1
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Loubiere V, de Almeida BP, Pagani M, Stark A. Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila. Nat Commun 2024; 15:8584. [PMID: 39362902 PMCID: PMC11450171 DOI: 10.1038/s41467-024-52921-2] [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: 10/15/2023] [Accepted: 09/24/2024] [Indexed: 10/05/2024] Open
Abstract
Genomic enhancers are key transcriptional regulators which, upon the binding of sequence-specific transcription factors, activate their cognate target promoters. Although enhancers have been extensively studied in isolation, a substantial number of genes have more than one simultaneously active enhancer, and it remains unclear how these cooperate to regulate transcription. Using Drosophila melanogaster S2 cells as a model, we assay the activities of more than a thousand individual enhancers and about a million enhancer pairs toward housekeeping and developmental core promoters with STARR-seq. We report that housekeeping and developmental enhancers show distinct modes of enhancer-enhancer cooperativity: while housekeeping enhancers are additive such that their combined activity mirrors the sum of their individual activities, developmental enhancers are super-additive and combine multiplicatively. Super-additivity between developmental enhancers is promiscuous and neither depends on the enhancers' endogenous genomic contexts nor on specific transcription factor motif signatures. However, it can be further boosted by Twist and Trl motifs and saturates for the highest levels of enhancer activity. These results have important implications for our understanding of gene regulation in complex multi-enhancer developmental loci and genomically clustered housekeeping genes, providing a rationale to interpret the transcriptional impact of non-coding mutations at different loci.
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Affiliation(s)
- Vincent Loubiere
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Bernardo P de Almeida
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
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2
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Yao Q, Shen R, Shao Y, Tian Y, Han P, Zhang X, Zhu JK, Lu Y. Efficient and multiplex gene upregulation in plants through CRISPR-Cas-mediated knockin of enhancers. MOLECULAR PLANT 2024; 17:1472-1483. [PMID: 39049493 DOI: 10.1016/j.molp.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/01/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
Gene upregulation through genome editing is important for plant research and breeding. Targeted insertion of short transcriptional enhancers (STEs) into gene promoters may offer a universal solution akin to transgene-mediated overexpression while avoiding the drawbacks associated with transgenesis. Here, we introduce an "in locus activation" technique in rice that leverages well-characterized STEs for refined, heritable, and multiplexed gene upregulation. To address the scarcity of potent enhancers, we developed a large-scale mining approach and discovered a suite of STEs that are capable of enhancing gene expression in rice protoplasts. The in locus integration of these STEs into eight rice genes resulted in substantial transcriptional upregulation in the edited plants, with up to 869.1-fold increases in their transcript levels. Employing a variety of STEs, we achieved delicate control of gene expression, enabling the fine-tuning of key phenotypic traits such as plant height. Our approach also enabled efficient multiplexed gene upregulation, with up to four genes activated simultaneously, significantly enhancing the nicotinamide mononucleotide metabolic pathway. Importantly, heritability studies from the T0 to T3 generations confirmed the stable and heritable nature of STE-driven gene activation. Collectively, our work demonstrates that coupled with STE mining, leveraging genome editing for in locus activation and gene upregulation holds great promise to be widely adopted in fundamental plant research and crop breeding.
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Affiliation(s)
- Qi Yao
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Rundong Shen
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Yang Shao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifu Tian
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Peijin Han
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Xuening Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Yuming Lu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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3
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Sokolov V, Kyrchanova O, Klimenko N, Fedotova A, Ibragimov A, Maksimenko O, Georgiev P. New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity. Nucleic Acids Res 2024; 52:6886-6905. [PMID: 38769058 PMCID: PMC11229372 DOI: 10.1093/nar/gkae393] [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: 09/08/2023] [Revised: 04/20/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024] Open
Abstract
In Drosophila, a group of zinc finger architectural proteins recruits the CP190 protein to the chromatin, an interaction that is essential for the functional activity of promoters and insulators. In this study, we describe a new architectural C2H2 protein called Madf and Zinc-Finger Protein 1 (Mzfp1) that interacts with CP190. Mzfp1 has an unusual structure that includes six C2H2 domains organized in a C-terminal cluster and two tandem MADF domains. Mzfp1 predominantly binds to housekeeping gene promoters located in both euchromatin and heterochromatin genome regions. In vivo mutagenesis studies showed that Mzfp1 is an essential protein, and both MADF domains and the CP190 interaction region are required for its functional activity. The C2H2 cluster is sufficient for the specific binding of Mzfp1 to regulatory elements, while the second MADF domain is required for Mzfp1 recruitment to heterochromatin. Mzfp1 binds to the proximal part of the Fub boundary that separates regulatory domains of the Ubx and abd-A genes in the Bithorax complex. Mzfp1 participates in Fub functions in cooperation with the architectural proteins Pita and Su(Hw). Thus, Mzfp1 is a new architectural C2H2 protein involved in the organization of active promoters and insulators in Drosophila.
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Affiliation(s)
- Vladimir Sokolov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna Fedotova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Airat Ibragimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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4
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Vergara X, Manjón AG, de Haas M, Morris B, Schep R, Leemans C, Friskes A, Beijersbergen RL, Sanders MA, Medema RH, van Steensel B. Widespread chromatin context-dependencies of DNA double-strand break repair proteins. Nat Commun 2024; 15:5334. [PMID: 38909016 PMCID: PMC11193718 DOI: 10.1038/s41467-024-49232-x] [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: 02/19/2024] [Accepted: 05/28/2024] [Indexed: 06/24/2024] Open
Abstract
DNA double-strand breaks are repaired by multiple pathways, including non-homologous end-joining (NHEJ) and microhomology-mediated end-joining (MMEJ). The balance of these pathways is dependent on the local chromatin context, but the underlying mechanisms are poorly understood. By combining knockout screening with a dual MMEJ:NHEJ reporter inserted in 19 different chromatin environments, we identified dozens of DNA repair proteins that modulate pathway balance dependent on the local chromatin state. Proteins that favor NHEJ mostly synergize with euchromatin, while proteins that favor MMEJ generally synergize with distinct types of heterochromatin. Examples of the former are BRCA2 and POLL, and of the latter the FANC complex and ATM. Moreover, in a diversity of human cancer types, loss of several of these proteins alters the distribution of pathway-specific mutations between heterochromatin and euchromatin. Together, these results uncover a complex network of proteins that regulate MMEJ:NHEJ balance in a chromatin context-dependent manner.
