1
|
Colin L, Reyes C, Berthezene J, Maestroni L, Modolo L, Toselli E, Chanard N, Schaak S, Cuvier O, Gachet Y, Coulon S, Bernard P, Tournier S. Condensin positioning at telomeres by shelterin proteins drives sister-telomere disjunction in anaphase. eLife 2023; 12:RP89812. [PMID: 37988290 PMCID: PMC10662949 DOI: 10.7554/elife.89812] [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] [Indexed: 11/23/2023] Open
Abstract
The localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here, we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosome arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.
Collapse
Affiliation(s)
- Léonard Colin
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Celine Reyes
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Julien Berthezene
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Laetitia Maestroni
- CNRS, INSERM, Aix Marseille Université, Institut Paoli-Calmettes, CRCM, Equipe labellisée par la Ligue Nationale contre le CancerMarseilleFrance
| | - Laurent Modolo
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Esther Toselli
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Nicolas Chanard
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Stephane Schaak
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Olivier Cuvier
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Yannick Gachet
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Stephane Coulon
- CNRS, INSERM, Aix Marseille Université, Institut Paoli-Calmettes, CRCM, Equipe labellisée par la Ligue Nationale contre le CancerMarseilleFrance
| | - Pascal Bernard
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Sylvie Tournier
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| |
Collapse
|
2
|
Harris RJ, Heer M, Levasseur MD, Cartwright TN, Weston B, Mitchell JL, Coxhead JM, Gaughan L, Prendergast L, Rico D, Higgins JMG. Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation. Nat Commun 2023; 14:7243. [PMID: 37945563 PMCID: PMC10636195 DOI: 10.1038/s41467-023-43115-3] [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: 04/05/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Histone modifications influence the recruitment of reader proteins to chromosomes to regulate events including transcription and cell division. The idea of a histone code, where combinations of modifications specify unique downstream functions, is widely accepted and can be demonstrated in vitro. For example, on synthetic peptides, phosphorylation of Histone H3 at threonine-3 (H3T3ph) prevents the binding of reader proteins that recognize trimethylation of the adjacent lysine-4 (H3K4me3), including the TAF3 component of TFIID. To study these combinatorial effects in cells, we analyzed the genome-wide distribution of H3T3ph and H3K4me2/3 during mitosis. We find that H3T3ph anti-correlates with adjacent H3K4me2/3 in cells, and that the PHD domain of TAF3 can bind H3K4me2/3 in isolated mitotic chromatin despite the presence of H3T3ph. Unlike in vitro, H3K4 readers are still displaced from chromosomes in mitosis in Haspin-depleted cells lacking H3T3ph. H3T3ph is therefore unlikely to be responsible for transcriptional downregulation during cell division.
Collapse
Affiliation(s)
- Rebecca J Harris
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Maninder Heer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Mark D Levasseur
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Bethany Weston
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jennifer L Mitchell
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jonathan M Coxhead
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Luke Gaughan
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Lisa Prendergast
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad Sevilla-Universidad Pablo de Olavide-Junta de Andalucía, 41092, Seville, Spain.
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
| |
Collapse
|
3
|
Chang LH, Ghosh S, Papale A, Luppino JM, Miranda M, Piras V, Degrouard J, Edouard J, Poncelet M, Lecouvreur N, Bloyer S, Leforestier A, Joyce EF, Holcman D, Noordermeer D. Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries. Nat Commun 2023; 14:5615. [PMID: 37699887 PMCID: PMC10497529 DOI: 10.1038/s41467-023-41265-y] [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: 05/17/2023] [Accepted: 08/28/2023] [Indexed: 09/14/2023] Open
Abstract
Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs. We identify enrichment of three features of CTCF binding at strong TAD boundaries, consisting of strongly bound and closely spaced CTCF binding peaks, with a further enrichment of DNA-binding motifs within these peaks. Using multi-contact Nano-C analysis in cells with normal and perturbed CTCF binding, we establish that individual CTCF binding sites contribute to the blocking of loop extrusion, but in an incomplete manner. When clustered, individual CTCF binding sites thus create a stepwise insulation between neighboring TADs. Based on these results, we propose a model whereby multiple instances of temporal loop extrusion blocking create strong insulation between TADs.
