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Heer M, Giudice L, Mengoni C, Giugno R, Rico D. Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers. Nucleic Acids Res 2023; 51:e55. [PMID: 37021559 PMCID: PMC10250221 DOI: 10.1093/nar/gkad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 03/06/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023] Open
Abstract
Most cell type-specific genes are regulated by the interaction of enhancers with their promoters. The identification of enhancers is not trivial as enhancers are diverse in their characteristics and dynamic in their interaction partners. We present Esearch3D, a new method that exploits network theory approaches to identify active enhancers. Our work is based on the fact that enhancers act as a source of regulatory information to increase the rate of transcription of their target genes and that the flow of this information is mediated by the folding of chromatin in the three-dimensional (3D) nuclear space between the enhancer and the target gene promoter. Esearch3D reverse engineers this flow of information to calculate the likelihood of enhancer activity in intergenic regions by propagating the transcription levels of genes across 3D genome networks. Regions predicted to have high enhancer activity are shown to be enriched in annotations indicative of enhancer activity. These include: enhancer-associated histone marks, bidirectional CAGE-seq, STARR-seq, P300, RNA polymerase II and expression quantitative trait loci (eQTLs). Esearch3D leverages the relationship between chromatin architecture and transcription, allowing the prediction of active enhancers and an understanding of the complex underpinnings of regulatory networks. The method is available at: https://github.com/InfOmics/Esearch3D and https://doi.org/10.5281/zenodo.7737123.
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Affiliation(s)
- Maninder Heer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Luca Giudice
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Claudia Mengoni
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer. Nat Commun 2021; 12:7235. [PMID: 34903763 PMCID: PMC8668926 DOI: 10.1038/s41467-021-27492-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
Developmental genes are frequently controlled by multiple enhancers sharing similar specificities. As a result, deletions of such regulatory elements have often failed to reveal their full function. Here, we use the Pitx1 testbed locus to characterize in detail the regulatory and cellular identity alterations following the deletion of one of its enhancers (Pen). By combining single cell transcriptomics and an in-embryo cell tracing approach, we observe an increased fraction of Pitx1 non/low-expressing cells and a decreased fraction of Pitx1 high-expressing cells. We find that the over-representation of Pitx1 non/low-expressing cells originates from a failure of the Pitx1 locus to coordinate enhancer activities and 3D chromatin changes. This locus mis-activation induces a localized heterochrony and a concurrent loss of irregular connective tissue, eventually leading to a clubfoot phenotype. This data suggests that, in some cases, redundant enhancers may be used to locally enforce a robust activation of their host regulatory landscapes.
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Shukla R, Henkel ND, Alganem K, Hamoud AR, Reigle J, Alnafisah RS, Eby HM, Imami AS, Creeden JF, Miruzzi SA, Meller J, Mccullumsmith RE. Signature-based approaches for informed drug repurposing: targeting CNS disorders. Neuropsychopharmacology 2021; 46:116-130. [PMID: 32604402 PMCID: PMC7688959 DOI: 10.1038/s41386-020-0752-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/30/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022]
Abstract
CNS disorders, and in particular psychiatric illnesses, lack definitive disease-altering therapeutics. The limited understanding of the mechanisms driving these illnesses with the slow pace and high cost of drug development exacerbates this issue. For these reasons, drug repurposing - both a less expensive and time-efficient practice compared to de novo drug development - has been a promising strategy to overcome the paucity of treatments available for these debilitating disorders. While empirical drug-repurposing has been a routine practice in clinical psychiatry, innovative, informed, and cost-effective repurposing efforts using big data ("omics") have been designed to characterize drugs by structural and transcriptomic signatures. These strategies, in conjunction with ontological integration, provide an important opportunity to address knowledge-based challenges associated with drug development for CNS disorders. In this review, we discuss various signature-based in silico approaches to drug repurposing, its integration with multiple omics platforms, and how this data can be used for clinically relevant, evidence-based drug repurposing. These tools provide an exciting translational avenue to merge omics-based drug discovery platforms with patient-specific disease signatures, ultimately facilitating the identification of new therapies for numerous psychiatric disorders.