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Affiliation(s)
- Xabier Vergara
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Anna G Manjón
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Marcel de Haas
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Ben Morris
- NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ruben Schep
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Christ Leemans
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Anoek Friskes
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Roderick L Beijersbergen
- NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mathijs A Sanders
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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5
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Zhimulev I, Vatolina T, Levitsky V, Tsukanov A. Developmental and Housekeeping Genes: Two Types of Genetic Organization in the Drosophila Genome. Int J Mol Sci 2024; 25:4068. [PMID: 38612878 PMCID: PMC11012173 DOI: 10.3390/ijms25074068] [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: 12/29/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
We developed a procedure for locating genes on Drosophila melanogaster polytene chromosomes and described three types of chromosome structures (gray bands, black bands, and interbands), which differed markedly in morphological and genetic properties. This was reached through the use of our original methods of molecular and genetic analysis, electron microscopy, and bioinformatics data processing. Analysis of the genome-wide distribution of these properties led us to a bioinformatics model of the Drosophila genome organization, in which the genome was divided into two groups of genes. One was constituted by 65, in which the genome was divided into two groups, 62 genes that are expressed in most cell types during life cycle and perform basic cellular functions (the so-called "housekeeping genes"). The other one was made up of 3162 genes that are expressed only at particular stages of development ("developmental genes"). These two groups of genes are so different that we may state that the genome has two types of genetic organization. Different are the timings of their expression, chromatin packaging levels, the composition of activating and deactivating proteins, the sizes of these genes, the lengths of their introns, the organization of the promoter regions of the genes, the locations of origin recognition complexes (ORCs), and DNA replication timings.
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Affiliation(s)
- Igor Zhimulev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia;
| | - Tatyana Vatolina
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia;
| | - Victor Levitsky
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia; (V.L.); (A.T.)
| | - Anton Tsukanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia; (V.L.); (A.T.)
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6
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Wei KHC, Chatla K, Bachtrog D. Single-cell RNA-seq of Drosophila miranda testis reveals the evolution and trajectory of germline sex chromosome regulation. PLoS Biol 2024; 22:e3002605. [PMID: 38687805 PMCID: PMC11135767 DOI: 10.1371/journal.pbio.3002605] [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: 12/21/2022] [Revised: 05/29/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Although sex chromosomes have evolved from autosomes, they often have unusual regulatory regimes that are sex- and cell-type-specific such as dosage compensation (DC) and meiotic sex chromosome inactivation (MSCI). The molecular mechanisms and evolutionary forces driving these unique transcriptional programs are critical for genome evolution but have been, in the case of MSCI in Drosophila, subject to continuous debate. Here, we take advantage of the younger sex chromosomes in D. miranda (XR and the neo-X) to infer how former autosomes acquire sex-chromosome-specific regulatory programs using single-cell and bulk RNA sequencing and ribosome profiling, in a comparative evolutionary context. We show that contrary to mammals and worms, the X down-regulation through germline progression is most consistent with the shutdown of DC instead of MSCI, resulting in half gene dosage at the end of meiosis for all 3 X's. Moreover, lowly expressed germline and meiotic genes on the neo-X are ancestrally lowly expressed, instead of acquired suppression after sex linkage. For the young neo-X, DC is incomplete across all tissue and cell types and this dosage imbalance is rescued by contributions from Y-linked gametologs which produce transcripts that are translated to compensate both gene and protein dosage. We find an excess of previously autosomal testis genes becoming Y-specific, showing that the neo-Y and its masculinization likely resolve sexual antagonism. Multicopy neo-sex genes are predominantly expressed during meiotic stages of spermatogenesis, consistent with their amplification being driven to interfere with mendelian segregation. Altogether, this study reveals germline regulation of evolving sex chromosomes and elucidates the consequences these unique regulatory mechanisms have on the evolution of sex chromosome architecture.
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Affiliation(s)
- Kevin H-C. Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
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7
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Malfait J, Wan J, Spicuglia S. Epromoters are new players in the regulatory landscape with potential pleiotropic roles. Bioessays 2023; 45:e2300012. [PMID: 37246247 DOI: 10.1002/bies.202300012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
Precise spatiotemporal control of gene expression during normal development and cell differentiation is achieved by the combined action of proximal (promoters) and distal (enhancers) cis-regulatory elements. Recent studies have reported that a subset of promoters, termed Epromoters, works also as enhancers to regulate distal genes. This new paradigm opened novel questions regarding the complexity of our genome and raises the possibility that genetic variation within Epromoters has pleiotropic effects on various physiological and pathological traits by differentially impacting multiple proximal and distal genes. Here, we discuss the different observations pointing to an important role of Epromoters in the regulatory landscape and summarize the evidence supporting a pleiotropic impact of these elements in disease. We further hypothesize that Epromoter might represent a major contributor to phenotypic variation and disease.
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Affiliation(s)
- Juliette Malfait
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Jing Wan
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
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8
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Dejosez M, Dall'Agnese A, Ramamoorthy M, Platt J, Yin X, Hogan M, Brosh R, Weintraub AS, Hnisz D, Abraham BJ, Young RA, Zwaka TP. Regulatory architecture of housekeeping genes is driven by promoter assemblies. Cell Rep 2023; 42:112505. [PMID: 37182209 PMCID: PMC10329844 DOI: 10.1016/j.celrep.2023.112505] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/22/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Genes that are key to cell identity are generally regulated by cell-type-specific enhancer elements bound by transcription factors, some of which facilitate looping to distant gene promoters. In contrast, genes that encode housekeeping functions, whose regulation is essential for normal cell metabolism and growth, generally lack interactions with distal enhancers. We find that Ronin (Thap11) assembles multiple promoters of housekeeping and metabolic genes to regulate gene expression. This behavior is analogous to how enhancers are brought together with promoters to regulate cell identity genes. Thus, Ronin-dependent promoter assemblies provide a mechanism to explain why housekeeping genes can forgo distal enhancer elements and why Ronin is important for cellular metabolism and growth control. We propose that clustering of regulatory elements is a mechanism common to cell identity and housekeeping genes but is accomplished by different factors binding distinct control elements to establish enhancer-promoter or promoter-promoter interactions, respectively.
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Affiliation(s)
- Marion Dejosez
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Alessandra Dall'Agnese
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mahesh Ramamoorthy
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Jesse Platt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Xing Yin
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Megan Hogan
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Ran Brosh
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brian J Abraham
- St. Jude Research Children's Hospital, Memphis, TN 38105, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Thomas P Zwaka
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA.
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9
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Jullien D, Guillou E, Bernat-Fabre S, Payet A, Bourbon HMG, Boube M. Inducible degradation of the Drosophila Mediator subunit Med19 reveals its role in regulating developmental but not constitutively-expressed genes. PLoS One 2022; 17:e0275613. [PMID: 36445897 PMCID: PMC9707739 DOI: 10.1371/journal.pone.0275613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
The multi-subunit Mediator complex plays a critical role in gene expression by bridging enhancer-bound transcription factors and the RNA polymerase II machinery. Although experimental case studies suggest differential roles of Mediator subunits, a comprehensive view of the specific set of genes regulated by individual subunits in a developing tissue is still missing. Here we address this fundamental question by focusing on the Med19 subunit and using the Drosophila wing imaginal disc as a developmental model. By coupling auxin-inducible degradation of endogenous Med19 in vivo with RNA-seq, we got access to the early consequences of Med19 elimination on gene expression. Differential gene expression analysis reveals that Med19 is not globally required for mRNA transcription but specifically regulates positively or negatively less than a quarter of the expressed genes. By crossing our transcriptomic data with those of Drosophila gene expression profile database, we found that Med19-dependent genes are highly enriched with spatially-regulated genes while the expression of most constitutively expressed genes is not affected upon Med19 loss. Whereas globally downregulation does not exceed upregulation, we identified a functional class of genes encoding spatially-regulated transcription factors, and more generally developmental regulators, responding unidirectionally to Med19 loss with an expression collapse. Moreover, we show in vivo that the Notch-responsive wingless and the E(spl)-C genes require Med19 for their expression. Combined with experimental evidences suggesting that Med19 could function as a direct transcriptional effector of Notch signaling, our data support a model in which Med19 plays a critical role in the transcriptional activation of developmental genes in response to cell signaling pathways.
