, Escrivá H, Gómez-Skarmeta JL. A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation. Nat Genet 2016; 48:336-41. [PMID: 26829752 DOI: 10.1038/ng.3497] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/30/2015] [Indexed: 12/19/2022]
Abstract
The HoxA and HoxD gene clusters of jawed vertebrates are organized into bipartite three-dimensional chromatin structures that separate long-range regulatory inputs coming from the anterior and posterior Hox-neighboring regions. This architecture is instrumental in allowing vertebrate Hox genes to pattern disparate parts of the body, including limbs. Almost nothing is known about how these three-dimensional topologies originated. Here we perform extensive 4C-seq profiling of the Hox cluster in embryos of amphioxus, an invertebrate chordate. We find that, in contrast to the architecture in vertebrates, the amphioxus Hox cluster is organized into a single chromatin interaction domain that includes long-range contacts mostly from the anterior side, bringing distant cis-regulatory elements into contact with Hox genes. We infer that the vertebrate Hox bipartite regulatory system is an evolutionary novelty generated by combining ancient long-range regulatory contacts from DNA in the anterior Hox neighborhood with new regulatory inputs from the posterior side.
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Affiliation(s)
- Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Ibai Irastorza-Azcarate
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | | | - Carlos Gómez-Marín
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Elisa de la Calle-Mustienes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Stéphanie Bertrand
- Université Pierre et Marie Curie Université Paris 6, CNRS, UMR 7232, Biologie Integrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls-sur-Mer, Banyuls-sur-Mer, France
| | - Sergio G Diaz
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Daniel Aldea
- Université Pierre et Marie Curie Université Paris 6, CNRS, UMR 7232, Biologie Integrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls-sur-Mer, Banyuls-sur-Mer, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | | | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Hector Escrivá
- Université Pierre et Marie Curie Université Paris 6, CNRS, UMR 7232, Biologie Integrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls-sur-Mer, Banyuls-sur-Mer, France
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
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27
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Maeso I, Tena JJ. Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework. Semin Cell Dev Biol 2015; 57:2-10. [PMID: 26673387 DOI: 10.1016/j.semcdb.2015.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/02/2015] [Accepted: 12/05/2015] [Indexed: 12/22/2022]
Abstract
Cis-regulatory changes are arguably the primary evolutionary source of animal morphological diversity. With the recent explosion of genome-wide comparisons of the cis-regulatory content in different animal species is now possible to infer general principles underlying enhancer evolution. However, these studies have also revealed numerous discrepancies and paradoxes, suggesting that the mechanistic causes and modes of cis-regulatory evolution are still not well understood and are probably much more complex than generally appreciated. Here, we argue that the mutational mechanisms and genomic regions generating new regulatory activities must comply with the constraints imposed by the molecular properties of cis-regulatory elements (CREs) and the organizational features of long-range chromatin interactions. Accordingly, we propose a new integrative evolutionary framework for cis-regulatory evolution based on two major premises for the origin of novel enhancer activity: (i) an accessible chromatin environment and (ii) compatibility with the 3D structure and interactions of pre-existing CREs. Mechanisms and DNA sequences not fulfilling these premises, will be less likely to have a measurable impact on gene expression and as such, will have a minor contribution to the evolution of gene regulation. Finally, we discuss current comparative cis-regulatory data under the light of this new evolutionary model, and propose that the two most prominent mechanisms for the evolution of cis-regulatory changes are the overprinting of ancestral CREs and the exaptation of transposable elements.
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Affiliation(s)
- Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), Universidad Pablo de Olavide, 41013 Seville, Spain.
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), Universidad Pablo de Olavide, 41013 Seville, Spain.
