1
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Kawasaki K, Fukaya T. Regulatory landscape of enhancer-mediated transcriptional activation. Trends Cell Biol 2024; 34:826-837. [PMID: 38355349 DOI: 10.1016/j.tcb.2024.01.008] [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: 10/31/2023] [Revised: 12/21/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Enhancers are noncoding regulatory elements that instruct spatial and temporal specificity of gene transcription in response to a variety of intrinsic and extrinsic signals during development. Although it has long been postulated that enhancers physically interact with target promoters through the formation of stable loops, recent studies have changed this static view: sequence-specific transcription factors (TFs) and coactivators are dynamically recruited to enhancers and assemble so-called transcription hubs. Dynamic assembly of transcription hubs appears to serve as a key scaffold to integrate regulatory information encoded by surrounding genome and biophysical properties of transcription machineries. In this review, we outline emerging new models of transcriptional regulation by enhancers and discuss future perspectives.
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Affiliation(s)
- Koji Kawasaki
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
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2
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Kim J, Wang H, Ercan S. Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558239. [PMID: 37786717 PMCID: PMC10541618 DOI: 10.1101/2023.09.18.558239] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
In mammals, cohesin and CTCF organize the 3D genome into topologically associated domains (TADs) to regulate communication between cis -regulatory elements. Many organisms, including S. cerevisiae , C. elegans , and A. thaliana contain cohesin but lack CTCF. Here, we used C. elegans to investigate the function of cohesin in 3D genome organization in the absence of CTCF. Using Hi-C data, we observe cohesin-dependent features called "fountains", which are also reported in zebrafish and mice. These are population average reflections of DNA loops originating from distinct genomic regions and are ∼20-40 kb in C. elegans . Hi-C analysis upon cohesin and WAPL depletion support the idea that cohesin is preferentially loaded at NIPBL occupied sites and loop extrudes in an effectively two-sided manner. ChIP-seq analyses show that cohesin translocation along the fountain trajectory depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C contact patterns at individual fountains suggest that cohesin processivity is unequal on each side, possibly due to collision with cohesin loaded from surrounding sites. The putative cohesin loading sites are closest to active enhancers and fountain strength is associated with transcription. Compared to mammals, average processivity of C. elegans cohesin is ∼10-fold shorter and NIPBL binding does not depend on cohesin. We propose that preferential loading and loop extrusion by cohesin is an evolutionarily conserved mechanism that regulates the 3D interactions of enhancers in animal genomes.
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3
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Lam JC, Aboreden NG, Midla SC, Wang S, Huang A, Keller CA, Giardine B, Henderson KA, Hardison RC, Zhang H, Blobel GA. YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle. Nat Genet 2024; 56:1938-1952. [PMID: 39210046 DOI: 10.1038/s41588-024-01871-y] [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: 11/10/2023] [Accepted: 07/16/2024] [Indexed: 09/04/2024]
Abstract
Few transcription factors have been examined for their direct roles in physically connecting enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells revealed its requirement for the maintenance of numerous enhancer-promoter loops, but not compartments or domains. Despite its reported ability to interact with cohesin, the formation of YY1-dependent enhancer-promoter loops does not involve stalling of cohesin-mediated loop extrusion. Integrating mitosis-to-G1-phase dynamics, we observed partial retention of YY1 on mitotic chromatin, predominantly at gene promoters, followed by rapid rebinding during mitotic exit, coinciding with enhancer-promoter loop establishment. YY1 degradation during the mitosis-to-G1-phase interval revealed a set of enhancer-promoter loops that require YY1 for establishment during G1-phase entry but not for maintenance in interphase, suggesting that cell cycle stage influences YY1's architectural function. Thus, as revealed here for YY1, chromatin architectural functions of transcription factors can vary in their interplay with CTCF and cohesin as well as by cell cycle stage.
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Affiliation(s)
- Jessica C Lam
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas G Aboreden
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susannah C Midla
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Siqing Wang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Genomics Research Incubator, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Kate A Henderson
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Ealo T, Sanchez-Gaya V, Respuela P, Muñoz-San Martín M, Martin-Batista E, Haro E, Rada-Iglesias A. Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition. Nat Commun 2024; 15:7258. [PMID: 39179577 PMCID: PMC11344162 DOI: 10.1038/s41467-024-51602-4] [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: 01/23/2024] [Accepted: 08/10/2024] [Indexed: 08/26/2024] Open
Abstract
The specificity of gene expression during development requires the insulation of regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed to clusters of CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow some physical crosstalk across regulatory domains, which is at odds with the specific and precise expression of developmental genes. Here we show that developmental genes and nearby clusters of CTCF sites cooperatively foster the robust insulation of regulatory domains. By genetically dissecting a couple of representative loci in mouse embryonic stem cells, we show that CTCF sites prevent undesirable enhancer-gene contacts (i.e. physical insulation), while developmental genes preferentially contribute to regulatory insulation through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into the insulation of regulatory domains, which in turn might help interpreting the pathological consequences of certain structural variants.
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Affiliation(s)
- Thais Ealo
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
| | - Victor Sanchez-Gaya
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain.
| | - Patricia Respuela
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
| | - María Muñoz-San Martín
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
- Service of Neurology, University Hospital Marqués de Valdecilla, Universidad de Cantabria and IDIVAL, Santander, Spain
| | | | - Endika Haro
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain.
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain.
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5
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Whitney PH, Lionnet T. The method in the madness: Transcriptional control from stochastic action at the single-molecule scale. Curr Opin Struct Biol 2024; 87:102873. [PMID: 38954990 PMCID: PMC11373363 DOI: 10.1016/j.sbi.2024.102873] [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: 01/12/2024] [Revised: 05/07/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024]
Abstract
Cell states result from the ordered activation of gene expression by transcription factors. Transcription factors face opposing design constraints: they need to be dynamic to trigger rapid cell state transitions, but also stable enough to maintain terminal cell identities indefinitely. Recent progress in live-cell single-molecule microscopy has helped define the biophysical principles underlying this paradox. Beyond transcription factor activity, single-molecule experiments have revealed that at nearly every level of transcription regulation, control emerges from multiple short-lived stochastic interactions, rather than deterministic, stable interactions typical of other biochemical pathways. This architecture generates consistent outcomes that can be rapidly choreographed. Here, we highlight recent results that demonstrate how order in transcription regulation emerges from the apparent molecular-scale chaos and discuss remaining conceptual challenges.
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Affiliation(s)
- Peter H Whitney
- Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA; Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Timothée Lionnet
- Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA; Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA.
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6
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Jensen CL, Chen LF, Swigut T, Crocker OJ, Yao D, Bassik MC, Ferrell JE, Boettiger AN, Wysocka J. Long range regulation of transcription scales with genomic distance in a gene specific manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604327. [PMID: 39071420 PMCID: PMC11275926 DOI: 10.1101/2024.07.19.604327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
While critical for tuning the timing and level of transcription, enhancer communication with distal promoters is not well understood. Here we bypass the need for sequence-specific transcription factors and recruit activators directly using CARGO-VPR, an approach for targeting dCas9-VPR using a multiplexed array of RNA guides. We show that this approach achieves effective activator recruitment to arbitrary genomic sites, even those inaccessible by single dCas9. We utilize CARGO-VPR across the Prdm8-Fgf5 locus in mESCs, where neither gene is expressed. We demonstrate that while activator recruitment to any tested region results in transcriptional induction of at least one gene, the expression level strongly depends on the genomic distance between the promoter and activator recruitment site. However, the expression-distance relationship for each gene scales distinctly in a manner not attributable to differences in 3D contact frequency, promoter DNA sequence or presence of the repressive chromatin marks at the locus.