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Affiliation(s)
- Rammohan Shukla
- Department of Neurosciences, University of Toledo, Toledo, OH, USA.
| | | | - Khaled Alganem
- Department of Neurosciences, University of Toledo, Toledo, OH, USA
| | | | - James Reigle
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Hunter M Eby
- Department of Neurosciences, University of Toledo, Toledo, OH, USA
| | - Ali S Imami
- Department of Neurosciences, University of Toledo, Toledo, OH, USA
| | - Justin F Creeden
- Department of Neurosciences, University of Toledo, Toledo, OH, USA
| | - Scott A Miruzzi
- Department of Neurosciences, University of Toledo, Toledo, OH, USA
| | - Jaroslaw Meller
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Electrical Engineering and Computing Systems, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Informatics, Nicolaus Copernicus University, Torun, Poland
| | - Robert E Mccullumsmith
- Department of Neurosciences, University of Toledo, Toledo, OH, USA
- Neurosciences Institute, ProMedica, Toledo, OH, USA
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Alquezar‐Planas DE, Löber U, Cui P, Quedenau C, Chen W, Greenwood AD. DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David E. Alquezar‐Planas
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Australian Museum Research InstituteAustralian Museum Sydney NSW Australia
| | - Ulrike Löber
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- The Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Experimental and Clinical Research Center A Cooperation of Charité – Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine Berlin Germany
| | - Pin Cui
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Claudia Quedenau
- Genomics Max Delbrück Center for Molecular Medicine Berlin Germany
| | - Wei Chen
- Berlin Institute for Medical Systems BiologyMax‐Delbrück Center for Molecular Medicine Berlin Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Department of Veterinary Medicine Freie Universität Berlin Berlin Germany
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Sparks AM, Watt K, Sinclair R, Pilkington JG, Pemberton JM, McNeilly TN, Nussey DH, Johnston SE. The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries). PLoS Genet 2019; 15:e1008461. [PMID: 31697674 PMCID: PMC6863570 DOI: 10.1371/journal.pgen.1008461] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 11/19/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Much of our knowledge of the drivers of immune variation, and how these responses vary over time, comes from humans, domesticated livestock or laboratory organisms. While the genetic basis of variation in immune responses have been investigated in these systems, there is a poor understanding of how genetic variation influences immunity in natural, untreated populations living in complex environments. Here, we examine the genetic architecture of variation in immune traits in the Soay sheep of St Kilda, an unmanaged population of sheep infected with strongyle gastrointestinal nematodes. We assayed IgA, IgE and IgG antibodies against the prevalent nematode Teladorsagia circumcincta in the blood plasma of > 3,000 sheep collected over 26 years. Antibody levels were significantly heritable (h2 = 0.21 to 0.57) and highly stable over an individual’s lifespan. IgA levels were strongly associated with a region on chromosome 24 explaining 21.1% and 24.5% of heritable variation in lambs and adults, respectively. This region was adjacent to two candidate loci, Class II Major Histocompatibility Complex Transactivator (CIITA) and C-Type Lectin Domain Containing 16A (CLEC16A). Lamb IgA levels were also associated with the immunoglobulin heavy constant loci (IGH) complex, and adult IgE levels and lamb IgA and IgG levels were associated with the major histocompatibility complex (MHC). This study provides evidence of high heritability of a complex immunological trait under natural conditions and provides the first evidence from a genome-wide study that large effect genes located outside the MHC region exist for immune traits in the wild. Understanding how immune responses vary in natural populations can give an insight into how infection affects the ability of hosts and parasites to survive and reproduce, and how this drives evolutionary and ecological dynamics. Yet, very little is known about how immune responses vary over an individual’s lifetime and how genes contribute to this variation under natural conditions. Our study investigates the genetic architecture of variation in three antibody types, IgA, IgE and IgG in a wild population of Soay sheep on the St Kilda archipelago in North-West Scotland. Using data collected over 26 years, we show that antibody levels have a heritable basis in lambs and adults and are stable over an individual’s lifetime. We also identify several genomic regions with large effects on immune responses. Our study offers the first insights into the genetic control of immunity in a wild population, which is essential to understand how immune profiles vary in challenging natural conditions and how natural selection maintains genetic variation in complex immune traits.