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28
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Structure, function and evolution of topologically associating domains (TADs) at HOX loci. FEBS Lett 2015; 589:2869-76. [PMID: 25913784 DOI: 10.1016/j.febslet.2015.04.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 11/24/2022]
Abstract
Hox genes encode transcription factors necessary for patterning the major developing anterior to posterior embryonic axis. In addition, during vertebrate evolution, various subsets of this gene family were co-opted along with the emergence of novel body structures, such as the limbs or the external genitalia. The morphogenesis of these axial structures thus relies in part upon the precisely controlled transcription of specific Hox genes, a mechanism involving multiple long-range enhancers. Recently, it was reported that such regulatory mechanisms were largely shared between different developing tissues, though with some specificities, suggesting the recruitment of ancestral regulatory modalities from one tissue to another. The analysis of chromatin architectures at HoxD and HoxA loci revealed the existence of two flanking topologically associating domains (TADs), precisely encompassing the adjacent regulatory landscapes. Here, we discuss the function of these TADs in the control of Hox gene regulation and we speculate about their capacity to serve as structural frameworks for the emergence of novel enhancers. In this view, TADs may have been used as genomic niches to evolve pleiotropic regulations found at many developmental loci.
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29
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Abstract
There is no obvious morphological counterpart of the autopod (wrist/ankle and digits) in living fishes. Comparative molecular data may provide insight into understanding both the homology of elements and the evolutionary developmental mechanisms behind the fin to limb transition. In mouse limbs the autopod is built by a "late" phase of Hoxd and Hoxa gene expression, orchestrated by a set of enhancers located at the 5' end of each cluster. Despite a detailed mechanistic understanding of mouse limb development, interpretation of Hox expression patterns and their regulation in fish has spawned multiple hypotheses as to the origin and function of "autopod" enhancers throughout evolution. Using phylogenetic footprinting, epigenetic profiling, and transgenic reporters, we have identified and functionally characterized hoxD and hoxA enhancers in the genomes of zebrafish and the spotted gar, Lepisosteus oculatus, a fish lacking the whole genome duplication of teleosts. Gar and zebrafish "autopod" enhancers drive expression in the distal portion of developing zebrafish pectoral fins, and respond to the same functional cues as their murine orthologs. Moreover, gar enhancers drive reporter gene expression in both the wrist and digits of mouse embryos in patterns that are nearly indistinguishable from their murine counterparts. These functional genomic data support the hypothesis that the distal radials of bony fish are homologous to the wrist and/or digits of tetrapods.
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Lonfat N, Montavon T, Darbellay F, Gitto S, Duboule D. Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci. Science 2014; 346:1004-6. [DOI: 10.1126/science.1257493] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Kjosness KM, Hines JE, Lovejoy CO, Reno PL. The pisiform growth plate is lost in humans and supports a role for Hox in growth plate formation. J Anat 2014; 225:527-38. [PMID: 25279687 PMCID: PMC4292754 DOI: 10.1111/joa.12235] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2014] [Indexed: 12/29/2022] Open
Abstract
The human pisiform is a small, nodular, although functionally significant, bone of the wrist. In most other mammals, including apes and Australopithecus afarensis, pisiforms are elongate. An underappreciated fact is that the typical mammalian pisiform forms from two ossification centers. We hypothesize that: (i) the presence of a secondary ossification center in mammalian pisiforms indicates the existence of a growth plate; and (ii) human pisiform reduction results from growth plate loss. To address these hypotheses, we surveyed African ape pisiform ossification and confirmed the presence of a late-forming secondary ossification center in chimpanzees and gorillas. Identification of the initial ossification center occurs substantially earlier in apes relative to humans, raising questions concerning the homology of the human pisiform and the two mammalian ossification centers. Second, we conducted histological and immunohistochemical analyses of pisiform ossification in mice. We confirm the presence of two ossification centers separated by organized columnar and hypertrophic chondrocyte zones. Flattened chondrocytes were highly mitotic, indicating the presence of a growth plate. Hox genes have been proposed to play a fundamental role in growth plate patterning. The existence of a pisiform growth plate presents an interesting test case for the association between Hox expression and growth plate formation, and could explain the severe effects on the pisiform observed in Hoxa11 and Hoxd11 knockout mice. Consistent with this hypothesis, we show that Hoxd11 is expressed adjacent to the pisiform in late-stage embryonic mouse limbs supporting a role for Hox genes in growth plate specification. This raises questions concerning the mechanisms regulating Hox expression in the developing carpus.