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Affiliation(s)
- Denis Jullien
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
- * E-mail: (MB); (DJ)
| | - Emmanuelle Guillou
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Sandra Bernat-Fabre
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Adeline Payet
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Henri-Marc G. Bourbon
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
| | - Muriel Boube
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit UMR 5077, Federal University of Toulouse, Toulouse, France
- RESTORE Research Center, Université de Toulouse, INSERM 1301, CNRS 5070, EFS, ENVT, Toulouse, France
- * E-mail: (MB); (DJ)
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10
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Herman N, Kadener S, Shifman S. The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes. EMBO Rep 2022; 23:e54720. [PMID: 36245419 PMCID: PMC9724677 DOI: 10.15252/embr.202254720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
Insulator proteins located at the boundaries of topological associated domains (TAD) are involved in higher-order chromatin organization and transcription regulation. However, it is still not clear how long-range contacts contribute to transcriptional regulation. Here, we show that relative-of-WOC (ROW) is essential for the long-range transcription regulation mediated by the boundary element-associated factor of 32kD (BEAF-32). We find that ROW physically interacts with heterochromatin proteins (HP1b and HP1c) and the insulator protein (BEAF-32). These proteins interact at TAD boundaries where ROW, through its AT-hook motifs, binds AT-rich sequences flanked by BEAF-32-binding sites and motifs. Knockdown of row downregulates genes that are long-range targets of BEAF-32 and bound indirectly by ROW (without binding motif). Analyses of high-throughput chromosome conformation capture (Hi-C) data reveal long-range interactions between promoters of housekeeping genes bound directly by ROW and promoters of developmental genes bound indirectly by ROW. Thus, our results show cooperation between BEAF-32 and the ROW complex, including HP1 proteins, to regulate the transcription of developmental and inducible genes through long-range interactions.
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Affiliation(s)
- Neta Herman
- Department of Genetics, The Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | | | - Sagiv Shifman
- Department of Genetics, The Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
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11
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Pokusaeva VO, Diez AR, Espinar L, Pérez AT, Filion GJ. Strand asymmetry influences mismatch resolution during a single-strand annealing. Genome Biol 2022; 23:93. [PMID: 35414014 PMCID: PMC9001825 DOI: 10.1186/s13059-022-02665-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/30/2022] [Indexed: 02/08/2023] Open
Abstract
Background Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the contributions of DNA repair from those of DNA damage. Results Here, we develop a genome-wide assay whereby the same DNA lesion is repaired in different genomic contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated if the break is repaired through single-strand annealing. The resolution of the mismatch showed a 60–80% bias in favor of the strand with the longest 3′ flap. The location of the lesion in the genome and the type of mismatch had little influence on the bias. Instead, we observe a complete reversal of the bias when the longest 3′ flap is moved to the opposite strand by changing the position of the double-strand break in the reporter. Conclusions These results suggest that the processing of the double-strand break has a major influence on the repair of mismatches during a single-strand annealing. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02665-3.
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Affiliation(s)
- Victoria O Pokusaeva
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Present Address: Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Aránzazu Rosado Diez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Present Address: H12O-CNIO Lung Cancer Clinical Research Unit, i + 12 Research Institute, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Lorena Espinar
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Albert Torelló Pérez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Guillaume J Filion
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,University Pompeu Fabra (UPF), Barcelona, Spain. .,Present Address: Department Biological Sciences, University of Toronto Scarborough, Toronto, Canada.
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12
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Chathoth KT, Mikheeva LA, Crevel G, Wolfe JC, Hunter I, Beckett-Doyle S, Cotterill S, Dai H, Harrison A, Zabet NR. The role of insulators and transcription in 3D chromatin organization of flies. Genome Res 2022; 32:682-698. [PMID: 35354608 PMCID: PMC8997359 DOI: 10.1101/gr.275809.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/17/2022] [Indexed: 11/25/2022]
Abstract
The DNA in many organisms, including humans, is shown to be organized in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here, we show that depletion of BEAF-32, Cp190, Chro, and Dref leads to changes in TAD organization and chromatin loops. Their depletion predominantly affects TAD borders located in regions moderately enriched in repressive modifications and depleted in active ones, whereas TAD borders located in euchromatin are resilient to these knockdowns. Furthermore, transcriptomic data has revealed hundreds of genes displaying differential expression in these knockdowns and showed that the majority of differentially expressed genes are located within reorganized TADs. Our work identifies a novel and functional role for architectural proteins at TAD borders in Drosophila and a link between TAD reorganization and subsequent changes in gene expression.
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Affiliation(s)
- Keerthi T Chathoth
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Liudmila A Mikheeva
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom.,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom.,Department of Mathematical Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Gilles Crevel
- Department Basic Medical Sciences, St. Georges University London, London SW17 0RE, United Kingdom
| | - Jareth C Wolfe
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom.,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom.,School of Computer Science and Electronic Engineering, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Ioni Hunter
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Saskia Beckett-Doyle
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Sue Cotterill
- Department Basic Medical Sciences, St. Georges University London, London SW17 0RE, United Kingdom
| | - Hongsheng Dai
- Department of Mathematical Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Andrew Harrison
- Department of Mathematical Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom.,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom
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13
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Ilyin AA, Kononkova AD, Golova AV, Shloma VV, Olenkina O, Nenasheva V, Abramov Y, Kotov AA, Maksimov D, Laktionov P, Pindyurin A, Galitsyna A, Ulianov S, Khrameeva E, Gelfand M, Belyakin S, Razin S, Shevelyov Y. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3203-3225. [PMID: 35166842 PMCID: PMC8989536 DOI: 10.1093/nar/gkac109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis – in bamΔ86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters’ detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.
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Affiliation(s)
| | | | | | | | | | - Valentina V Nenasheva
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Yuri A Abramov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Alexei A Kotov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Daniil A Maksimov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Petr P Laktionov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ekaterina E Khrameeva
- Correspondence may also be addressed to Ekaterina Khrameeva. Tel: +7 495 2801481; Fax: +7 495 2801481;
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Stepan N Belyakin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Yuri Y Shevelyov
- To whom correspondence should be addressed. Tel: +7 499 1960809; Fax: +7 499 1960221;
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14
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Hong CKY, Cohen BA. Genomic environments scale the activities of diverse core promoters. Genome Res 2022; 32:85-96. [PMID: 34961747 PMCID: PMC8744677 DOI: 10.1101/gr.276025.121] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/15/2021] [Indexed: 11/24/2022]
Abstract
A classical model of gene regulation is that enhancers provide specificity whereas core promoters provide a modular site for the assembly of the basal transcriptional machinery. However, examples of core promoter specificity have led to an alternate hypothesis in which specificity is achieved by core promoters with different sequence motifs that respond differently to genomic environments containing different enhancers and chromatin landscapes. To distinguish between these models, we measured the activities of hundreds of diverse core promoters in four different genomic locations and, in a complementary experiment, six different core promoters at thousands of locations across the genome. Although genomic locations had large effects on expression, the intrinsic activities of different classes of promoters were preserved across genomic locations, suggesting that core promoters are modular regulatory elements whose activities are independently scaled up or down by different genomic locations. This scaling of promoter activities is nonlinear and depends on the genomic location and the strength of the core promoter. Our results support the classical model of regulation in which diverse core promoter motifs set the intrinsic strengths of core promoters, which are then amplified or dampened by the activities of their genomic environments.