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Affiliation(s)
- Alexandra M. Sparks
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
| | - Kathryn Watt
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rona Sinclair
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jill G. Pilkington
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Josephine M. Pemberton
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, United Kingdom
| | - Daniel H. Nussey
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Susan E. Johnston
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma. Int J Mol Sci 2019; 20:ijms20143582. [PMID: 31336658 PMCID: PMC6679006 DOI: 10.3390/ijms20143582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/06/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022] Open
Abstract
Understanding the gene regulatory network governing cancer initiation and progression is necessary, although it remains largely unexplored. Enhancer elements represent the center of this regulatory circuit. The study aims to identify the gene expression change driven by copy number variation in enhancer elements of pancreatic adenocarcinoma (PAAD). The pancreatic tissue specific enhancer and target gene data were taken from EnhancerAtlas. The gene expression and copy number data were taken from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) and copy number variations (CNVs) were identified between matched tumor-normal samples of PAAD. Significant CNVs were matched onto enhancer coordinates by using genomic intersection functionality from BEDTools. By combining the gene expression and CNV data, we identified 169 genes whose expression shows a positive correlation with the CNV of enhancers. We further identified 16 genes which are regulated by a super enhancer and 15 genes which have high prognostic potential (Z-score > 1.96). Cox proportional hazard analysis of these genes indicates that these are better predictors of survival. Taken together, our integrative analytical approach identifies enhancer CNV-driven gene expression change in PAAD, which could lead to better understanding of PAAD pathogenesis and to the design of enhancer-based cancer treatment strategies.
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Liu J, Rutten L, Limpens E, van der Molen T, van Velzen R, Chen R, Chen Y, Geurts R, Kohlen W, Kulikova O, Bisseling T. A Remote cis-Regulatory Region Is Required for NIN Expression in the Pericycle to Initiate Nodule Primordium Formation in Medicago truncatula. THE PLANT CELL 2019; 31:68-83. [PMID: 30610167 PMCID: PMC6391699 DOI: 10.1105/tpc.18.00478] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/13/2018] [Accepted: 01/04/2019] [Indexed: 05/22/2023]
Abstract
The legume-rhizobium symbiosis results in nitrogen-fixing root nodules, and their formation involves both intracellular infection initiated in the epidermis and nodule organogenesis initiated in inner root cell layers. NODULE INCEPTION (NIN) is a nodule-specific transcription factor essential for both processes. These NIN-regulated processes occur at different times and locations in the root, demonstrating a complex pattern of spatiotemporal regulation. We show that regulatory sequences sufficient for the epidermal infection process are located within a 5 kb region directly upstream of the NIN start codon in Medicago truncatula Furthermore, we identify a remote upstream cis-regulatory region required for the expression of NIN in the pericycle, and we show that this region is essential for nodule organogenesis. This region contains putative cytokinin response elements and is conserved in eight more legume species. Both the cytokinin receptor 1, which is essential for nodule primordium formation, and the B-type response regulator RR1 are expressed in the pericycle in the susceptible zone of the uninoculated root. This, together with the identification of the cytokinin-responsive elements in the NIN promoter, strongly suggests that NIN expression is initially triggered by cytokinin signaling in the pericycle to initiate nodule primordium formation.