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Affiliation(s)
- Kelsey M Kjosness
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
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Gredler ML, Seifert AW, Cohn MJ. Morphogenesis and Patterning of the Phallus and Cloaca in the American Alligator, Alligator mississippiensis. Sex Dev 2014; 9:53-67. [DOI: 10.1159/000364817] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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33
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Samee MAH, Sinha S. Quantitative modeling of a gene's expression from its intergenic sequence. PLoS Comput Biol 2014; 10:e1003467. [PMID: 24604095 PMCID: PMC3945089 DOI: 10.1371/journal.pcbi.1003467] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 12/18/2013] [Indexed: 11/18/2022] Open
Abstract
Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we report the first quantitative model of a gene's expression pattern as a function of its locus. We model the expression readout of a locus in two tiers: 1) combinatorial regulation by transcription factors bound to each enhancer is predicted by a thermodynamics-based model and 2) independent contributions from multiple enhancers are linearly combined to fit the gene expression pattern. The model does not require any prior knowledge about enhancers contributing toward a gene's expression. We demonstrate that the model captures the complex multi-domain expression patterns of anterior-posterior patterning genes in the early Drosophila embryo. Altogether, we model the expression patterns of 27 genes; these include several gap genes, pair-rule genes, and anterior, posterior, trunk, and terminal genes. We find that the model-selected enhancers for each gene overlap strongly with its experimentally characterized enhancers. Our findings also suggest the presence of sequence-segments in the locus that would contribute ectopic expression patterns and hence were "shut down" by the model. We applied our model to identify the transcription factors responsible for forming the stripe boundaries of the studied genes. The resulting network of regulatory interactions exhibits a high level of agreement with known regulatory influences on the target genes. Finally, we analyzed whether and why our assumption of enhancer independence was necessary for the genes we studied. We found a deterioration of expression when binding sites in one enhancer were allowed to influence the readout of another enhancer. Thus, interference between enhancer activities was a possible factor necessitating enhancer independence in our model.
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Affiliation(s)
- Md. Abul Hassan Samee
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (MAHS); (SS)
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (MAHS); (SS)
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Freitas R, Gómez-Skarmeta JL, Rodrigues PN. New frontiers in the evolution of fin development. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:540-52. [DOI: 10.1002/jez.b.22563] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 01/10/2014] [Accepted: 01/19/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Renata Freitas
- IBMC-Instituto de Biologia Celular e Molecular; Porto Portugal
| | | | - Pedro Nuno Rodrigues
- IBMC-Instituto de Biologia Celular e Molecular; Porto Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; Porto Portugal
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Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
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Berlivet S, Paquette D, Dumouchel A, Langlais D, Dostie J, Kmita M. Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genet 2013; 9:e1004018. [PMID: 24385922 PMCID: PMC3873244 DOI: 10.1371/journal.pgen.1004018] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/25/2013] [Indexed: 12/19/2022] Open
Abstract
HoxA genes exhibit central roles during development and causal mutations have been found in several human syndromes including limb malformation. Despite their importance, information on how these genes are regulated is lacking. Here, we report on the first identification of bona fide transcriptional enhancers controlling HoxA genes in developing limbs and show that these enhancers are grouped into distinct topological domains at the sub-megabase scale (sub-TADs). We provide evidence that target genes and regulatory elements physically interact with each other through contacts between sub-TADs rather than by the formation of discreet “DNA loops”. Interestingly, there is no obvious relationship between the functional domains of the enhancers within the limb and how they are partitioned among the topological domains, suggesting that sub-TAD formation does not rely on enhancer activity. Moreover, we show that suppressing the transcriptional activity of enhancers does not abrogate their contacts with HoxA genes. Based on these data, we propose a model whereby chromatin architecture defines the functional landscapes of enhancers. From an evolutionary standpoint, our data points to the convergent evolution of HoxA and HoxD regulation in the fin-to-limb transition, one of the major morphological innovations in vertebrates. Hox genes encode transcription factors with crucial roles during development. These genes are grouped in four different clusters names HoxA, B, C, and D. Mutations in genes of the HoxA and D clusters have been found in several human syndromes, affecting in some cases limb development. Despite their essential role and contrary to the genes of the HoxD cluster, little is known about how the HoxA genes are regulated. Here, we identified a large set of regulatory elements controlling HoxA genes during limb development. By studying spatial chromatin organization at the HoxA region, we found that the regulatory elements are spatially clustered regardless of their activity. Clustering of enhancers define tissue-specific chromatin domains that interact specifically with each other and with active genes in the limb. Our findings give support to the emerging concept that chromatin architecture defines the functional properties of genomes. Additionally, our study suggests a common constraint of the chromatin topology in the evolution of HoxA and HoxD regulation in the emergence of the hand/foot, which is one of the major morphological innovations in vertebrates.