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Affiliation(s)
- Clarice K Y Hong
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, Missouri 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, Missouri 63110, USA
| | - Barak A Cohen
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, Missouri 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, Missouri 63110, USA
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15
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Li L, Waymack R, Gad M, Wunderlich Z. Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo. Genetics 2021; 219:iyab154. [PMID: 34849867 PMCID: PMC8664596 DOI: 10.1093/genetics/iyab154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/12/2021] [Indexed: 11/13/2022] Open
Abstract
Proper development depends on precise spatiotemporal gene expression patterns. Most developmental genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical "sharp" developmental promoter, while the other resembles a "broad" promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter, indicating that promoters provide both redundancy and specificity. By analyzing the reporter dynamics, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the combination of promoter and enhancer. Using locus-sized reporters, we discovered that enhancers with no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is due both to enhancer preference and a need for redundancy and that "broad" promoters with dispersed transcription start sites are common among developmental genes. They also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where other variables shape a gene's overall expression pattern.
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Affiliation(s)
- Lily Li
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel Waymack
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mario Gad
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
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16
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Santiago-Algarra D, Souaid C, Singh H, Dao LTM, Hussain S, Medina-Rivera A, Ramirez-Navarro L, Castro-Mondragon JA, Sadouni N, Charbonnier G, Spicuglia S. Epromoters function as a hub to recruit key transcription factors required for the inflammatory response. Nat Commun 2021; 12:6660. [PMID: 34795220 PMCID: PMC8602369 DOI: 10.1038/s41467-021-26861-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
Gene expression is controlled by the involvement of gene-proximal (promoters) and distal (enhancers) regulatory elements. Our previous results demonstrated that a subset of gene promoters, termed Epromoters, work as bona fide enhancers and regulate distal gene expression. Here, we hypothesized that Epromoters play a key role in the coordination of rapid gene induction during the inflammatory response. Using a high-throughput reporter assay we explored the function of Epromoters in response to type I interferon. We find that clusters of IFNa-induced genes are frequently associated with Epromoters and that these regulatory elements preferentially recruit the STAT1/2 and IRF transcription factors and distally regulate the activation of interferon-response genes. Consistently, we identified and validated the involvement of Epromoter-containing clusters in the regulation of LPS-stimulated macrophages. Our findings suggest that Epromoters function as a local hub recruiting the key TFs required for coordinated regulation of gene clusters during the inflammatory response.
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Affiliation(s)
- David Santiago-Algarra
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Charbel Souaid
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Himanshu Singh
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Lan T M Dao
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Vinmec Research Institute of Stem cell and Gene technology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Saadat Hussain
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Lucia Ramirez-Navarro
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Jaime A Castro-Mondragon
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway
| | - Nori Sadouni
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Guillaume Charbonnier
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France.
- Equipe Labellisée Ligue Contre le Cancer, Paris, France.
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17
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Pavani G, Amendola M. Targeted Gene Delivery: Where to Land. Front Genome Ed 2021; 2:609650. [PMID: 34713234 PMCID: PMC8525409 DOI: 10.3389/fgeed.2020.609650] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-editing technologies have the potential to correct most genetic defects involved in blood disorders. In contrast to mutation-specific editing, targeted gene insertion can correct most of the mutations affecting the same gene with a single therapeutic strategy (gene replacement) or provide novel functions to edited cells (gene addition). Targeting a selected genomic harbor can reduce insertional mutagenesis risk, while enabling the exploitation of endogenous promoters, or selected chromatin contexts, to achieve specific transgene expression levels/patterns and the modulation of disease-modifier genes. In this review, we will discuss targeted gene insertion and the advantages and limitations of different genomic harbors currently under investigation for various gene therapy applications.
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Affiliation(s)
- Giulia Pavani
- INTEGRARE, UMR_S951, Genethon, Inserm, Univ Evry, Univ Paris-Saclay, Evry, France
| | - Mario Amendola
- INTEGRARE, UMR_S951, Genethon, Inserm, Univ Evry, Univ Paris-Saclay, Evry, France
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18
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Schep R, Brinkman EK, Leemans C, Vergara X, van der Weide RH, Morris B, van Schaik T, Manzo SG, Peric-Hupkes D, van den Berg J, Beijersbergen RL, Medema RH, van Steensel B. Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance. Mol Cell 2021; 81:2216-2230.e10. [PMID: 33848455 PMCID: PMC8153251 DOI: 10.1016/j.molcel.2021.03.032] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/23/2020] [Accepted: 03/19/2021] [Indexed: 01/01/2023]
Abstract
DNA double-strand break (DSB) repair is mediated by multiple pathways. It is thought that the local chromatin context affects the pathway choice, but the underlying principles are poorly understood. Using a multiplexed reporter assay in combination with Cas9 cutting, we systematically measure the relative activities of three DSB repair pathways as a function of chromatin context in >1,000 genomic locations. This reveals that non-homologous end-joining (NHEJ) is broadly biased toward euchromatin, while the contribution of microhomology-mediated end-joining (MMEJ) is higher in specific heterochromatin contexts. In H3K27me3-marked heterochromatin, inhibition of the H3K27 methyltransferase EZH2 reverts the balance toward NHEJ. Single-stranded template repair (SSTR), often used for precise CRISPR editing, competes with MMEJ and is moderately linked to chromatin context. These results provide insight into the impact of chromatin on DSB repair pathway balance and guidance for the design of Cas9-mediated genome editing experiments.
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Affiliation(s)
- Ruben Schep
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Eva K Brinkman
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Christ Leemans
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Xabier Vergara
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Robin H van der Weide
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Robotics Screening Center, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Tom van Schaik
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Stefano G Manzo
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Daniel Peric-Hupkes
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Jeroen van den Berg
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Robotics Screening Center, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - René H Medema
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
| | - Bas van Steensel
- Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Department of Cell Biology, Erasmus University Medical Centre, 3015 CN, Rotterdam, the Netherlands.