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Affiliation(s)
- Jieyu Liu
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Luuk Rutten
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Erik Limpens
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Tjitse van der Molen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Rujin Chen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Yuhui Chen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Olga Kulikova
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
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Hirsch N, Eshel R, Bar Yaacov R, Shahar T, Shmulevich F, Dahan I, Levaot N, Kaplan T, Lupiáñez DG, Birnbaum RY. Unraveling the transcriptional regulation of TWIST1 in limb development. PLoS Genet 2018; 14:e1007738. [PMID: 30372441 PMCID: PMC6233932 DOI: 10.1371/journal.pgen.1007738] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 11/13/2018] [Accepted: 10/03/2018] [Indexed: 12/13/2022] Open
Abstract
The transcription factor TWIST1 plays a vital role in mesoderm development, particularly in limb and craniofacial formation. Accordingly, haploinsufficiency of TWIST1 can cause limb and craniofacial malformations as part of Saethre-Chotzen syndrome. However, the molecular basis of TWIST1 transcriptional regulation during development has yet to be elucidated. Here, we characterized active enhancers in the TWIST1-HDAC9 locus that drive transcription in the developing limb and branchial arches. Using available p300 and H3K27ac ChIP-seq data, we identified 12 enhancer candidates, located both within and outside the coding sequences of the neighboring gene, Histone deacetyase 9 (HDAC9). Using zebrafish and mouse enhancer assays, we showed that eight of these candidates have limb/fin and branchial arch enhancer activity that resemble Twist1 expression. Using 4C-seq, we showed that the Twist1 promoter region interacts with three enhancers (eTw-5, 6, 7) in the limb bud and branchial arch of mouse embryos at day 11.5. Furthermore, we found that two transcription factors, LMX1B and TFAP2, bind these enhancers and modulate their enhancer activity. Finally, using CRISPR/Cas9 genome editing, we showed that homozygous deletion of eTw5-7 enhancers reduced Twist1 expression in the limb bud and caused pre-axial polydactyly, a phenotype observed in Twist1+/- mice. Taken together, our findings reveal that each enhancer has a discrete activity pattern, and together comprise a spatiotemporal regulatory network of Twist1 transcription in the developing limbs/fins and branchial arches. Our study suggests that mutations in TWIST1 enhancers could lead to reduced TWIST1 expression, resulting in phenotypic outcome as seen with TWIST1 coding mutations.
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Affiliation(s)
- Naama Hirsch
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Reut Eshel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Reut Bar Yaacov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tal Shahar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Fania Shmulevich
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Idit Dahan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noam Levaot
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Darío G. Lupiáñez
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ramon Y. Birnbaum
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail:
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Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis. Nat Genet 2018; 50:1463-1473. [PMID: 30262816 PMCID: PMC10154999 DOI: 10.1038/s41588-018-0221-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 08/02/2018] [Indexed: 12/20/2022]
Abstract
The regulatory specificity of enhancers and their interaction with gene promoters is thought to be controlled by their sequence and the binding of transcription factors. By studying Pitx1, a regulator of hindlimb development, we show that dynamic changes in chromatin conformation can restrict the activity of enhancers. Inconsistent with its hindlimb-restricted expression, Pitx1 is controlled by an enhancer (Pen) that shows activity in forelimbs and hindlimbs. By Capture Hi-C and three-dimensional modeling of the locus, we demonstrate that forelimbs and hindlimbs have fundamentally different chromatin configurations, whereby Pen and Pitx1 interact in hindlimbs and are physically separated in forelimbs. Structural variants can convert the inactive into the active conformation, thereby inducing Pitx1 misexpression in forelimbs, causing partial arm-to-leg transformation in mice and humans. Thus, tissue-specific three-dimensional chromatin conformation can contribute to enhancer activity and specificity in vivo and its disturbance can result in gene misexpression and disease.
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De Souza RAG, Kosior N, Thomson SB, Mathelier A, Zhang AW, Bečanović K, Wasserman WW, Leavitt BR. Computational Analysis of Transcriptional Regulation Sites at the HTT Gene Locus. J Huntingtons Dis 2018; 7:223-237. [PMID: 30103339 DOI: 10.3233/jhd-170272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Huntington's disease is a late onset neurological disorder caused by a trinucleotide CAG repeat expansion mutation in the HTT gene encoding for the protein huntingtin. Despite considerable ongoing research, the wild-type function of huntingtin is not yet fully understood. OBJECTIVE To improve knowledge of HTT gene regulation at the transcriptional level and inform future studies aimed at uncovering the HTT gene's normal function. METHODS The HTT gene region was functionally characterized through an in silico analysis using publicly available data sets. ChIP-seq data sets and the online STRING database were used to identify putative transcription factor binding sites (TFBSs) and protein-protein interactions within the HTT promoter region. siRNA-mediated knockdown and ChIP-qPCR of STAT1, a TF identified from the in silico analysis, were used to validate the bioinformatics screen. RESULTS 16 regions containing potential regulatory genomic markers were identified. TFBSs for 59 transcription factors (TFs) were detected in one or more of the 16 candidate regions. Using these TFs, 15 clusters of protein-protein interactions were identified using STRING. siRNA-mediated knockdown of STAT1 resulted in an increase in HTT expression, and ChIP-qPCR detected enrichment of STAT1 binding at one of the predicted regions. These assays confirmed the utility of the bioinformatic analysis. CONCLUSIONS Putative regulatory regions outside of the immediate HTT promoter region have been identified with specific protein-protein interactions. Future work will focus on in vitro and in vivo studies to examine the effect of modulating identified TFBSs and altering the levels of specific TFs of interest in regulating HTT gene expression.