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7
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Fu Y, Zhao T, Clark F, Nomikou S, Tsirigos A, Lionnet T. Connecting Chromatin Structures to Gene Regulation Using Dynamic Polymer Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.07.566032. [PMID: 37986912 PMCID: PMC10659377 DOI: 10.1101/2023.11.07.566032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The transfer of regulatory information between distal loci on chromatin is thought to involve physical proximity, but key biophysical features of these contacts remain unclear. For instance, it is unknown how close and for how long two loci need to be in order to productively interact. The main challenge is that it is currently impossible to measure chromatin dynamics with high spatiotemporal resolution at scale. Polymer simulations provide an accessible and rigorous way to test biophysical models of chromatin regulation, yet there is a lack of simple and general methods for extracting the values of model parameters. Here we adapt the Nelder-Mead simplex optimization algorithm to select the best polymer model matching a given Hi-C dataset, using the MYC locus as an example. The model's biophysical parameters predict a compartmental rearrangement of the MYC locus in leukemia, which we validate with single-cell measurements. Leveraging trajectories predicted by the model, we find that loci with similar Hi-C contact frequencies can exhibit widely different contact dynamics. Interestingly, the frequency of productive interactions between loci exhibits a non-linear relationship with their Hi-C contact frequency when we enforce a specific capture radius and contact duration. These observations are consistent with recent experimental observations and suggest that the dynamic ensemble of chromatin configurations, rather than average contact matrices, is required to fully predict productive long-range chromatin interactions.
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8
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Yang JH, Hansen AS. Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. Nat Rev Mol Cell Biol 2024; 25:574-591. [PMID: 38413840 DOI: 10.1038/s41580-024-00710-6] [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] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.
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Affiliation(s)
- Jin H Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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9
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Brandani GB, Gu C, Gopi S, Takada S. Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci. PNAS NEXUS 2024; 3:pgae226. [PMID: 38881841 PMCID: PMC11179106 DOI: 10.1093/pnasnexus/pgae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024]
Abstract
Chromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in orchestrating various genomic functions. To aid our understanding of the principles underlying chromatin organization, we introduce Hi-C metainference, a Bayesian approach that integrates Hi-C contact frequencies into multiscale prior models of chromatin. This approach combines both bottom-up (the physics-based prior) and top-down (the data-driven posterior) strategies to characterize the 3D organization of a target genomic locus. We first demonstrate the capability of this method to accurately reconstruct the structural ensemble and the dynamics of a system from contact information. We then apply the approach to investigate the Sox2, Pou5f1, and Nanog loci of mouse embryonic stem cells using a bottom-up chromatin model at 1 kb resolution. We observe that the studied loci are conformationally heterogeneous and organized as crumpled globules, favoring contacts between distant enhancers and promoters. Using nucleosome-resolution simulations, we then reveal how the Nanog gene is functionally organized across the multiple scales of chromatin. At the local level, we identify diverse tetranucleosome folding motifs with a characteristic distribution along the genome, predominantly open at cis-regulatory elements and compact in between. At the larger scale, we find that enhancer-promoter contacts are driven by the transient condensation of chromatin into compact domains stabilized by extensive internucleosome interactions. Overall, this work highlights the condensed, but dynamic nature of chromatin in vivo, contributing to a deeper understanding of gene structure-function relationships.
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Affiliation(s)
- Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Chenyang Gu
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Soundhararajan Gopi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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10
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Rengifo Rojas C, Cercy J, Perillous S, Gonthier-Guéret C, Montibus B, Maupetit-Méhouas S, Espinadel A, Dupré M, Hong CC, Hata K, Nakabayashi K, Plagge A, Bouschet T, Arnaud P, Vaillant I, Court F. Biallelic non-productive enhancer-promoter interactions precede imprinted expression of Kcnk9 during mouse neural commitment. HGG ADVANCES 2024; 5:100271. [PMID: 38297831 PMCID: PMC10869267 DOI: 10.1016/j.xhgg.2024.100271] [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: 10/17/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
It is only partially understood how constitutive allelic methylation at imprinting control regions (ICRs) interacts with other regulation levels to drive timely parental allele-specific expression along large imprinted domains. The Peg13-Kcnk9 domain is an imprinted domain with important brain functions. To gain insights into its regulation during neural commitment, we performed an integrative analysis of its allele-specific epigenetic, transcriptomic, and cis-spatial organization using a mouse stem cell-based corticogenesis model that recapitulates the control of imprinted gene expression during neurodevelopment. We found that, despite an allelic higher-order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, enhancer-Kcnk9 promoter contacts occurred on both alleles, although they were productive only on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side and suggests a more nuanced role for allelic CTCF binding at some ICRs.
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Affiliation(s)
- Cecilia Rengifo Rojas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jil Cercy
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sophie Perillous
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Céline Gonthier-Guéret
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bertille Montibus
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stéphanie Maupetit-Méhouas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Astrid Espinadel
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marylou Dupré
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan; Department of Human Molecular Genetics, Gunma University Graduate School of Medicine 3-39-22 Showa, Maebashi, Gunma 371-8511, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Antonius Plagge
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Philippe Arnaud
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Isabelle Vaillant
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Franck Court
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
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11
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Kim KL, Rahme GJ, Goel VY, El Farran CA, Hansen AS, Bernstein BE. Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation. Mol Cell 2024; 84:1365-1376.e7. [PMID: 38452764 PMCID: PMC10997458 DOI: 10.1016/j.molcel.2024.02.007] [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: 10/03/2023] [Revised: 01/03/2024] [Accepted: 02/08/2024] [Indexed: 03/09/2024]
Abstract
Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying structures and mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth factor (FGF) oncogenes but is disrupted by DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The boundary contains an array of CTCF sites that enforce adjacent TADs, one containing FGF genes and the other containing ANO1 and its putative enhancers, which are specifically active in GIST and its likely cell of origin. We show that coordinate disruption of four CTCF motifs in the boundary fuses the adjacent TADs, allows the ANO1 enhancer to contact FGF3, and causes its robust induction. High-resolution micro-C maps reveal specific contact between transcription initiation sites in the ANO1 enhancer and FGF3 promoter that quantitatively scales with FGF3 induction such that modest changes in contact frequency result in strong changes in expression, consistent with a causal relationship.
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Affiliation(s)
- Kyung Lock Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Gilbert J Rahme
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Viraat Y Goel
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Chadi A El Farran
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Anders S Hansen
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Bradley E Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA.
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12
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Chen Z, Snetkova V, Bower G, Jacinto S, Clock B, Dizehchi A, Barozzi I, Mannion BJ, Alcaina-Caro A, Lopez-Rios J, Dickel DE, Visel A, Pennacchio LA, Kvon EZ. Increased enhancer-promoter interactions during developmental enhancer activation in mammals. Nat Genet 2024; 56:675-685. [PMID: 38509385 PMCID: PMC11203181 DOI: 10.1038/s41588-024-01681-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.
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Affiliation(s)
- Zhuoxin Chen
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Valentina Snetkova
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grace Bower
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Atrin Dizehchi
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
- School of Health Sciences, Universidad Loyola Andalucía, Seville, Spain
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Octant, Inc, Emeryville, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA.