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19
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Zhu I, Song W, Ovcharenko I, Landsman D. A model of active transcription hubs that unifies the roles of active promoters and enhancers. Nucleic Acids Res 2021; 49:4493-4505. [PMID: 33872375 PMCID: PMC8096258 DOI: 10.1093/nar/gkab235] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 12/31/2022] Open
Abstract
An essential questions of gene regulation is how large number of enhancers and promoters organize into gene regulatory loops. Using transcription-factor binding enrichment as an indicator of enhancer strength, we identified a portion of H3K27ac peaks as potentially strong enhancers and found a universal pattern of promoter and enhancer distribution: At actively transcribed regions of length of ∼200-300 kb, the numbers of active promoters and enhancers are inversely related. Enhancer clusters are associated with isolated active promoters, regardless of the gene's cell-type specificity. As the number of nearby active promoters increases, the number of enhancers decreases. At regions where multiple active genes are closely located, there are few distant enhancers. With Hi-C analysis, we demonstrate that the interactions among the regulatory elements (active promoters and enhancers) occur predominantly in clusters and multiway among linearly close elements and the distance between adjacent elements shows a preference of ∼30 kb. We propose a simple rule of spatial organization of active promoters and enhancers: Gene transcriptions and regulations mainly occur at local active transcription hubs contributed dynamically by multiple elements from linearly close enhancers and/or active promoters. The hub model can be represented with a flower-shaped structure and implies an enhancer-like role of active promoters.
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Affiliation(s)
- Iris Zhu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Ovcharenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
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20
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Floc'hlay S, Wong ES, Zhao B, Viales RR, Thomas-Chollier M, Thieffry D, Garfield DA, Furlong EEM. Cis-acting variation is common across regulatory layers but is often buffered during embryonic development. Genome Res 2021; 31:211-224. [PMID: 33310749 PMCID: PMC7849415 DOI: 10.1101/gr.266338.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Precise patterns of gene expression are driven by interactions between transcription factors, regulatory DNA sequences, and chromatin. How DNA mutations affecting any one of these regulatory "layers" are buffered or propagated to gene expression remains unclear. To address this, we quantified allele-specific changes in chromatin accessibility, histone modifications, and gene expression in F1 embryos generated from eight Drosophila crosses at three embryonic stages, yielding a comprehensive data set of 240 samples spanning multiple regulatory layers. Genetic variation (allelic imbalance) impacts gene expression more frequently than chromatin features, with metabolic and environmental response genes being most often affected. Allelic imbalance in cis-regulatory elements (enhancers) is common and highly heritable, yet its functional impact does not generally propagate to gene expression. When it does, genetic variation impacts RNA levels through two alternative mechanisms involving either H3K4me3 or chromatin accessibility and H3K27ac. Changes in RNA are more predictive of variation in H3K4me3 than vice versa, suggesting a role for H3K4me3 downstream from transcription. The impact of a substantial proportion of genetic variation is consistent across embryonic stages, with 50% of allelic imbalanced features at one stage being also imbalanced at subsequent developmental stages. Crucially, buffering, as well as the magnitude and evolutionary impact of genetic variants, is influenced by regulatory complexity (i.e., number of enhancers regulating a gene), with transcription factors being most robust to cis-acting, but most influenced by trans-acting, variation.
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Affiliation(s)
- Swann Floc'hlay
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Emily S Wong
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales 2052, Australia
| | - Bingqing Zhao
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Rebecca R Viales
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Morgane Thomas-Chollier
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Denis Thieffry
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
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21
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Lewis SH, Ross L, Bain SA, Pahita E, Smith SA, Cordaux R, Miska EA, Lenhard B, Jiggins FM, Sarkies P. ------Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods. PLoS Genet 2020; 16:e1008864. [PMID: 32584820 PMCID: PMC7343188 DOI: 10.1371/journal.pgen.1008864] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/08/2020] [Accepted: 05/15/2020] [Indexed: 12/23/2022] Open
Abstract
Cytosine methylation is an ancient epigenetic modification yet its function and extent within genomes is highly variable across eukaryotes. In mammals, methylation controls transposable elements and regulates the promoters of genes. In insects, DNA methylation is generally restricted to a small subset of transcribed genes, with both intergenic regions and transposable elements (TEs) depleted of methylation. The evolutionary origin and the function of these methylation patterns are poorly understood. Here we characterise the evolution of DNA methylation across the arthropod phylum. While the common ancestor of the arthropods had low levels of TE methylation and did not methylate promoters, both of these functions have evolved independently in centipedes and mealybugs. In contrast, methylation of the exons of a subset of transcribed genes is ancestral and widely conserved across the phylum, but has been lost in specific lineages. A similar set of genes is methylated in all species that retained exon-enriched methylation. We show that these genes have characteristic patterns of expression correlating to broad transcription initiation sites and well-positioned nucleosomes, providing new insights into potential mechanisms driving methylation patterns over hundreds of millions of years.
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Affiliation(s)
- Samuel H. Lewis
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Laura Ross
- Institute of Evolutionary Biology, Edinburgh, United Kingdom
| | - Stevie A. Bain
- Institute of Evolutionary Biology, Edinburgh, United Kingdom
| | - Eleni Pahita
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Stephen A. Smith
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions Universite de Poitiers, France
| | - Eric A. Miska
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, United Kingdom
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
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22
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Zhang T, Pilko A, Wollman R. Loci specific epigenetic drug sensitivity. Nucleic Acids Res 2020; 48:4797-4810. [PMID: 32246716 PMCID: PMC7229858 DOI: 10.1093/nar/gkaa210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/10/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
Therapeutic targeting of epigenetic modulators offers a novel approach to the treatment of multiple diseases. The cellular consequences of chemical compounds that target epigenetic regulators (epi-drugs) are complex. Epi-drugs affect global cellular phenotypes and cause local changes to gene expression due to alteration of a gene chromatin environment. Despite increasing use in the clinic, the mechanisms responsible for cellular changes are unclear. Specifically, to what degree the effects are a result of cell-wide changes or disease related locus specific effects is unknown. Here we developed a platform to systematically and simultaneously investigate the sensitivity of epi-drugs at hundreds of genomic locations by combining DNA barcoding, unique split-pool encoding, and single cell expression measurements. Internal controls are used to isolate locus specific effects separately from any global consequences these drugs have. Using this platform we discovered wide-spread loci specific sensitivities to epi-drugs for three distinct epi-drugs that target histone deacetylase, DNA methylation and bromodomain proteins. By leveraging ENCODE data on chromatin modification, we identified features of chromatin environments that are most likely to be affected by epi-drugs. The measurements of loci specific epi-drugs sensitivities will pave the way to the development of targeted therapy for personalized medicine.
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Affiliation(s)
- Thanutra Zhang
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
| | - Anna Pilko
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
- Departments of Integrative Biology and Physiology and Chemistry and Biochemistry, University of California UCLA, CA, USA
| | - Roy Wollman
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
- Departments of Integrative Biology and Physiology and Chemistry and Biochemistry, University of California UCLA, CA, USA
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23
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King TD, Johnson JE, Bateman JR. Position Effects Influence Transvection in Drosophila melanogaster. Genetics 2019; 213:1289-1299. [PMID: 31611231 PMCID: PMC6893391 DOI: 10.1534/genetics.119.302583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/03/2019] [Indexed: 01/14/2023] Open
Abstract
Transvection is an epigenetic phenomenon wherein regulatory elements communicate between different chromosomes in trans, and is thereby dependent upon the three-dimensional organization of the genome. Transvection is best understood in Drosophila, where homologous chromosomes are closely paired in most somatic nuclei, although similar phenomena have been observed in other species. Previous data have supported that the Drosophila genome is generally permissive to enhancer action in trans, a form of transvection where an enhancer on one homolog activates gene expression from a promoter on a paired homolog. However, the capacity of different genomic positions to influence the quantitative output of transvection has yet to be addressed. To investigate this question, we employed a transgenic system that assesses and compares enhancer action in cis and in trans at defined chromosomal locations. Using the strong synthetic eye-specific enhancer GMR, we show that loci supporting strong cis-expression tend to support robust enhancer action in trans, whereas locations with weaker cis-expression show reduced transvection in a fluorescent reporter assay. Our subsequent analysis is consistent with a model wherein the chromatin state of the transgenic insertion site is a primary determinant of the degree to which enhancer action in trans will be supported, whereas other factors such as locus-specific variation in somatic homolog pairing are of less importance in influencing position effects on transvection.