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Affiliation(s)
- Soizik Berlivet
- Unité de génétique et développement, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Denis Paquette
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Annie Dumouchel
- Unité de génétique et développement, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - David Langlais
- Unité de génétique moléculaire, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - Josée Dostie
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
- * E-mail: (JD); (MK)
| | - Marie Kmita
- Unité de génétique et développement, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
- Department of Medicine, University of Montréal, Montréal, Québec, Canada
- * E-mail: (JD); (MK)
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37
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Sheth R, Bastida MF, Kmita M, Ros M. "Self-regulation," a new facet of Hox genes' function. Dev Dyn 2013; 243:182-91. [PMID: 23913823 DOI: 10.1002/dvdy.24019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 07/13/2013] [Accepted: 07/15/2013] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Precise temporal and spatial expression of the clustered Hox genes is essential for patterning the developing embryo. Temporal activation of Hox genes was shown to be cluster-autonomous. However, gene clustering appears dispensable for spatial colinear expression. Generally, a set of Hox genes expressed in a group of cells instructs these cells about their fate such that the differential expression of Hox genes results in morphological diversity. The spatial colinearity is considered to rely both on local and long-range cis regulation. RESULTS Here, we report on the global deregulation of HoxA and HoxD expression patterns upon inactivation of a subset of HOXA and HOXD proteins. CONCLUSIONS Our data suggest the existence of a "self-regulation" mechanism, a process by which HOX proteins establish and/or maintain the spatial domains of the Hox gene family and we propose that the functionally dominant HOX proteins could contribute to generating the spatial parameters of Hox expression in a given tissue, i.e., HOX controlling the establishment of the ultimate HOX code.
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Affiliation(s)
- Rushikesh Sheth
- Instituto de Biomedicina y Biotecnologéa de Cantabria, . CSIC-SODERCAN-Universidad de Cantabria, Santander, Spain; Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
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38
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Soshnikova N. Hox genes regulation in vertebrates. Dev Dyn 2013; 243:49-58. [PMID: 23832853 DOI: 10.1002/dvdy.24014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/30/2013] [Accepted: 07/01/2013] [Indexed: 12/16/2022] Open
Abstract
Hox genes encode transcription factors defining cellular identities along the major and secondary body axes. Their coordinated expression in both space and time is critical for embryonic patterning. Accordingly, Hox genes transcription is tightly controlled at multiple levels, and involves an intricate combination of local and long-range cis-regulatory elements. Recent studies revealed that in addition to transcription factors, dynamic patterns of histone marks and higher-order chromatin structure are important determinants of Hox gene regulation. Furthermore, the emerging picture suggests an involvement of various species of non-coding RNA in targeting activating and repressive complexes to Hox clusters. I review these recent developments and discuss their relevance to the control of Hox gene expression in vivo, as well as to our understanding of transcriptional regulatory mechanisms.
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39
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DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP. The genomic landscape of cohesin-associated chromatin interactions. Genome Res 2013; 23:1224-34. [PMID: 23704192 PMCID: PMC3730097 DOI: 10.1101/gr.156570.113] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/20/2013] [Indexed: 12/19/2022]
Abstract
Cohesin is implicated in establishing tissue-specific DNA loops that target enhancers to promoters, and also localizes to sites bound by the insulator protein CTCF, which blocks enhancer-promoter communication. However, cohesin-associated interactions have not been characterized on a genome-wide scale. Here we performed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subunit SMC1A in developing mouse limb. We identified 2264 SMC1A interactions, of which 1491 (65%) involved sites co-occupied by CTCF. SMC1A participates in tissue-specific enhancer-promoter interactions and interactions that demarcate regions of correlated regulatory output. In contrast to previous studies, we also identified interactions between promoters and distal sites that are maintained in multiple tissues but are poised in embryonic stem cells and resolve to tissue-specific activated or repressed chromatin states in the mouse embryo. Our results reveal the diversity of cohesin-associated interactions in the genome and highlight their role in establishing the regulatory architecture of development.