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13
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Liu R, Xu R, Yan S, Li P, Jia C, Sun H, Sheng K, Wang Y, Zhang Q, Guo J, Xin X, Li X, Guo D. Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells. Front Genet 2024; 15:1377238. [PMID: 38586584 PMCID: PMC10995239 DOI: 10.3389/fgene.2024.1377238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition and significance of the three-dimensional chromatin structure, summarize the technologies available for studying it, and describe the research progress on the chromatin spatial structure of dendritic cells, macrophages, T cells, B cells, and neutrophils.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Dianhao Guo
- School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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14
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Wang Z, Zhang Z, Luo S, Zhou T, Zhang J. Power-law behavior of transcriptional bursting regulated by enhancer-promoter communication. Genome Res 2024; 34:106-118. [PMID: 38171575 PMCID: PMC10903953 DOI: 10.1101/gr.278631.123] [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: 04/12/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Revealing how transcriptional bursting kinetics are genomically encoded is challenging because genome structures are stochastic at the organization level and are suggestively linked to gene transcription. To address this challenge, we develop a generic theoretical framework that integrates chromatin dynamics, enhancer-promoter (E-P) communication, and gene-state switching to study transcriptional bursting. The theory predicts that power law can be a general rule to quantitatively describe bursting modulations by E-P spatial communication. Specifically, burst frequency and burst size are up-regulated by E-P communication strength, following power laws with positive exponents. Analysis of the scaling exponents further reveals that burst frequency is preferentially regulated. Bursting kinetics are down-regulated by E-P genomic distance with negative power-law exponents, and this negative modulation desensitizes at large distances. The mutual information between burst frequency (or burst size) and E-P spatial distance further reveals essential characteristics of the information transfer from E-P communication to transcriptional bursting kinetics. These findings, which are in agreement with experimental observations, not only reveal fundamental principles of E-P communication in transcriptional bursting but also are essential for understanding cellular decision-making.
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Affiliation(s)
- Zihao Wang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Zhenquan Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Songhao Luo
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China;
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jiajun Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China;
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
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15
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Doughty BR, Hinks MM, Schaepe JM, Marinov GK, Thurm AR, Rios-Martinez C, Parks BE, Tan Y, Marklund E, Dubocanin D, Bintu L, Greenleaf WJ. Single-molecule chromatin configurations link transcription factor binding to expression in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578660. [PMID: 38352517 PMCID: PMC10862896 DOI: 10.1101/2024.02.02.578660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state, and gene expression levels remain opaque. We applied single-molecule footprinting (SMF) to measure the simultaneous occupancy of TFs, nucleosomes, and components of the transcription machinery on engineered enhancer/promoter constructs with variable numbers of TF binding sites for both a synthetic and an endogenous TF. We find that activation domains enhance a TF's capacity to compete with nucleosomes for binding to DNA in a BAF-dependent manner, TF binding on nucleosome-free DNA is consistent with independent binding between TFs, and average TF occupancy linearly contributes to promoter activation rates. We also decompose TF strength into separable binding and activation terms, which can be tuned and perturbed independently. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the binding microstates observed at the enhancer and subsequent time-dependent gene expression. This work provides a template for quantitative dissection of distinct contributors to gene activation, including the activity of chromatin remodelers, TF activation domains, chromatin acetylation, TF concentration, TF binding affinity, and TF binding site configuration.
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Affiliation(s)
| | - Michaela M Hinks
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Julia M Schaepe
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Georgi K Marinov
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Abby R Thurm
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
| | | | - Benjamin E Parks
- Computer Science Department, Stanford University, Stanford, CA 94305, USA
| | - Yingxuan Tan
- Computer Science Department, Stanford University, Stanford, CA 94305, USA
| | - Emil Marklund
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Danilo Dubocanin
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Lacramioara Bintu
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - William J Greenleaf
- Genetics Department, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94205, USA
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16
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Hung TC, Kingsley DM, Boettiger AN. Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. Nat Genet 2024; 56:306-314. [PMID: 38238628 DOI: 10.1038/s41588-023-01641-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/06/2023] [Indexed: 02/15/2024]
Abstract
Although promoters and their enhancers are frequently contained within a topologically associating domain (TAD), some developmentally important genes have their promoter and enhancers within different TADs. Hypotheses about molecular mechanisms enabling cross-TAD interactions remain to be assessed. To test these hypotheses, we used optical reconstruction of chromatin architecture to characterize the conformations of the Pitx1 locus on single chromosomes in developing mouse limbs. Our data support a model in which neighboring boundaries are stacked as a result of loop extrusion, bringing boundary-proximal cis-elements into contact. This stacking interaction also contributes to the appearance of architectural stripes in the population average maps. Through molecular dynamics simulations, we found that increasing boundary strengths facilitates the formation of the stacked boundary conformation, counter-intuitively facilitating border bypass. This work provides a revised view of the TAD borders' function, both facilitating and preventing cis-regulatory interactions, and introduces a framework to distinguish border-crossing from border-respecting enhancer-promoter pairs.
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Affiliation(s)
- Tzu-Chiao Hung
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Hariprakash JM, Salviato E, La Mastra F, Sebestyén E, Tagliaferri I, Silva RS, Lucini F, Farina L, Cinquanta M, Rancati I, Riboni M, Minardi SP, Roz L, Gorini F, Lanzuolo C, Casola S, Ferrari F. Leveraging Tissue-Specific Enhancer-Target Gene Regulatory Networks Identifies Enhancer Somatic Mutations That Functionally Impact Lung Cancer. Cancer Res 2024; 84:133-153. [PMID: 37855660 PMCID: PMC10758689 DOI: 10.1158/0008-5472.can-23-1129] [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: 04/13/2023] [Revised: 08/29/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with the genomic sequence. Enhancer alterations have been associated with various pathological conditions, including cancer. However, the identification and characterization of somatic mutations in noncoding regulatory regions with a functional effect on tumorigenesis and prognosis remain a major challenge. Here, we present a strategy for detecting and characterizing enhancer mutations in a genome-wide analysis of patient cohorts, across three lung cancer subtypes. Lung tissue-specific enhancers were defined by integrating experimental data and public epigenomic profiles, and the genome-wide enhancer-target gene regulatory network of lung cells was constructed by integrating chromatin three-dimensional architecture data. Lung cancers possessed a similar mutation burden at tissue-specific enhancers and exons but with differences in their mutation signatures. Functionally relevant alterations were prioritized on the basis of the pathway-level integration of the effect of a mutation and the frequency of mutations on individual enhancers. The genes enriched for mutated enhancers converged on the regulation of key biological processes and pathways relevant to tumor biology. Recurrent mutations in individual enhancers also affected the expression of target genes, with potential relevance for patient prognosis. Together, these findings show that noncoding regulatory mutations have a potential relevance for cancer pathogenesis and can be exploited for patient classification. SIGNIFICANCE Mapping enhancer-target gene regulatory interactions and analyzing enhancer mutations at the level of their target genes and pathways reveal convergence of recurrent enhancer mutations on biological processes involved in tumorigenesis and prognosis.
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Affiliation(s)
| | - Elisa Salviato
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Endre Sebestyén
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Federica Lucini
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Lorenzo Farina
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Ilaria Rancati
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Luca Roz
- Fondazione IRCCS—Istituto Nazionale Tumori, Milan, Italy
| | - Francesca Gorini
- INGM, National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi,” Milan, Italy
| | - Chiara Lanzuolo
- INGM, National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi,” Milan, Italy
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy
| | - Stefano Casola
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Francesco Ferrari
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza,” National Research Council (IGM-CNR), Pavia, Italy
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18
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Wang Z, Luo S, Zhang Z, Zhou T, Zhang J. 4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction. PLoS Comput Biol 2023; 19:e1011722. [PMID: 38109463 PMCID: PMC10760824 DOI: 10.1371/journal.pcbi.1011722] [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: 04/14/2023] [Revised: 01/02/2024] [Accepted: 11/28/2023] [Indexed: 12/20/2023] Open
Abstract
Recent experimental evidence strongly supports that three-dimensional (3D) long-range enhancer-promoter (E-P) interactions have important influences on gene-expression dynamics, but it is unclear how the interaction information is translated into gene expression over time (4D). To address this question, we developed a general theoretical framework (named as a 4D nucleome equation), which integrates E-P interactions on chromatin and biochemical reactions of gene transcription. With this equation, we first present the distribution of mRNA counts as a function of the E-P genomic distance and then reveal a power-law scaling of the expression level in this distance. Interestingly, we find that long-range E-P interactions can induce bimodal and trimodal mRNA distributions. The 4D nucleome equation also allows for model selection and parameter inference. When this equation is applied to the mouse embryonic stem cell smRNA-FISH data and the E-P genomic-distance data, the predicted E-P contact probability and mRNA distribution are in good agreement with experimental results. Further statistical inference indicates that the E-P interactions prefer to modulate the mRNA level by controlling promoter activation and transcription initiation rates. Our model and results provide quantitative insights into both spatiotemporal gene-expression determinants (i.e., long-range E-P interactions) and cellular fates during development.