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Affiliation(s)
- Thomas D King
- Biology Department, Bowdoin College, Brunswick, Maine 04011
| | | | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, Maine 04011
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24
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Rennie S, Dalby M, Lloret-Llinares M, Bakoulis S, Dalager Vaagensø C, Heick Jensen T, Andersson R. Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. Nucleic Acids Res 2019; 46:5455-5469. [PMID: 29659982 PMCID: PMC6009668 DOI: 10.1093/nar/gky244] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/22/2018] [Indexed: 12/19/2022] Open
Abstract
Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in Drosophila melanogaster. We find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed. We observe quantitative relationships between enhancer potential, expression level and core promoter strength, providing an explanation for indirectly related histone modifications that are reflecting expression levels. Lowly abundant unstable RNAs initiated from weak core promoters are key characteristics of gene-distal developmental enhancers, while the housekeeping enhancer strengths of gene promoters reflect their expression strengths. The seemingly separable layer of regulation by gene promoters with housekeeping enhancer potential is also indicated by chromatin interaction data. Our results suggest a unified promoter architecture of many D. melanogaster regulatory elements, that is universal across Metazoa, whose regulatory functions seem to be related to their core promoter elements.
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Affiliation(s)
- Sarah Rennie
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Maria Dalby
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Stylianos Bakoulis
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Christian Dalager Vaagensø
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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25
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Parey E, Crombach A. Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. Genome Biol Evol 2019; 11:660-677. [PMID: 30689829 PMCID: PMC6411481 DOI: 10.1093/gbe/evz019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2019] [Indexed: 12/30/2022] Open
Abstract
In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin-associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. These five types were given color names in reference to the Greek word chroma. They are defined by distinct but overlapping combinations of proteins and differ in biological and biochemical properties, including transcriptional activity, replication timing, and histone modifications. In this work, we assess the evolutionary relationships of chromatin-associated proteins and present an integrated view of the evolution and conservation of the fruit fly Drosophila melanogaster chromatin landscape. We combine homology prediction across a wide range of species with gene age inference methods to determine the origin of each chromatin-associated protein. This provides insight into the evolution of the different chromatin types. Our results indicate that for the euchromatic types, YELLOW and RED, young associated proteins are more specialized than old ones; and for genes found in either chromatin type, intron/exon structure is lineage-specific. Next, we provide evidence that a subset of GREEN-associated proteins is involved in a centromere drive in D. melanogaster. Our results on BLUE chromatin support the hypothesis that the emergence of Polycomb Group proteins is linked to eukaryotic multicellularity. In light of these results, we discuss how the regulatory complexification of chromatin links to the origins of eukaryotic multicellularity.
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Affiliation(s)
- Elise Parey
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Anton Crombach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Inria, Antenne Lyon La Doua, Villeurbanne, France.,Université de Lyon, INSA-Lyon, LIRIS, UMR 5205, Villeurbanne, France
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26
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Transcription factors and 3D genome conformation in cell-fate decisions. Nature 2019; 569:345-354. [PMID: 31092938 DOI: 10.1038/s41586-019-1182-7] [Citation(s) in RCA: 290] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/19/2019] [Indexed: 12/31/2022]
Abstract
How cells adopt different identities has long fascinated biologists. Signal transduction in response to environmental cues results in the activation of transcription factors that determine the gene-expression program characteristic of each cell type. Technological advances in the study of 3D chromatin folding are bringing the role of genome conformation in transcriptional regulation to the fore. Characterizing this role of genome architecture has profound implications, not only for differentiation and development but also for diseases including developmental malformations and cancer. Here we review recent studies indicating that the interplay between transcription and genome conformation is a driving force for cell-fate decisions.
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27
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Leemans C, van der Zwalm MCH, Brueckner L, Comoglio F, van Schaik T, Pagie L, van Arensbergen J, van Steensel B. Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. Cell 2019; 177:852-864.e14. [PMID: 30982597 PMCID: PMC6506275 DOI: 10.1016/j.cell.2019.03.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/23/2019] [Accepted: 03/04/2019] [Indexed: 12/28/2022]
Abstract
It is largely unclear whether genes that are naturally embedded in lamina-associated domains (LADs) are inactive due to their chromatin environment or whether LADs are merely secondary to the lack of transcription. We show that hundreds of human promoters become active when moved from their native LAD position to a neutral context in the same cells, indicating that LADs form a repressive environment. Another set of promoters inside LADs is able to "escape" repression, although their transcription elongation is attenuated. By inserting reporters into thousands of genomic locations, we demonstrate that escaper promoters are intrinsically less sensitive to LAD repression. This is not simply explained by promoter strength but by the interplay between promoter sequence and local chromatin features that vary strongly across LADs. Enhancers also differ in their sensitivity to LAD chromatin. This work provides a general framework for the systematic understanding of gene regulation by repressive chromatin.
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Affiliation(s)
- Christ Leemans
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marloes C H van der Zwalm
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Laura Brueckner
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Federico Comoglio
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tom van Schaik
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ludo Pagie
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joris van Arensbergen
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands.
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28
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Vizcaya-Molina E, Klein CC, Serras F, Mishra RK, Guigó R, Corominas M. Damage-responsive elements in Drosophila regeneration. Genome Res 2018; 28:1852-1866. [PMID: 30459214 PMCID: PMC6280756 DOI: 10.1101/gr.233098.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/10/2018] [Indexed: 12/21/2022]
Abstract
One of the most important questions in regenerative biology is to unveil how and when genes change expression and trigger regeneration programs. The resetting of gene expression patterns during response to injury is governed by coordinated actions of genomic regions that control the activity of multiple sequence-specific DNA binding proteins. Using genome-wide approaches to interrogate chromatin function, we here identify the elements that regulate tissue recovery in Drosophila imaginal discs, which show a high regenerative capacity after genetically induced cell death. Our findings indicate there is global coregulation of gene expression as well as a regeneration program driven by different types of regulatory elements. Novel enhancers acting exclusively within damaged tissue cooperate with enhancers co-opted from other tissues and other developmental stages, as well as with endogenous enhancers that show increased activity after injury. Together, these enhancers host binding sites for regulatory proteins that include a core set of conserved transcription factors that control regeneration across metazoans.