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Affiliation(s)
- Rebecca A G De Souza
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Natalia Kosior
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Sarah B Thomson
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Allen W Zhang
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Kristina Bečanović
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Wyeth W Wasserman
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Blair R Leavitt
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
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Razin SV, Gavrilov AA. Structural–Functional Domains of the Eukaryotic Genome. BIOCHEMISTRY (MOSCOW) 2018; 83:302-312. [DOI: 10.1134/s0006297918040028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/27/2017] [Indexed: 08/30/2023]
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12
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Robson MI, de Las Heras JI, Czapiewski R, Sivakumar A, Kerr ARW, Schirmer EC. Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments. Genome Res 2017; 27:1126-1138. [PMID: 28424353 PMCID: PMC5495065 DOI: 10.1101/gr.212308.116] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 04/12/2017] [Indexed: 01/15/2023]
Abstract
The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome reorganization at the nuclear periphery dominated by release of loci frequently important for T-cell function. To assess how these changes at the nuclear periphery influence wider genome organization, our DamID data sets were contrasted with TADs and compartments. Features of specific repositioning events were then tested by fluorescence in situ hybridization during T-cell activation. First, considerable overlap between TADs and LADs was observed with the TAD repositioning as a unit. Second, A1 and A2 subcompartments are segregated in 3D space through differences in proximity to LADs along chromosomes. Third, genes and a putative enhancer in LADs that were released from the periphery during T-cell activation became preferentially associated with A2 subcompartments and were constrained to the relative proximity of the lamina. Thus, lamina associations influence internal nuclear organization, and changes in LADs during T-cell activation may provide an important additional mode of gene regulation.
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Affiliation(s)
- Michael I Robson
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Jose I de Las Heras
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Rafal Czapiewski
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Aishwarya Sivakumar
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Alastair R W Kerr
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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13
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Ampuja M, Rantapero T, Rodriguez-Martinez A, Palmroth M, Alarmo EL, Nykter M, Kallioniemi A. Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer. BMC Genomics 2017; 18:68. [PMID: 28077088 PMCID: PMC5225521 DOI: 10.1186/s12864-016-3428-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/16/2016] [Indexed: 02/07/2023] Open
Abstract
Background Bone morphogenetic protein 4 (BMP4) plays an important role in cancer pathogenesis. In breast cancer, it reduces proliferation and increases migration in a cell line-dependent manner. To characterize the transcriptional mediators of these phenotypes, we performed RNA-seq and DNase-seq analyses after BMP4 treatment in MDA-MB-231 and T-47D breast cancer cells that respond to BMP4 with enhanced migration and decreased cell growth, respectively. Results The RNA-seq data revealed gene expression changes that were consistent with the in vitro phenotypes of the cell lines, particularly in MDA-MB-231, where migration-related processes were enriched. These results were confirmed when enrichment of BMP4-induced open chromatin regions was analyzed. Interestingly, the chromatin in transcription start sites of differentially expressed genes was already open in unstimulated cells, thus enabling rapid recruitment of transcription factors to the promoters as a response to stimulation. Further analysis and functional validation identified MBD2, CBFB, and HIF1A as downstream regulators of BMP4 signaling. Silencing of these transcription factors revealed that MBD2 was a consistent activator of target genes in both cell lines, CBFB an activator in cells with reduced proliferation phenotype, and HIF1A a repressor in cells with induced migration phenotype. Conclusions Integrating RNA-seq and DNase-seq data showed that the phenotypic responses to BMP4 in breast cancer cell lines are reflected in transcriptomic and chromatin levels. We identified and experimentally validated downstream regulators of BMP4 signaling that relate to the different in vitro phenotypes and thus demonstrate that the downstream BMP4 response is regulated in a cell type-specific manner. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3428-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M Ampuja
- BioMediTech, University of Tampere, Tampere, Finland. .,Fimlab Laboratories, Tampere, Finland.