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Affiliation(s)
- Zihao Wang
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Songhao Luo
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Zhenquan Zhang
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jiajun Zhang
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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19
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Arnold M, Stengel KR. Emerging insights into enhancer biology and function. Transcription 2023; 14:68-87. [PMID: 37312570 PMCID: PMC10353330 DOI: 10.1080/21541264.2023.2222032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
Cell type-specific gene expression is coordinated by DNA-encoded enhancers and the transcription factors (TFs) that bind to them in a sequence-specific manner. As such, these enhancers and TFs are critical mediators of normal development and altered enhancer or TF function is associated with the development of diseases such as cancer. While initially defined by their ability to activate gene transcription in reporter assays, putative enhancer elements are now frequently defined by their unique chromatin features including DNase hypersensitivity and transposase accessibility, bidirectional enhancer RNA (eRNA) transcription, CpG hypomethylation, high H3K27ac and H3K4me1, sequence-specific transcription factor binding, and co-factor recruitment. Identification of these chromatin features through sequencing-based assays has revolutionized our ability to identify enhancer elements on a genome-wide scale, and genome-wide functional assays are now capitalizing on this information to greatly expand our understanding of how enhancers function to provide spatiotemporal coordination of gene expression programs. Here, we highlight recent technological advances that are providing new insights into the molecular mechanisms by which these critical cis-regulatory elements function in gene control. We pay particular attention to advances in our understanding of enhancer transcription, enhancer-promoter syntax, 3D organization and biomolecular condensates, transcription factor and co-factor dependencies, and the development of genome-wide functional enhancer screens.
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Affiliation(s)
- Mirjam Arnold
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kristy R. Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Montefiore Einstein Cancer Center, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY, USA
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA
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20
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Sept CE, Tak YE, Cerda-Smith CG, Hutchinson HM, Goel V, Blanchette M, Bhakta MS, Hansen AS, Joung JK, Johnstone S, Eyler CE, Aryee MJ. High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563340. [PMID: 37961446 PMCID: PMC10634716 DOI: 10.1101/2023.10.20.563340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
DNA looping is vital for establishing many enhancer-promoter interactions. While CTCF is known to anchor many cohesin-mediated loops, the looped chromatin fiber appears to predominantly exist in a poorly characterized actively extruding state. To better characterize extruding chromatin loop structures, we used CTCF MNase HiChIP data to determine both CTCF binding at high resolution and 3D contact information. Here we present FactorFinder, a tool that identifies CTCF binding sites at near base-pair resolution. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics, and find that active enhancers and RNA Pol II impede cohesin extrusion, facilitating an enrichment of enhancer-promoter contacts in the partially extruded loop state. We propose a model of topological regulation whereby the transient, partially extruded states play active roles in transcription.
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Affiliation(s)
- Corriene E Sept
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Y Esther Tak
- Molecular Pathology Unit, Massachusetts General Hospital; Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School; Boston, MA 02115, USA
| | - Christian G Cerda-Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Haley M Hutchinson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Viraat Goel
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA 02139, USA
| | - Marco Blanchette
- Dovetail Genomics, Cantata Bio LLC, Scotts Valley, CA 95066, USA
| | - Mital S Bhakta
- Dovetail Genomics, Cantata Bio LLC, Scotts Valley, CA 95066, USA
| | - Anders S Hansen
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA 02139, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital; Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School; Boston, MA 02115, USA
| | - Sarah Johnstone
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Pathology, Dana-Farber Cancer Institute; Boston, MA 02215, USA
| | - Christine E Eyler
- Department of Radiation Oncology, Duke University School of Medicine; Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine; Durham, NC 27710, USA
| | - Martin J Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
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21
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Thomas HF, Buecker C. What is an enhancer? Bioessays 2023; 45:e2300044. [PMID: 37256273 DOI: 10.1002/bies.202300044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023]
Abstract
Tight control of the transcription process is essential for the correct spatial and temporal gene expression pattern during development and in homeostasis. Enhancers are at the core of correct transcriptional activation. The original definition of an enhancer is straightforward: a DNA sequence that activates transcription independent of orientation and direction. Dissection of numerous enhancer loci has shown that many enhancer-like elements might not conform to the original definition, suggesting that enhancers and enhancer-like elements might use multiple different mechanisms to contribute to transcriptional activation. Here, we review methodologies to identify enhancers and enhancer-like elements and discuss pitfalls and consequences for our understanding of transcriptional regulation.
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22
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Bravo González-Blas C, De Winter S, Hulselmans G, Hecker N, Matetovici I, Christiaens V, Poovathingal S, Wouters J, Aibar S, Aerts S. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat Methods 2023; 20:1355-1367. [PMID: 37443338 PMCID: PMC10482700 DOI: 10.1038/s41592-023-01938-4] [Citation(s) in RCA: 114] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikolai Hecker
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jasper Wouters
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
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23
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Lyu J, Chen C. LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis. Genome Biol 2023; 24:184. [PMID: 37559123 PMCID: PMC10413806 DOI: 10.1186/s13059-023-03025-5] [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: 12/19/2022] [Accepted: 07/28/2023] [Indexed: 08/11/2023] Open
Abstract
Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with the limited RT/SSS efficiency compromising RNA detectability. Here, we develop a new scRNA-seq method, Linearly Amplified Single-stranded-RNA-derived Transcriptome sequencing (LAST-seq), which directly amplifies the original single-stranded RNA molecules without prior RT/SSS. LAST-seq offers a high single-molecule capture efficiency and a low level of technical noise for single-cell transcriptome analyses. Using LAST-seq, we characterize transcriptional bursting kinetics in human cells, revealing a role of topologically associating domains in transcription regulation.
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Affiliation(s)
- Jun Lyu
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chongyi Chen
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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24
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Senapati S, Irshad IU, Sharma AK, Kumar H. Fundamental insights into the correlation between chromosome configuration and transcription. Phys Biol 2023; 20:051002. [PMID: 37467757 DOI: 10.1088/1478-3975/ace8e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain, and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research.
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Affiliation(s)
- Swayamshree Senapati
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
| | - Inayat Ullah Irshad
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
| | - Ajeet K Sharma
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, Jammu 181221, India
| | - Hemant Kumar
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
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25
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Ochiai H, Ohishi H, Sato Y, Kimura H. Organization of transcription and 3D genome as revealed by live-cell imaging. Curr Opin Struct Biol 2023; 81:102615. [PMID: 37257205 DOI: 10.1016/j.sbi.2023.102615] [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: 01/24/2023] [Revised: 04/03/2023] [Accepted: 05/01/2023] [Indexed: 06/02/2023]
Abstract
Higher-order genomic structures play a critical role in regulating gene expression by influencing the spatial proximity of promoters and enhancers. Live-cell imaging studies have demonstrated that three-dimensional genome structures undergo dynamic changes over time. Transcription is also dynamic, with genes frequently switching between active and inactive states. Recent observations suggest that the formation of condensates, composed of transcription-related factors, RNA, and RNA-binding proteins, around genes can regulate transcription. Advancements in technology have facilitated the visualization of the intricate spatiotemporal relationship between higher-order genomic structures, condensate formation, and transcriptional activity in living cells.
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Affiliation(s)
- Hiroshi Ochiai
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan.
| | - Hiroaki Ohishi
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan
| | - Yuko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.