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Affiliation(s)
- Elena Vizcaya-Molina
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
| | - Cecilia C Klein
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona 08028, Catalonia, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Catalonia, Spain
| | - Florenci Serras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
| | - Rakesh K Mishra
- The Centre for Cellular and Molecular Biology (CCMB), Hyderabad 500007, India
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Catalonia, Spain
| | - Montserrat Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
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29
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Pindyurin AV, Ilyin AA, Ivankin AV, Tselebrovsky MV, Nenasheva VV, Mikhaleva EA, Pagie L, van Steensel B, Shevelyov YY. The large fraction of heterochromatin in Drosophila neurons is bound by both B-type lamin and HP1a. Epigenetics Chromatin 2018; 11:65. [PMID: 30384843 PMCID: PMC6211408 DOI: 10.1186/s13072-018-0235-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background In most mammalian cell lines, chromatin located at the nuclear periphery is represented by condensed heterochromatin, as evidenced by microscopy observations and DamID mapping of lamina-associated domains (LADs) enriched in dimethylated Lys9 of histone H3 (H3K9me2). However, in Kc167 cell culture, the only Drosophilla cell type where LADs have previously been mapped, they are neither H3K9me2-enriched nor overlapped with the domains of heterochromatin protein 1a (HP1a). Results Here, using cell type-specific DamID we mapped genome-wide LADs, HP1a and Polycomb (Pc) domains from the central brain, Repo-positive glia, Elav-positive neurons and the fat body of Drosophila third instar larvae. Strikingly, contrary to Kc167 cells of embryonic origin, in neurons and, to a lesser extent, in glia and the fat body, HP1a domains appear to overlap strongly with LADs in both the chromosome arms and pericentromeric regions. Accordingly, centromeres reside closer to the nuclear lamina in neurons than in Kc167 cells. As expected, active gene promoters are mostly not present in LADs, HP1a and Pc domains. These domains are occupied by silent or weakly expressed genes with genes residing in the HP1a-bound LADs expressed at the lowest level. Conclusions In various differentiated Drosophila cell types, we discovered the existence of peripheral heterochromatin, similar to that observed in mammals. Our findings support the model that peripheral heterochromatin matures enhancing the repression of unwanted genes as cells terminally differentiate. Electronic supplementary material The online version of this article (10.1186/s13072-018-0235-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexey V Pindyurin
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands. .,Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, 630090. .,Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, Novosibirsk, Russia, 630090.
| | - Artem A Ilyin
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182
| | - Anton V Ivankin
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, 630090
| | - Mikhail V Tselebrovsky
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182.,QC Biochemistry Lab, Yaroslavl Pharmaceutical Complex for Production of Finished Dosage Forms, R-Pharm Group, Yaroslavl, Russia, 150061
| | - Valentina V Nenasheva
- Department of Viral and Cellular Molecular Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182
| | - Elena A Mikhaleva
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands.,Department of Cell Biology, Erasmus University Medical Center, 3015 GE, Rotterdam, The Netherlands
| | - Yuri Y Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182.
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30
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Nicolas D, Zoller B, Suter DM, Naef F. Modulation of transcriptional burst frequency by histone acetylation. Proc Natl Acad Sci U S A 2018; 115:7153-7158. [PMID: 29915087 PMCID: PMC6142243 DOI: 10.1073/pnas.1722330115] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many mammalian genes are transcribed during short bursts of variable frequencies and sizes that substantially contribute to cell-to-cell variability. However, which molecular mechanisms determine bursting properties remains unclear. To probe putative mechanisms, we combined temporal analysis of transcription along the circadian cycle with multiple genomic reporter integrations, using both short-lived luciferase live microscopy and single-molecule RNA-FISH. Using the Bmal1 circadian promoter as our model, we observed that rhythmic transcription resulted predominantly from variations in burst frequency, while the genomic position changed the burst size. Thus, burst frequency and size independently modulated Bmal1 transcription. We then found that promoter histone-acetylation level covaried with burst frequency, being greatest at peak expression and lowest at trough expression, while remaining unaffected by the genomic location. In addition, specific deletions of ROR-responsive elements led to constitutively elevated histone acetylation and burst frequency. We then investigated the suggested link between histone acetylation and burst frequency by dCas9p300-targeted modulation of histone acetylation, revealing that acetylation levels influence burst frequency more than burst size. The correlation between acetylation levels at the promoter and burst frequency was also observed in endogenous circadian genes and in embryonic stem cell fate genes. Thus, our data suggest that histone acetylation-mediated control of transcription burst frequency is a common mechanism to control mammalian gene expression.
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Affiliation(s)
- Damien Nicolas
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Benjamin Zoller
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - David M Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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31
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Dao LTM, Spicuglia S. Transcriptional regulation by promoters with enhancer function. Transcription 2018; 9:307-314. [PMID: 29889606 PMCID: PMC6150634 DOI: 10.1080/21541264.2018.1486150] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/01/2018] [Indexed: 12/31/2022] Open
Abstract
Promoters with enhancer activity have been described recently. In this point of view, we will discuss current findings highlighting the commonality of this type of regulatory elements, their genetic and epigenetic characteristics, their potential biological roles in the regulation of gene expression and the underlining molecular mechanisms. ABBREVIATIONS TSS: transcription start site; IFN: interferon; STARR-seq: Self-Transcribing Active Regulatory Region sequencing; MPRA: Massively Parallel Reporter Assay; ChIP: chromatin immunoprecipitation; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; lncRNA: long non-coding RNA.
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Affiliation(s)
- Lan T. M. Dao
- Vinmec Research Institute of Stem cell and Gene technology (VRISG), Hanoi, Vietnam
| | - Salvatore Spicuglia
- Aix-Marseille University, INSERM, TAGC, UMR, Marseille, France
- Equipe Labéllisée Ligue Contre le Cancer
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32
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Cortini R, Filion GJ. Theoretical principles of transcription factor traffic on folded chromatin. Nat Commun 2018; 9:1740. [PMID: 29712907 PMCID: PMC5928121 DOI: 10.1038/s41467-018-04130-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/05/2018] [Indexed: 01/02/2023] Open
Abstract
All organisms regulate transcription of their genes. To understand this process, a complete understanding of how transcription factors find their targets in cellular nuclei is essential. The DNA sequence and other variables are known to influence this binding, but the distribution of transcription factor binding patterns remains mostly unexplained in metazoan genomes. Here, we investigate the role of chromosome conformation in the trajectories of transcription factors. Using molecular dynamics simulations, we uncover the principles of their diffusion on chromatin. Chromosome contacts play a conflicting role: at low density they enhance transcription factor traffic, but at high density they lower it by volume exclusion. Consistently, we observe that in human cells, highly occupied targets, where protein binding is promiscuous, are found at sites engaged in chromosome loops within uncompacted chromatin. In summary, we provide a framework for understanding the search trajectories of transcription factors, highlighting the key contribution of genome conformation. How transcription factors find their targets in vivo is still poorly understood. Here the authors use molecular dynamics simulations to investigate how transcription factors diffuse on chromatin, providing a theoretical framework for understanding the key role of genome conformation in this process.