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Affiliation(s)
- Laura E. DeMare
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Jing Leng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Justin Cotney
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Steven K. Reilly
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Jun Yin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Richard Sarro
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - James P. Noonan
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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40
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Montavon T, Duboule D. Chromatin organization and global regulation of Hox gene clusters. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120367. [PMID: 23650639 PMCID: PMC3682730 DOI: 10.1098/rstb.2012.0367] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
During development, a properly coordinated expression of Hox genes, within their different genomic clusters is critical for patterning the body plans of many animals with a bilateral symmetry. The fascinating correspondence between the topological organization of Hox clusters and their transcriptional activation in space and time has served as a paradigm for understanding the relationships between genome structure and function. Here, we review some recent observations, which revealed highly dynamic changes in the structure of chromatin at Hox clusters, in parallel with their activation during embryonic development. We discuss the relevance of these findings for our understanding of large-scale gene regulation.
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Affiliation(s)
- Thomas Montavon
- National Research Centre 'Frontiers in Genetics', School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, Switzerland
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41
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Reno PL, Horton WE, Lovejoy CO. Metapodial or phalanx? An evolutionary and developmental perspective on the homology of the first ray's proximal segment. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:276-85. [PMID: 23640850 DOI: 10.1002/jez.b.22506] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 03/29/2013] [Accepted: 04/01/2013] [Indexed: 12/30/2022]
Abstract
The first mammalian metapodial (MP1) has periodically been argued to actually be a phalanx, because the first ray has one less element than the four posterior rays, and because the MP1 growth plate is proximal like those of all phalanges, rather than distal as in metapodials 2-5. However, growth plates are formed at both ends in non-therian tetrapod metapodials, and phylogenetic analysis demonstrates that growth plate loss is a therian synapomorphy that postdates the establishment of the mammalian phalangeal formula. These data, along with results of developmental and morphological studies, suggest that the MP1 is not a phalanx. The singular, proximal growth plates in MPs 2-5 are likely to be an adaptation to dynamic erect quadrupedal gait which was characterized by conversion of the posterior metapodials into rigid struts with the carpus/tarsus. While the adaptive significance of the reversed ossification of MP1 is less clear, we present three functional/developmental hypotheses.
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Affiliation(s)
- Philip L Reno
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA.
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42
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Davis MC. The Deep Homology of the Autopod: Insights from Hox Gene Regulation. Integr Comp Biol 2013; 53:224-32. [DOI: 10.1093/icb/ict029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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43
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Rosin JM, Abassah-Oppong S, Cobb J. Comparative transgenic analysis of enhancers from the human SHOX and mouse Shox2 genomic regions. Hum Mol Genet 2013; 22:3063-76. [DOI: 10.1093/hmg/ddt163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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44
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Marinić M, Aktas T, Ruf S, Spitz F. An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. Dev Cell 2013; 24:530-42. [PMID: 23453598 DOI: 10.1016/j.devcel.2013.01.025] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 11/26/2012] [Accepted: 01/31/2013] [Indexed: 12/26/2022]
Abstract
Fgf8 encodes a key signaling factor, and its precise regulation is essential for embryo patterning. Here, we identified the regulatory modules that control Fgf8 expression during mammalian embryogenesis. These enhancers are interspersed with unrelated genes along a large region of 220 kb; yet they act on Fgf8 only. Intriguingly, this region also contains additional genuine enhancer activities that are not transformed into gene expression. Using genomic engineering strategies, we showed that these multiple and distinct regulatory modules act as a coherent unit and influence genes depending on their position rather than on their promoter sequence. These findings highlight how the structure of a locus regulates the autonomous intrinsic activities of the regulatory elements it contains and contributes to their tissue and target specificities. We discuss the implications of such regulatory systems regarding the evolution of gene expression and the impact of human genomic structural variations.