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26
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Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho HS, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn RA, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. Nat Genet 2023; 55:1336-1346. [PMID: 37488417 PMCID: PMC11012226 DOI: 10.1038/s41588-023-01450-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Comprehensive enhancer discovery is challenging because most enhancers, especially those contributing to complex diseases, have weak effects on gene expression. Our gene regulatory network modeling identified that nonlinear enhancer gene regulation during cell state transitions can be leveraged to improve the sensitivity of enhancer discovery. Using human embryonic stem cell definitive endoderm differentiation as a dynamic transition system, we conducted a mid-transition CRISPRi-based enhancer screen. We discovered a comprehensive set of enhancers for each of the core endoderm-specifying transcription factors. Many enhancers had strong effects mid-transition but weak effects post-transition, consistent with the nonlinear temporal responses to enhancer perturbation predicted by the modeling. Integrating three-dimensional genomic information, we were able to develop a CTCF-loop-constrained Interaction Activity model that can better predict functional enhancers compared to models that rely on Hi-C-based enhancer-promoter contact frequency. Our study provides generalizable strategies for sensitive and systematic enhancer discovery in both normal and pathological cell state transitions.
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Affiliation(s)
- Renhe Luo
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Jielin Yan
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Jin Woo Oh
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Wang Xi
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Dustin Shigaki
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Wilfred Wong
- Computational & Systems Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Hyein S Cho
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
| | - Dylan Murphy
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York City, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Ronald Cutler
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bess P Rosen
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Julian Pulecio
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
| | - Dapeng Yang
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
| | - Rachel A Glenn
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Tingxu Chen
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Qing V Li
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Effie Apostolou
- Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA.
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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27
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Friman ET, Flyamer IM, Marenduzzo D, Boyle S, Bickmore WA. Ultra-long-range interactions between active regulatory elements. Genome Res 2023; 33:1269-1283. [PMID: 37451823 PMCID: PMC10547262 DOI: 10.1101/gr.277567.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Contacts between enhancers and promoters are thought to relate to their ability to activate transcription. Investigating factors that contribute to such chromatin interactions is therefore important for understanding gene regulation. Here, we have determined contact frequencies between millions of pairs of cis-regulatory elements from chromosome conformation capture data sets and analyzed a collection of hundreds of DNA-binding factors for binding at regions of enriched contacts. This analysis revealed enriched contacts at sites bound by many factors associated with active transcription. We show that active regulatory elements, independent of cohesin and polycomb, interact with each other across distances of tens of megabases in vertebrate and invertebrate genomes and that interactions correlate and change with activity. However, these ultra-long-range interactions are not dependent on RNA polymerase II transcription or individual transcription cofactors. Using simulations, we show that a model of chromatin and multivalent binding factors can give rise to long-range interactions via bridging-induced clustering. We propose that long-range interactions between cis-regulatory elements are driven by at least three distinct processes: cohesin-mediated loop extrusion, polycomb contacts, and clustering of active regions.
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Affiliation(s)
- Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
| | - Ilya M Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
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28
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Tan J, Shenker-Tauris N, Rodriguez-Hernaez J, Wang E, Sakellaropoulos T, Boccalatte F, Thandapani P, Skok J, Aifantis I, Fenyö D, Xia B, Tsirigos A. Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening. Nat Biotechnol 2023; 41:1140-1150. [PMID: 36624151 PMCID: PMC10329734 DOI: 10.1038/s41587-022-01612-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/14/2022] [Indexed: 01/11/2023]
Abstract
Investigating how chromatin organization determines cell-type-specific gene expression remains challenging. Experimental methods for measuring three-dimensional chromatin organization, such as Hi-C, are costly and have technical limitations, restricting their broad application particularly in high-throughput genetic perturbations. We present C.Origami, a multimodal deep neural network that performs de novo prediction of cell-type-specific chromatin organization using DNA sequence and two cell-type-specific genomic features-CTCF binding and chromatin accessibility. C.Origami enables in silico experiments to examine the impact of genetic changes on chromatin interactions. We further developed an in silico genetic screening approach to assess how individual DNA elements may contribute to chromatin organization and to identify putative cell-type-specific trans-acting regulators that collectively determine chromatin architecture. Applying this approach to leukemia cells and normal T cells, we demonstrate that cell-type-specific in silico genetic screening, enabled by C.Origami, can be used to systematically discover novel chromatin regulation circuits in both normal and disease-related biological systems.
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Affiliation(s)
- Jimin Tan
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
| | - Nina Shenker-Tauris
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- The Jackson Laboratory for Genomics Medicine, Farmington, CT, USA
| | | | - Francesco Boccalatte
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Palaniraja Thandapani
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Jane Skok
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Iannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Bo Xia
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA.
- Society of Fellows, Harvard University, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA.
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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29
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Wang R, Xu Q, Wang C, Tian K, Wang H, Ji X. Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions. Nucleic Acids Res 2023; 51:6784-6805. [PMID: 37264934 PMCID: PMC10359638 DOI: 10.1093/nar/gkad401] [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: 12/15/2022] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the cohesin in chromatin and identified transcription factors, RNA-binding proteins and chromatin regulators associated with cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with cohesin that warrant further investigation.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qiqin Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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30
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Ramasamy S, Aljahani A, Karpinska MA, Cao TBN, Velychko T, Cruz JN, Lidschreiber M, Oudelaar AM. The Mediator complex regulates enhancer-promoter interactions. Nat Struct Mol Biol 2023:10.1038/s41594-023-01027-2. [PMID: 37430065 DOI: 10.1038/s41594-023-01027-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 05/30/2023] [Indexed: 07/12/2023]
Abstract
Enhancer-mediated gene activation generally requires physical proximity between enhancers and their target gene promoters. However, the molecular mechanisms by which interactions between enhancers and promoters are formed are not well understood. Here, we investigate the function of the Mediator complex in the regulation of enhancer-promoter interactions, by combining rapid protein depletion and high-resolution MNase-based chromosome conformation capture approaches. We show that depletion of Mediator leads to reduced enhancer-promoter interaction frequencies, which are associated with a strong decrease in gene expression. In addition, we find increased interactions between CTCF-binding sites upon Mediator depletion. These changes in chromatin architecture are associated with a redistribution of the Cohesin complex on chromatin and a reduction in Cohesin occupancy at enhancers. Together, our results indicate that the Mediator and Cohesin complexes contribute to enhancer-promoter interactions and provide insights into the molecular mechanisms by which communication between enhancers and promoters is regulated.
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Affiliation(s)
- Shyam Ramasamy
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Abrar Aljahani
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Magdalena A Karpinska
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - T B Ngoc Cao
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Taras Velychko
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - J Neos Cruz
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - A Marieke Oudelaar
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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31
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Syed SA, Shqillo K, Nand A, Zhan Y, Dekker J, Imbalzano AN. Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544859. [PMID: 37398486 PMCID: PMC10312757 DOI: 10.1101/2023.06.13.544859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Protein arginine methyltransferase 5 (Prmt5) is an essential regulator of embryonic development and adult progenitor cell functions. Prmt5 expression is mis-regulated in many cancers, and the development of Prmt5 inhibitors as cancer therapeutics is an active area of research. Prmt5 functions via effects on gene expression, splicing, DNA repair, and other critical cellular processes. We examined whether Prmt5 functions broadly as a genome-wide regulator of gene transcription and higher-order chromatin interactions during the initial stages of adipogenesis using ChIP-Seq, RNA-seq, and Hi-C using 3T3-L1 cells, a frequently utilized model for adipogenesis. We observed robust genome-wide Prmt5 chromatin-binding at the onset of differentiation. Prmt5 localized to transcriptionally active genomic regions, acting as both a positive and a negative regulator. A subset of Prmt5 binding sites co-localized with mediators of chromatin organization at chromatin loop anchors. Prmt5 knockdown decreased insulation strength at the boundaries of topologically associating domains (TADs) adjacent to sites with Prmt5 and CTCF co-localization. Genes overlapping such weakened TAD boundaries showed transcriptional dysregulation. This study identifies Prmt5 as a broad regulator of gene expression, including regulation of early adipogenic factors, and reveals an unappreciated requirement for Prmt5 in maintaining strong insulation at TAD boundaries and overall chromatin organization.
