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Scholz BA, Sumida N, de Lima CDM, Chachoua I, Martino M, Tzelepis I, Nikoshkov A, Zhao H, Mehmood R, Sifakis EG, Bhartiya D, Göndör A, Ohlsson R. WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating. Nat Genet 2019; 51:1723-1731. [DOI: 10.1038/s41588-019-0535-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/23/2019] [Indexed: 01/10/2023]
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Abstract
Transcriptional enhancers constitute a subclass of regulatory elements that facilitate transcription. Such regions are generally organized by short stretches of DNA enriched in transcription factor-binding sites but also can include very large regions containing clusters of enhancers, termed super-enhancers. These regions increase the probability or the rate (or both) of transcription generally in
cis and sometimes over very long distances by altering chromatin states and the activity of Pol II machinery at promoters. Although enhancers were discovered almost four decades ago, their inner workings remain enigmatic. One important opening into the underlying principle has been provided by observations that enhancers make physical contacts with their target promoters to facilitate the loading of the RNA polymerase complex. However, very little is known about how such chromatin loops are regulated and how they govern transcription in the three-dimensional context of the nuclear architecture. Here, we present current themes of how enhancers may boost gene expression in three dimensions and we identify currently unresolved key questions.
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Affiliation(s)
- Anita Göndör
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Rolf Ohlsson
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nat Methods 2016; 13:1013-1020. [PMID: 27749837 DOI: 10.1038/nmeth.4031] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/19/2016] [Indexed: 01/10/2023]
Abstract
Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis. Integration of ATAC-see with flow cytometry enables automated quantitation and prospective cell isolation as a function of chromatin accessibility, and it reveals a cell-cycle dependence of chromatin accessibility that is especially dynamic in G1 phase. The integration of imaging and epigenomics provides a general and scalable approach for deciphering the spatiotemporal architecture of gene control.
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Affiliation(s)
- Xingqi Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Ying Shen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Will Draper
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Jason D Buenrostro
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA
| | - Ulrike Litzenburger
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Rajarshi P Ghosh
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Alexandra East-Seletsky
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, California, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Jan T Liphardt
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
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Zhao H, Sifakis E, Sumida N, Millán-Ariño L, Scholz B, Svensson J, Chen X, Ronnegren A, Mallet de Lima C, Varnoosfaderani F, Shi C, Loseva O, Yammine S, Israelsson M, Rathje LS, Németi B, Fredlund E, Helleday T, Imreh M, Göndör A. PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription. Mol Cell 2015; 59:984-97. [DOI: 10.1016/j.molcel.2015.07.019] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 05/20/2015] [Accepted: 07/21/2015] [Indexed: 11/28/2022]
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Chen X, Yammine S, Shi C, Tark-Dame M, Göndör A, Ohlsson R. The visualization of large organized chromatin domains enriched in the H3K9me2 mark within a single chromosome in a single cell. Epigenetics 2015; 9:1439-45. [PMID: 25482057 DOI: 10.4161/15592294.2014.971633] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Despite considerable efforts, our understanding of the organization of higher order chromatin conformations in single cells and how these relate to chromatin marks remains poor. We have earlier invented the Chromatin In Situ Proximity (ChrISP) technique to determine proximities between chromatin fibers within a single chromosome. Here we used ChrISP to identify chromosome 11-specific hubs that are enriched in the H3K9me2 mark and that project toward the nuclear membrane in finger-like structures. Conversely, chromosome 11-specfic chromatin hubs, visualized by the presence of either H3K9me1 or H3K9me3 marks, are chromosome-wide and largely absent at the nuclear periphery. As the nuclear periphery-specific chromatin hubs were lost in the induced reduction of H3K9me2 levels, they likely represent Large Organization Chromatin in Lysine Methylation (LOCK) domains, previously identified by ChIP-seq analysis. Strikingly, the downregulation of the H3K9me2/3 marks also led to the chromosome-wide compaction of chromosome 11, suggesting a pleiotropic function of these features not recognized before. The ChrISP-mediated visualization of dynamic chromatin states in single cells thus provides an analysis of chromatin structures with a resolution far exceeding that of any other light microscopic technique.
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Affiliation(s)
- Xingqi Chen
- a Department of Microbiology; Tumor and Cell Biology ; Stockholm , Sweden
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