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Affiliation(s)
- Ruggero Cortini
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universidad Pompeu Fabra (UPF), 08003, Barcelona, Spain.
| | - Guillaume J Filion
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universidad Pompeu Fabra (UPF), 08003, Barcelona, Spain.
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33
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Medina-Rivera A, Santiago-Algarra D, Puthier D, Spicuglia S. Widespread Enhancer Activity from Core Promoters. Trends Biochem Sci 2018; 43:452-468. [PMID: 29673772 DOI: 10.1016/j.tibs.2018.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 01/04/2023]
Abstract
Gene expression in higher eukaryotes is precisely regulated in time and space through the interplay between promoters and gene-distal regulatory regions, known as enhancers. The original definition of enhancers implies the ability to activate gene expression remotely, while promoters entail the capability to locally induce gene expression. Despite the conventional distinction between them, promoters and enhancers share many genomic and epigenomic features. One intriguing finding in the gene regulation field comes from the observation that many core promoter regions display enhancer activity. Recent high-throughput reporter assays along with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-related approaches have indicated that this phenomenon is common and might have a strong impact on our global understanding of genome organisation and gene expression regulation.
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Affiliation(s)
- Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - David Santiago-Algarra
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France; Equipe Labéllisée, Ligue Contre le Cancer, Paris, France
| | - Denis Puthier
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France; Equipe Labéllisée, Ligue Contre le Cancer, Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France; Equipe Labéllisée, Ligue Contre le Cancer, Paris, France.
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Lioy VS, Cournac A, Marbouty M, Duigou S, Mozziconacci J, Espéli O, Boccard F, Koszul R. Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins. Cell 2018; 172:771-783.e18. [PMID: 29358050 DOI: 10.1016/j.cell.2017.12.027] [Citation(s) in RCA: 207] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/02/2017] [Accepted: 12/19/2017] [Indexed: 12/26/2022]
Abstract
As in eukaryotes, bacterial genomes are not randomly folded. Bacterial genetic information is generally carried on a circular chromosome with a single origin of replication from which two replication forks proceed bidirectionally toward the opposite terminus region. Here, we investigate the higher-order architecture of the Escherichia coli genome, showing its partition into two structurally distinct entities by a complex and intertwined network of contacts: the replication terminus (ter) region and the rest of the chromosome. Outside of ter, the condensin MukBEF and the ubiquitous nucleoid-associated protein (NAP) HU promote DNA contacts in the megabase range. Within ter, the MatP protein prevents MukBEF activity, and contacts are restricted to ∼280 kb, creating a domain with distinct structural properties. We also show how other NAPs contribute to nucleoid organization, such as H-NS, which restricts short-range interactions. Combined, these results reveal the contributions of major evolutionarily conserved proteins in a bacterial chromosome organization.
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Affiliation(s)
- Virginia S Lioy
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Axel Cournac
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France
| | - Martial Marbouty
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France
| | - Stéphane Duigou
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Julien Mozziconacci
- Sorbonne Universités, Laboratoire de Physique Théorique de la Matière Condensée, UMR 7600, Université Pierre et Marie Curie, 75005 Paris, France
| | - Olivier Espéli
- Centre Interdisciplinaire de Recherche en Biologie, Collège de France, UMR-CNRS 7241, INSERM U1050, Paris, France
| | - Frédéric Boccard
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
| | - Romain Koszul
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France.
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35
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Abstract
Promoters and enhancers have long been regarded as distinct elements, a notion that has been challenged more recently. Two new studies now identify promoters that function as long-range enhancers in vivo to regulate the transcription of distal genes.
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Affiliation(s)
- Rui R Catarino
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Christoph Neumayr
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
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36
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Schauer T, Ghavi‐Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong EEM, Becker PB. Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. EMBO Rep 2017; 18:1854-1868. [PMID: 28794204 PMCID: PMC5623837 DOI: 10.15252/embr.201744292] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 11/09/2022] Open
Abstract
X chromosome dosage compensation in Drosophila requires chromosome-wide coordination of gene activation. The male-specific lethal dosage compensation complex (DCC) identifies and binds to X-chromosomal high-affinity sites (HAS) from which it boosts transcription. A sub-class of HAS, PionX sites, represent first contacts on the X. Here, we explored the chromosomal interactions of representative PionX sites by high-resolution 4C and determined the global chromosome conformation by Hi-C in sex-sorted embryos. Male and female X chromosomes display similar nuclear architecture, concordant with clustered, constitutively active genes. PionX sites, like HAS, are evenly distributed in the active compartment and engage in short- and long-range interactions beyond compartment boundaries. Long-range, inter-domain interactions between DCC binding sites are stronger in males, suggesting that the complex refines chromatin organization. By de novo induction of DCC in female cells, we monitored the extent of activation surrounding PionX sites. This revealed a remarkable range of DCC action not only in linear proximity, but also at megabase distance if close in space, suggesting that DCC profits from pre-existing chromosome folding to activate genes.
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Affiliation(s)
- Tamás Schauer
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
| | - Yad Ghavi‐Helm
- European Molecular Biology LaboratoryGenome Biology UnitHeidelbergGermany
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular BiologyIllkirchFrance
| | - Christian Albig
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
| | - Catherine Regnard
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
| | - Giacomo Cavalli
- Institute of Human GeneticsCNRSMontpellierFrance
- University of MontpellierMontpellierFrance
| | - Eileen EM Furlong
- European Molecular Biology LaboratoryGenome Biology UnitHeidelbergGermany
| | - Peter B Becker
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
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37
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Nikolaou C. Invisible cities: segregated domains in the yeast genome with distinct structural and functional attributes. Curr Genet 2017; 64:247-258. [PMID: 28780612 DOI: 10.1007/s00294-017-0731-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 02/07/2023]
Abstract
Recent advances in our understanding of the three-dimensional organization of the eukaryotic nucleus have rendered the spatial distribution of genes increasingly relevant. In a recent work (Tsochatzidou et al., Nucleic Acids Res 45:5818-5828, 2017), we proposed the existence of a functional compartmentalization of the yeast genome according to which, genes occupying the chromosomal regions at the nuclear periphery have distinct structural, functional and evolutionary characteristics compared to their centromeric-proximal counterparts. Around the same time, it was also shown that the genome of Saccharomyces cerevisiae is organized in topologically associated domains (TADs), which are largely associated with the replication timing. In this work, we proceed to investigate whether such units of three-dimensional genomic organization can be linked to transcriptional activity as a driving force for the shaping of genomic architecture. Through the application of a simple boundary-calling criterion in genome-wide 3C data, we define ~100 TAD-like domains which can be clustered in six different classes with radically different nucleosomal organizations, significant variations in transcription factor binding and uneven chromosomal distribution. Approximately ~20% of the genome is found to be confined in regions with "closed" chromatin structure around gene promoters. Most interestingly, we find both "open" and "closed" regions to be segregated, in the sense that they tend to avoid inter-chromosomal interactions. Our data further enforce the notion of a marked compartmentalization of the yeast genome in isolated territories, with implications in its function and evolution.
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Affiliation(s)
- Christoforos Nikolaou
- Computational Genomics Group, Department of Biology, University of Crete, 70013, Herakleion, Greece.
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