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Affiliation(s)
- Sabriya A Syed
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Kristina Shqillo
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Ankita Nand
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Ye Zhan
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Job Dekker
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
- Howard Hughes Medical Institute, Chevy Chase, MD USA
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
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32
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Mach P, Giorgetti L. Integrative approaches to study enhancer-promoter communication. Curr Opin Genet Dev 2023; 80:102052. [PMID: 37257410 PMCID: PMC10293802 DOI: 10.1016/j.gde.2023.102052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 06/02/2023]
Abstract
The spatiotemporal control of gene expression in complex multicellular organisms relies on noncoding regulatory sequences such as enhancers, which activate transcription of target genes often over large genomic distances. Despite the advances in the identification and characterization of enhancers, the principles and mechanisms by which enhancers select and control their target genes remain largely unknown. Here, we review recent interdisciplinary and quantitative approaches based on emerging techniques that aim to address open questions in the field, notably how regulatory information is encoded in the DNA sequence, how this information is transferred from enhancers to promoters, and how these processes are regulated in time.
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Affiliation(s)
- Pia Mach
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland. https://twitter.com/@MachPia
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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33
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Flores V, Farabella I, Nir G. Genome-wide tracing to decipher nuclear organization. Curr Opin Cell Biol 2023; 82:102175. [PMID: 37263058 DOI: 10.1016/j.ceb.2023.102175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023]
Abstract
Nuclear organization impacts gene expression activity and cell phenotype. Our current understanding is mainly derived from ensemble-level sequencing studies that reflect the 3D genome structure of millions of cells. These approaches have provided invaluable details on the 3D organizations of the genome and their relation to other nuclear landmarks. However, they mostly lack the ability to provide multimodal information simultaneously at the single-cell level. In recent years, cutting-edge imaging technologies have risen to the challenge of simultaneously describing multiple components of the nuclear space at the single-cell level, paving the way for a deeper understanding of the genome structure-function relationship. This review will focus on the development and utilization of such technologies to gain a multi-component view of the nucleus at single-cell resolution, dissecting the complexity and heterogeneity of nuclear organization.
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Affiliation(s)
- Victoria Flores
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Irene Farabella
- Integrative Nuclear Architecture Laboratory, Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy.
| | - Guy Nir
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
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34
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Kawasaki K, Fukaya T. Functional coordination between transcription factor clustering and gene activity. Mol Cell 2023; 83:1605-1622.e9. [PMID: 37207625 DOI: 10.1016/j.molcel.2023.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/15/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
The prevailing view of metazoan gene regulation is that transcription is facilitated through the formation of static activator complexes at distal regulatory regions. Here, we employed quantitative single-cell live-imaging and computational analysis to provide evidence that the dynamic assembly and disassembly process of transcription factor (TF) clusters at enhancers is a major source of transcriptional bursting in developing Drosophila embryos. We further show that the regulatory connectivity between TF clustering and burst induction is highly regulated through intrinsically disordered regions (IDRs). Addition of a poly-glutamine tract to the maternal morphogen Bicoid demonstrated that extended IDR length leads to ectopic TF clustering and burst induction from its endogenous target genes, resulting in defects in body segmentation during embryogenesis. Moreover, we successfully visualized the presence of "shared" TF clusters during the co-activation of two distant genes, which provides a concrete molecular explanation for the newly proposed "topological operon" hypothesis in metazoan gene regulation.
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Affiliation(s)
- Koji Kawasaki
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
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35
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Rajderkar S, Barozzi I, Zhu Y, Hu R, Zhang Y, Li B, Alcaina Caro A, Fukuda-Yuzawa Y, Kelman G, Akeza A, Blow MJ, Pham Q, Harrington AN, Godoy J, Meky EM, von Maydell K, Hunter RD, Akiyama JA, Novak CS, Plajzer-Frick I, Afzal V, Tran S, Lopez-Rios J, Talkowski ME, Lloyd KCK, Ren B, Dickel DE, Visel A, Pennacchio LA. Topologically associating domain boundaries are required for normal genome function. Commun Biol 2023; 6:435. [PMID: 37081156 PMCID: PMC10119121 DOI: 10.1038/s42003-023-04819-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1-3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.
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Affiliation(s)
- Sudha Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ana Alcaina Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide Junta de Andalucía, 41013, Seville, Spain
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adyam Akeza
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Quan Pham
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Anne N Harrington
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Janeth Godoy
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Eman M Meky
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide Junta de Andalucía, 41013, Seville, Spain
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, Davis, CA, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA.
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36
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Schaeffer M, Nollmann M. Contributions of 3D chromatin structure to cell-type-specific gene regulation. Curr Opin Genet Dev 2023; 79:102032. [PMID: 36893484 DOI: 10.1016/j.gde.2023.102032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 03/09/2023]
Abstract
Eukaryotic genomes are organized in 3D in a multiscale manner, and different mechanisms acting at each of these scales can contribute to transcriptional regulation. However, the large single-cell variability in 3D chromatin structures represents a challenge to understand how transcription may be differentially regulated between cell types in a robust and efficient manner. Here, we describe the different mechanisms by which 3D chromatin structure was shown to contribute to cell-type-specific transcriptional regulation. Excitingly, several novel methodologies able to measure 3D chromatin conformation and transcription in single cells in their native tissue context, or to detect the dynamics of cis-regulatory interactions, are starting to allow quantitative dissection of chromatin structure noise and relate it to how transcription may be regulated between different cell types and cell states.
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Affiliation(s)
- Marie Schaeffer
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, Montpellier, France.
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37
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Chen LF, Lee J, Boettiger A. Recent progress and challenges in single-cell imaging of enhancer-promoter interaction. Curr Opin Genet Dev 2023; 79:102023. [PMID: 36854248 DOI: 10.1016/j.gde.2023.102023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/13/2023] [Accepted: 01/25/2023] [Indexed: 02/27/2023]
Abstract
In the past two years, approaches relying on high-resolution microscopy and live-cell imaging have increasingly contributed to our understanding of the 3D genome organization and its importance for transcriptional control. Here, we describe recent progress that has highlighted how flexible and heterogeneous 3D chromatin structure is, on the length scales relevant to transcriptional control. We describe work that has investigated how robust transcriptional outcomes may be derived from such flexible organization without the need for clearly distinct structures in active and silent cells. We survey the latest state of the art in directly observing the dynamics of chromatin interactions, and suggest how some recent, apparently contradictory conclusions may be reconciled.
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Affiliation(s)
- Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University, USA
| | - Joo Lee
- Department of Developmental Biology, Stanford University, USA
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38
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Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho H, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn R, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531569. [PMID: 36945628 PMCID: PMC10028945 DOI: 10.1101/2023.03.07.531569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Comprehensive enhancer discovery is challenging because most enhancers, especially those affected in complex diseases, have weak effects on gene expression. Our network modeling revealed that nonlinear enhancer-gene regulation during cell state transitions can be leveraged to improve the sensitivity of enhancer discovery. Utilizing hESC definitive endoderm differentiation as a dynamic transition system, we conducted a mid-transition CRISPRi-based enhancer screen. The screen discovered a comprehensive set of enhancers (4 to 9 per locus) for each of the core endoderm lineage-specifying transcription factors, and many enhancers had strong effects mid-transition but weak effects post-transition. Through integrating enhancer activity measurements and three-dimensional enhancer-promoter interaction information, we were able to develop a CTCF loop-constrained Interaction Activity (CIA) model that can better predict functional enhancers compared to models that rely on Hi-C-based enhancer-promoter contact frequency. Our study provides generalizable strategies for sensitive and more comprehensive enhancer discovery in both normal and pathological cell state transitions.