| | - T Rantapero
- BioMediTech, University of Tampere, Tampere, Finland
| | - A Rodriguez-Martinez
- BioMediTech, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere, Finland
| | - M Palmroth
- BioMediTech, University of Tampere, Tampere, Finland
| | - E L Alarmo
- BioMediTech, University of Tampere, Tampere, Finland
| | - M Nykter
- BioMediTech, University of Tampere, Tampere, Finland
| | - A Kallioniemi
- BioMediTech, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere, Finland
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14
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Saber MM, Adeyemi Babarinde I, Hettiarachchi N, Saitou N. Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences. Genome Biol Evol 2016; 8:2076-92. [PMID: 27289096 PMCID: PMC4987104 DOI: 10.1093/gbe/evw132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions.
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Affiliation(s)
- Morteza Mahmoudi Saber
- Department of Biological Sciences, Graduate School of Science, University of Tokyo Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Isaac Adeyemi Babarinde
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Nilmini Hettiarachchi
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Naruya Saitou
- Department of Biological Sciences, Graduate School of Science, University of Tokyo Division of Population Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
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15
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3D genomics imposes evolution of the domain model of eukaryotic genome organization. Chromosoma 2016; 126:59-69. [DOI: 10.1007/s00412-016-0604-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/11/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
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16
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Pindyurin AV, de Jong J, Akhtar W. TRIP through the chromatin: a high throughput exploration of enhancer regulatory landscapes. Genomics 2015; 106:171-177. [PMID: 26080039 DOI: 10.1016/j.ygeno.2015.06.009] [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: 02/02/2015] [Revised: 05/01/2015] [Accepted: 06/09/2015] [Indexed: 11/25/2022]
Abstract
Enhancers are regulatory elements that promote gene expression in a spatio-temporal way and are involved in a wide range of developmental and disease processes. Both the identification and subsequent functional dissection of enhancers are key steps in understanding these processes. Several high-throughput approaches were recently developed for these purposes; however, in almost all cases enhancers are being tested outside their native chromatin context. Until recently, the analysis of enhancer activities at their native genomic locations was low throughput, laborious and time-consuming. Here, we discuss the potential of a powerful approach, TRIP, to study the functioning of enhancers in their native chromatin environments by introducing sensor constructs directly in the genome. TRIP allows for simultaneously analyzing the quantitative readout of numerous sensor constructs integrated at random locations in the genome. The high-throughput and flexible nature of TRIP opens up potential to study different aspects of enhancer biology at an unprecedented level.
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Affiliation(s)
- Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Johann de Jong
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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17
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Correlation between Reversal of DNA Methylation and Clinical Symptoms in Psoriatic Epidermis Following Narrow-Band UVB Phototherapy. J Invest Dermatol 2015; 135:2077-2083. [PMID: 25830654 PMCID: PMC4580729 DOI: 10.1038/jid.2015.128] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/11/2015] [Accepted: 03/19/2015] [Indexed: 11/24/2022]
Abstract
Epigenetic modifications by DNA methylation are associated with a wide range of diseases. Previous studies in psoriasis have concentrated on epigenetic changes in immune cells or in total skin biopsies that include stromal-associated changes. In order to improve our understanding of the role of DNA methylation in psoriasis, we sought to obtain a comprehensive DNA methylation signature specific for the epidermal component of psoriasis and to analyze methylation changes during therapy. Genome-wide DNA methylation profiling of epidermal cells from 12 patients undergoing narrow-band UVB phototherapy and 12 corresponding healthy controls revealed a distinct DNA methylation pattern in psoriasis compared with controls. A total of 3,665 methylation variable positions (MVPs) were identified with an overall hypomethylation in psoriasis patient samples. DNA methylation pattern was reversed at the end of phototherapy in patients showing excellent clinical improvement. Only 7% of phototherapy-affected MVPs (150 out of 2,108) correlate with nearby gene expression. Enrichment of MVPs in enhancers indicates tissue-specific modulation of the transcriptional regulatory machinery in psoriasis. Our study identified key epigenetic events associated with psoriasis pathogenesis and helps understand the dynamic DNA methylation landscape in the human genome.