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Affiliation(s)
- Mirna Marinić
- Developmental Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg 69117, Germany
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45
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Schneider I, Shubin NH. The origin of the tetrapod limb: from expeditions to enhancers. Trends Genet 2013; 29:419-26. [PMID: 23434323 DOI: 10.1016/j.tig.2013.01.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 12/22/2012] [Accepted: 01/28/2013] [Indexed: 12/24/2022]
Abstract
More than three centuries ago natural philosophers, and later anatomists, recognized a fundamental organization to the skeleton of tetrapod limbs. Composed of three segments, stylopod, zeugopod, and autopod, this pattern has served as the basis for a remarkably broad adaptive radiation from wings and flippers to hands and digging organs. A central area of inquiry has been tracing the origins of the elements of this Bauplan in the fins of diverse fish. Can equivalents of the three segments, and the developmental processes that pattern them, be seen in fish fins? In addition, if so, how do these data inform theories of the transformation of fins into limbs? Answers to these questions come from linking discoveries in paleontology with those of developmental biology and genetics. Burgeoning discoveries in the regulatory biology of developmental genes and in the genomics of diverse species offer novel data to investigate these classical questions.
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Affiliation(s)
- Igor Schneider
- Instituto de Ciencias Biologicas, Universidade Federal do Para, 66075, Belem, Brazil.
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46
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Abstract
Our limbs evolved from fish fins as vertebrates colonized aquatic shallows and land. If we understood the genetics underlying this transition, could we build a limb on a fish? In this issue of Developmental Cell, Freitas et al. (2012) show that boosting Hoxd13 expression can bring zebrafish one step closer to terra firma.
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Affiliation(s)
- Igor Schneider
- Instituto de Ciencias Biologicas, Universidade Federal do Para, 66075 Belem, Brazil.
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47
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Noordermeer D, Duboule D. Chromatin looping and organization at developmentally regulated gene loci. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2013; 2:615-30. [PMID: 24014450 DOI: 10.1002/wdev.103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Developmentally regulated genes are often controlled by distant enhancers, silencers and insulators, to implement their correct transcriptional programs. In recent years, the development of 3C and derived techniques (4C, 5C, HiC, ChIA-PET, etc.) has confirmed that chromatin looping is an important mechanism for the transfer of regulatory information in mammalian cells. At many developmentally regulated gene loci, transcriptional activation is indeed accompanied by the formation of chromatin loops between genes and distant enhancers. Similarly, dynamic looping between insulator elements and changes in local 3D organization may be observed upon variation in transcriptional activity. Chromatin looping also occurs at silent gene loci, where its function remains less understood. In lineage-committed cells, partial 3D configurations are detected at loci that are activated at later stages. However, these partial configurations usually lack promoter-enhancer loops that accompany transcriptional activation, suggesting they have structural functions. Definitive evidence for a repressive role of chromatin looping is still lacking. Chromatin loops have been reported at repressed loci but, alternatively, they may act as a distraction for active loops. Together, these mechanisms allow fine-tuning of regulatory programs, thus providing further diversity in the transcriptional control of developmentally regulated gene loci.
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Affiliation(s)
- Daan Noordermeer
- National Research Centre Frontiers in Genetics, School of Life Sciences, Ecole Polytechnique Frale (EPFL), Lausanne, Switzerland
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48
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49
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Hoxd13 Contribution to the Evolution of Vertebrate Appendages. Dev Cell 2012; 23:1219-29. [DOI: 10.1016/j.devcel.2012.10.015] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 07/26/2012] [Accepted: 10/16/2012] [Indexed: 01/12/2023]
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50
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Impact of copy number variations (CNVs) on long-range gene regulation at the HoxD locus. Proc Natl Acad Sci U S A 2012; 109:20204-11. [PMID: 23134724 DOI: 10.1073/pnas.1217659109] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Copy number variations are genomic structural variants that are frequently associated with human diseases. Among these copy number variations, duplications of DNA segments are often assumed to lead to dosage effects by increasing the copy number of either genes or their regulatory elements. We produced a series of large targeted duplications within a conserved gene desert upstream of the murine HoxD locus. This DNA region, syntenic to human 2q31-32, contains a range of regulatory elements required for Hoxd gene transcription, and it is often disrupted and/or reorganized in human genetic conditions collectively known as the 2q31 syndrome. Unexpectedly, one such duplication led to a transcriptional down-regulation in developing digits by impairing physical interactions between the target genes and their upstream regulatory elements, thus phenocopying the effect obtained when these enhancer sequences are deleted. These results illustrate the detrimental consequences of interrupting highly conserved regulatory landscapes and reveal a mechanism where genomic duplications lead to partial loss of function of nearby located genes.
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