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39
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Owen JA, Horowitz JM. Size limits the sensitivity of kinetic schemes. Nat Commun 2023; 14:1280. [PMID: 36890153 PMCID: PMC9995461 DOI: 10.1038/s41467-023-36705-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 02/10/2023] [Indexed: 03/10/2023] Open
Abstract
Living things benefit from exquisite molecular sensitivity in many of their key processes, including DNA replication, transcription and translation, chemical sensing, and morphogenesis. At thermodynamic equilibrium, the basic biophysical mechanism for sensitivity is cooperative binding, for which it can be shown that the Hill coefficient, a sensitivity measure, cannot exceed the number of binding sites. Generalizing this fact, we find that for any kinetic scheme, at or away from thermodynamic equilibrium, a very simple structural quantity, the size of the support of a perturbation, always limits the effective Hill coefficient. We show how this bound sheds light on and unifies diverse sensitivity mechanisms, including kinetic proofreading and a nonequilibrium Monod-Wyman-Changeux (MWC) model proposed for the E. coli flagellar motor switch, representing in each case a simple, precise bridge between experimental observations and the models we write down. In pursuit of mechanisms that saturate the support bound, we find a nonequilibrium binding mechanism, nested hysteresis, with sensitivity exponential in the number of binding sites, with implications for our understanding of models of gene regulation and the function of biomolecular condensates.
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Affiliation(s)
- Jeremy A Owen
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, 08540, USA.
| | - Jordan M Horowitz
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI, 48104, USA.
- Department of Physics, University of Michigan, Ann Arbor, MI, 48109, USA.
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40
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Hamamoto K, Umemura Y, Makino S, Fukaya T. Dynamic interplay between non-coding enhancer transcription and gene activity in development. Nat Commun 2023; 14:826. [PMID: 36805453 PMCID: PMC9941499 DOI: 10.1038/s41467-023-36485-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 02/03/2023] [Indexed: 02/22/2023] Open
Abstract
Non-coding transcription at the intergenic regulatory regions is a prevalent feature of metazoan genomes, but its biological function remains uncertain. Here, we devise a live-imaging system that permits simultaneous visualization of gene activity along with intergenic non-coding transcription at single-cell resolution in Drosophila. Quantitative image analysis reveals that elongation of RNA polymerase II across the internal core region of enhancers leads to suppression of transcriptional bursting from linked genes. Super-resolution imaging and genome-editing analysis further demonstrate that enhancer transcription antagonizes molecular crowding of transcription factors, thereby interrupting the formation of a transcription hub at the gene locus. We also show that a certain class of developmental enhancers are structurally optimized to co-activate gene transcription together with non-coding transcription effectively. We suggest that enhancer function is flexibly tunable through the modulation of hub formation via surrounding non-coding transcription during development.
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Affiliation(s)
- Kota Hamamoto
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yusuke Umemura
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shiho Makino
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. .,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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41
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Kim S, Wysocka J. Deciphering the multi-scale, quantitative cis-regulatory code. Mol Cell 2023; 83:373-392. [PMID: 36693380 PMCID: PMC9898153 DOI: 10.1016/j.molcel.2022.12.032] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/24/2023]
Abstract
Uncovering the cis-regulatory code that governs when and how much each gene is transcribed in a given genome and cellular state remains a central goal of biology. Here, we discuss major layers of regulation that influence how transcriptional outputs are encoded by DNA sequence and cellular context. We first discuss how transcription factors bind specific DNA sequences in a dosage-dependent and cooperative manner and then proceed to the cofactors that facilitate transcription factor function and mediate the activity of modular cis-regulatory elements such as enhancers, silencers, and promoters. We then consider the complex and poorly understood interplay of these diverse elements within regulatory landscapes and its relationships with chromatin states and nuclear organization. We propose that a mechanistically informed, quantitative model of transcriptional regulation that integrates these multiple regulatory layers will be the key to ultimately cracking the cis-regulatory code.
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Affiliation(s)
- Seungsoo Kim
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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42
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de Wit E, Nora EP. New insights into genome folding by loop extrusion from inducible degron technologies. Nat Rev Genet 2023; 24:73-85. [PMID: 36180596 DOI: 10.1038/s41576-022-00530-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2022] [Indexed: 01/24/2023]
Abstract
Chromatin folds into dynamic loops that often span hundreds of kilobases and physically wire distant loci together for gene regulation. These loops are continuously created, extended and positioned by structural maintenance of chromosomes (SMC) protein complexes, such as condensin and cohesin, and their regulators, including CTCF, in a highly dynamic process known as loop extrusion. Genetic loss of extrusion factors is lethal, complicating their study. Inducible protein degradation technologies enable the depletion of loop extrusion factors within hours, leading to the rapid reconfiguration of chromatin folding. Here, we review how these technologies have changed our understanding of genome organization, upsetting long-held beliefs on its role in transcription. Finally, we examine recent models that attempt to reconcile observations after chronic versus acute perturbations, and discuss future developments in this rapidly developing field of research.
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Affiliation(s)
- Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Amsterdam, the Netherlands.
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Elphège P Nora
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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43
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Chakraborty S, Kopitchinski N, Zuo Z, Eraso A, Awasthi P, Chari R, Mitra A, Tobias IC, Moorthy SD, Dale RK, Mitchell JA, Petros TJ, Rocha PP. Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness. Nat Genet 2023; 55:280-290. [PMID: 36717694 PMCID: PMC10758292 DOI: 10.1038/s41588-022-01295-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 12/20/2022] [Indexed: 01/31/2023]
Abstract
How enhancers activate their distal target promoters remains incompletely understood. Here we dissect how CTCF-mediated loops facilitate and restrict such regulatory interactions. Using an allelic series of mouse mutants, we show that CTCF is neither required for the interaction of the Sox2 gene with distal enhancers, nor for its expression. Insertion of various combinations of CTCF motifs, between Sox2 and its distal enhancers, generated boundaries with varying degrees of insulation that directly correlated with reduced transcriptional output. However, in both epiblast and neural tissues, enhancer contacts and transcriptional induction could not be fully abolished, and insertions failed to disrupt implantation and neurogenesis. In contrast, Sox2 expression was undetectable in the anterior foregut of mutants carrying the strongest boundaries, and these animals fully phenocopied loss of SOX2 in this tissue. We propose that enhancer clusters with a high density of regulatory activity can better overcome physical barriers to maintain faithful gene expression and phenotypic robustness.
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Affiliation(s)
- Shreeta Chakraborty
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Nina Kopitchinski
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Zhenyu Zuo
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ariel Eraso
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Parirokh Awasthi
- Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - Raj Chari
- Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - Apratim Mitra
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ian C Tobias
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Sakthi D Moorthy
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy J Petros
- Unit on Cellular and Molecular Neurodevelopment, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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44
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van Mierlo G, Pushkarev O, Kribelbauer JF, Deplancke B. Chromatin modules and their implication in genomic organization and gene regulation. Trends Genet 2023; 39:140-153. [PMID: 36549923 DOI: 10.1016/j.tig.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/04/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulating gene expression remains obscure. Recent complementary observations revealed that interactions between CREs frequently result in the formation of small-scale functional modules within topologically associating domains. Such chromatin modules likely emerge from a complex interplay between regulatory machineries assembled at CREs, including site-specific binding of transcription factors. Here, we review the methods that allow identifying chromatin modules, summarize possible mechanisms that steer CRE interactions within these modules, and discuss outstanding challenges to uncover how chromatin modules fit in our current understanding of the functional 3D genome.