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18
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J. Grant D, A. Shakes L, M. Wolf H, C. Norford D, K. Chatterjee P. Exploring function of conserved non-coding DNA in its chromosomal context. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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19
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Abstract
Coordinated gene expression controlled by long-distance enhancers is orchestrated by DNA regulatory sequences involving transcription factors and layers of control mechanisms. The Shh gene and well-established regulators are an example of genomic composition in which enhancers reside in a large desert extending into neighbouring genes to control the spatiotemporal pattern of expression. Exploiting the local hopping activity of the Sleeping Beauty transposon, the lacZ reporter gene was dispersed throughout the Shh region to systematically map the genomic features responsible for expression activity. We found that enhancer activities are retained inside a genomic region that corresponds to the topological associated domain (TAD) defined by Hi-C. This domain of approximately 900 kb is in an open conformation over its length and is generally susceptible to all Shh enhancers. Similar to the distal enhancers, an enhancer residing within the Shh second intron activates the reporter gene located at distances of hundreds of kilobases away, suggesting that both proximal and distal enhancers have the capacity to survey the Shh topological domain to recognise potential promoters. The widely expressed Rnf32 gene lying within the Shh domain evades enhancer activities by a process that may be common among other housekeeping genes that reside in large regulatory domains. Finally, the boundaries of the Shh TAD do not represent the absolute expression limits of enhancer activity, as expression activity is lost stepwise at a number of genomic positions at the verges of these domains.
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Affiliation(s)
- Eve Anderson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK
| | - Paul S Devenney
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK
| | - Robert E Hill
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK
| | - Laura A Lettice
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK
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20
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Abstract
Transcription factor binding sites (TFBSs) on the DNA are generally accepted as the key nodes of gene control. However, the multitudes of TFBSs identified in genome-wide studies, some of them seemingly unconstrained in evolution, have prompted the view that in many cases TF binding may serve no biological function. Yet, insights from transcriptional biochemistry, population genetics and functional genomics suggest that rather than segregating into 'functional' or 'non-functional', TFBS inputs to their target genes may be generally cumulative, with varying degrees of potency and redundancy. As TFBS redundancy can be diminished by mutations and environmental stress, some of the apparently 'spurious' sites may turn out to be important for maintaining adequate transcriptional regulation under these conditions. This has significant implications for interpreting the phenotypic effects of TFBS mutations, particularly in the context of genome-wide association studies for complex traits.
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21
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Symmons O, Uslu VV, Tsujimura T, Ruf S, Nassari S, Schwarzer W, Ettwiller L, Spitz F. Functional and topological characteristics of mammalian regulatory domains. Genome Res 2014; 24:390-400. [PMID: 24398455 PMCID: PMC3941104 DOI: 10.1101/gr.163519.113] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/19/2013] [Indexed: 01/04/2023]
Abstract
Long-range regulatory interactions play an important role in shaping gene-expression programs. However, the genomic features that organize these activities are still poorly characterized. We conducted a large operational analysis to chart the distribution of gene regulatory activities along the mouse genome, using hundreds of insertions of a regulatory sensor. We found that enhancers distribute their activities along broad regions and not in a gene-centric manner, defining large regulatory domains. Remarkably, these domains correlate strongly with the recently described TADs, which partition the genome into distinct self-interacting blocks. Different features, including specific repeats and CTCF-binding sites, correlate with the transition zones separating regulatory domains, and may help to further organize promiscuously distributed regulatory influences within large domains. These findings support a model of genomic organization where TADs confine regulatory activities to specific but large regulatory domains, contributing to the establishment of specific gene expression profiles.
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Affiliation(s)
- Orsolya Symmons
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Veli Vural Uslu
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Taro Tsujimura
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sandra Ruf
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sonya Nassari
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Wibke Schwarzer
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Laurence Ettwiller
- Centre for Organismal Studies, University of Heidelberg, 69111 Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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22
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van Heyningen V, Bickmore W. Regulation from a distance: long-range control of gene expression in development and disease. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120372. [PMID: 23650642 DOI: 10.1098/rstb.2012.0372] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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