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Affiliation(s)
- Guido van Mierlo
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Olga Pushkarev
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Judith F Kribelbauer
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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45
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Abstract
In animals, the sequences for controlling gene expression do not concentrate just at the transcription start site of genes, but are frequently thousands to millions of base pairs distal to it. The interaction of these sequences with one another and their transcription start sites is regulated by factors that shape the three-dimensional (3D) organization of the genome within the nucleus. Over the past decade, indirect tools exploiting high-throughput DNA sequencing have helped to map this 3D organization, have identified multiple key regulators of its structure and, in the process, have substantially reshaped our view of how 3D genome architecture regulates transcription. Now, new tools for high-throughput super-resolution imaging of chromatin have directly visualized the 3D chromatin organization, settling some debates left unresolved by earlier indirect methods, challenging some earlier models of regulatory specificity and creating hypotheses about the role of chromatin structure in transcriptional regulation.
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46
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Luo S, Wang Z, Zhang Z, Zhou T, Zhang J. Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics. Nucleic Acids Res 2022; 51:68-83. [PMID: 36583343 PMCID: PMC9874261 DOI: 10.1093/nar/gkac1204] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/06/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Gene expression in mammalian cells is highly variable and episodic, resulting in a series of discontinuous bursts of mRNAs. A challenge is to understand how static promoter architecture and dynamic feedback regulations dictate bursting on a genome-wide scale. Although single-cell RNA sequencing (scRNA-seq) provides an opportunity to address this challenge, effective analytical methods are scarce. We developed an interpretable and scalable inference framework, which combined experimental data with a mechanistic model to infer transcriptional burst kinetics (sizes and frequencies) and feedback regulations. Applying this framework to scRNA-seq data generated from embryonic mouse fibroblast cells, we found Simpson's paradoxes, i.e. genome-wide burst kinetics exhibit different characteristics in two cases without and with distinguishing feedback regulations. We also showed that feedbacks differently modulate burst frequencies and sizes and conceal the effects of transcription start site distributions on burst kinetics. Notably, only in the presence of positive feedback, TATA genes are expressed with high burst frequencies and enhancer-promoter interactions mainly modulate burst frequencies. The developed inference method provided a flexible and efficient way to investigate transcriptional burst kinetics and the obtained results would be helpful for understanding cell development and fate decision.
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Affiliation(s)
| | | | - Zhenquan Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou, 510275, P. R. China,School of Mathematics, Sun Yat-sen University, Guangzhou, Guangdong Province, 510275, P. R. China
| | - Tianshou Zhou
- Correspondence may also be addressed to Tianshou Zhou. Tel: +86 20 84134958;
| | - Jiajun Zhang
- To whom correspondence should be addressed. Tel: +86 20 84111829;
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47
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Abstract
The control of gene expression in eukaryotes relies on how transcription factors and RNA polymerases manipulate the structure of chromatin. These interactions are especially important in development as gene expression programs change. Chromatin generally limits the accessibility of DNA, and thus exposing sequences at regulatory elements is critical for gene expression. However, it is challenging to understand how transcription factors manipulate chromatin structure and the sequence of regulatory events. The Drosophila embryo has provided a powerful setting to directly observe the establishment and elaboration of chromatin features and experimentally test the causality of transcriptional events that are shared among many metazoans. The large embryo is tractable by live imaging, and a variety of well-developed tools allow the manipulation of factors during early development. The early embryo develops as a syncytium with rapid nuclear divisions and no zygotic transcription, with largely featureless chromatin. Thus, studies in this system have revealed the progression of genome activation triggered by pioneer factors that initiate DNA exposure at regulatory elements and the establishment of chromatin domains, including heterochromatin, the nucleolus, and nuclear bodies. The de novo emergence of nuclear structures in the early embryo reveals features of chromatin dynamics that are likely to be central to transcriptional regulation in all cells.
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Affiliation(s)
- Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road Chevy Chase, MD 20815-6789, USA
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48
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Valton AL, Venev SV, Mair B, Khokhar ES, Tong AHY, Usaj M, Chan K, Pai AA, Moffat J, Dekker J. A cohesin traffic pattern genetically linked to gene regulation. Nat Struct Mol Biol 2022; 29:1239-1251. [PMID: 36482254 PMCID: PMC10228515 DOI: 10.1038/s41594-022-00890-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 11/01/2022] [Indexed: 12/13/2022]
Abstract
Cohesin-mediated loop extrusion has been shown to be blocked at specific cis-elements, including CTCF sites, producing patterns of loops and domain boundaries along chromosomes. Here we explore such cis-elements, and their role in gene regulation. We find that transcription termination sites of active genes form cohesin- and RNA polymerase II-dependent domain boundaries that do not accumulate cohesin. At these sites, cohesin is first stalled and then rapidly unloaded. Start sites of transcriptionally active genes form cohesin-bound boundaries, as shown before, but are cohesin-independent. Together with cohesin loading, possibly at enhancers, these sites create a pattern of cohesin traffic that guides enhancer-promoter interactions. Disrupting this traffic pattern, by removing CTCF, renders cells sensitive to knockout of genes involved in transcription initiation, such as the SAGA complexes, and RNA processing such DEAD/H-Box RNA helicases. Without CTCF, these factors are less efficiently recruited to active promoters.
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Affiliation(s)
- Anne-Laure Valton
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Barbara Mair
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Eraj Shafiq Khokhar
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amy H Y Tong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Chan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Xue Y, Wang J, He Y, Patra P, Gao YQ. Multi-scale gene regulation mechanism: Spatiotemporal transmission of genetic information. Curr Opin Struct Biol 2022; 77:102487. [PMID: 36274420 DOI: 10.1016/j.sbi.2022.102487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/09/2022] [Accepted: 09/18/2022] [Indexed: 12/14/2022]
Abstract
Gene expression is regulated by many factors, including transcription factors, chromatin three-dimensional topology, modifications of DNA and histone proteins, and non-coding RNAs. The execution of these complex mechanisms requires an effectively coordinated regulation system. In this review, we emphasize that the multi-scale heterogeneous DNA sequence plays a fundamental and important role for gene expression activity and usage of different means of epigenetic regulation. We illustrate here that the chromatin structure organization provides a stage for spatiotemporal regulation between different genes or gene modules and to realize their downstream functional cooperation. Such a perspective expands our understanding of the central dogma: In addition to one-dimensional sequence information, inter-gene interactions can also be transferred from DNA and RNA to protein levels.
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Affiliation(s)
- Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jingyao Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yueying He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Piya Patra
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
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Reed KSM, Davis ES, Bond ML, Cabrera A, Thulson E, Quiroga IY, Cassel S, Woolery KT, Hilton I, Won H, Love MI, Phanstiel DH. Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription. Cell Rep 2022; 41:111567. [PMID: 36323252 PMCID: PMC9707392 DOI: 10.1016/j.celrep.2022.111567] [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: 05/18/2022] [Revised: 08/19/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
To infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription, we mapped each feature in a genome-wide fashion across eight narrowly spaced time points of macrophage activation. Enhancers and genes connected by loops exhibit stronger correlations between histone H3K27 acetylation and expression than can be explained by genomic distance or physical proximity alone. At these looped enhancer-promoter pairs, changes in acetylation at distal enhancers precede changes in gene expression. Changes in gene expression exhibit a directional bias at differential loop anchors; gained loops are associated with increased expression of genes oriented away from the center of the loop, and lost loops are often accompanied by high levels of transcription within the loop boundaries themselves. These results are consistent with a reciprocal relationship where loops can facilitate increased transcription by connecting promoters to distal enhancers, whereas high levels of transcription can impede loop formation.
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Affiliation(s)
- Kathleen S M Reed
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Marielle L Bond
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Alan Cabrera
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Eliza Thulson
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ivana Yoseli Quiroga
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Shannon Cassel
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kamisha T Woolery
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Isaac Hilton
- Department of Bioengineering, Rice University, Houston, TX 77005, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Hyejung Won
- Department of Genetics and Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Douglas H Phanstiel
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA.
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