Collapse
Affiliation(s)
- Li-Hsin Chang
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, and National Institute of Health Research, Blood and Transplant Research Unit in Precision Cellular Therapeutics, OX3 9DS, Oxford, UK
| | - Sourav Ghosh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- Department of Pathology and Laboratory Medicine, Western University, N6A3K7, London, ON, Canada
| | - Andrea Papale
- École Normale Supérieure, IBENS, Université PSL, 75005, Paris, France
| | - Jennifer M Luppino
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mélanie Miranda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Vincent Piras
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides (LPS), 91405, Orsay, France
| | - Joanne Edouard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Mallory Poncelet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nathan Lecouvreur
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sébastien Bloyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Amélie Leforestier
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides (LPS), 91405, Orsay, France
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Holcman
- École Normale Supérieure, IBENS, Université PSL, 75005, Paris, France
- Churchill College, University of Cambridge, CB3 0DS, Cambridge, UK
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Jiang G, Tian Q, Shi P, Li Z, Li Y, Chen J, Wang W, Chen R, Zhong H, Wu G. Association of NCAP family genes with prognosis and immune infiltration of human sarcoma. Aging (Albany NY) 2023; 15:204683. [PMID: 37192046 DOI: 10.18632/aging.204683] [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: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/18/2023]
Abstract
OBJECTIVE This study was conducted to explore the correlation of NCAP family genes with expression, prognosis, and immune infiltration in human sarcoma. RESULTS Compared with normal human tissues, six NCAP family genes were highly expressed in sarcoma tissues, and high expression of the six genes were significantly associated with the poor prognosis of sarcoma patients. The expression of NCAPs in sarcoma was significantly related to the low infiltration level of macrophages and CD4+ T cells. GO and KEGG enrichment analysis showed that NCAPs and their interacting genes were mainly enriched in organelle fission for biological processes (BP), spindle for cellular component (CC), tubulin binding for molecular function (MF), and 'Cell cycle' pathway. METHODS We explored the expression of NCAP family members by ONCOMINE, and GEPIA databases. Additionally, the prognostic value of NCAP family genes in sarcoma was detected by Kaplan-Meier Plotter and GEPIA databases. Moreover, we explored the relationship between NCAP family gene expression level and immune infiltration using the TIMER database. Finally, we performed GO and KEGG analysis for NCAPs-related genes by DAVID database. CONCLUSION The six members of NCAP gene family can be used as biomarkers to predict the prognosis of sarcoma. They were also correlated with the low immune infiltration in sarcoma.
Collapse
Affiliation(s)
- Guangyao Jiang
- Department of Orthopedics, People’s Hospital of Pingchang County, Pingchang, Sichuan 636400, China
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Qunyan Tian
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Peikai Shi
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518000, China
| | - Zhigao Li
- Department of General Surgery, People’s Hospital of Pingchang County, Pingchang, Sichuan 636400, China
| | - Yan Li
- Department of Orthopedics, People’s Hospital of Pingchang County, Pingchang, Sichuan 636400, China
| | - Junjie Chen
- Department of Orthopedics, Longhui People’s Hospital, Shaoyang, Hunan 422200, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Ruiqi Chen
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Hua Zhong
- Department of Orthopedics, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong 510900, China
| | - Gen Wu
- Department of Orthopedics, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong 510900, China
| |
Collapse
|
6
|
Abstract
Cellular senescence is implicated in a wide range of physiological and pathological conditions throughout an organism's entire lifetime. In particular, it has become evident that senescence plays a causative role in aging and age-associated disorders. This is not due simply to the loss of function of senescent cells. Instead, the substantial alterations of the cellular activities of senescent cells, especially the array of secretory factors, impact the surrounding tissues or even entire organisms. Such non-cell-autonomous functionality is largely coordinated by tissue-specific genes, constituting a cell fate-determining state. Senescence can be viewed as a gain-of-function phenotype or a process of cell identity shift. Cellular functionality or lineage-specific gene expression is tightly linked to the cell type-specific epigenetic landscape, reinforcing the heterogeneity of senescence across cell types. Here, we aim to define the senescence cellular functionality and epigenetic features that may contribute to the gain-of-function phenotype.
Collapse
Affiliation(s)
- Ioana Olan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom; ,
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom; ,
| |
Collapse
|
7
|
Arruda NL, Bryan AF, Dowen JM. PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome. Epigenetics Chromatin 2022; 15:30. [PMID: 35986423 PMCID: PMC9392266 DOI: 10.1186/s13072-022-00463-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/28/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Cohesin is an important structural regulator of the genome, regulating both three-dimensional genome organization and gene expression. The core cohesin trimer interacts with various HEAT repeat accessory subunits, yielding cohesin complexes of distinct compositions and potentially distinct functions. The roles of the two mutually exclusive HEAT repeat subunits PDS5A and PDS5B are not well understood. RESULTS Here, we determine that PDS5A and PDS5B have highly similar localization patterns across the mouse embryonic stem cell (mESC) genome and they show a strong overlap with other cohesin HEAT repeat accessory subunits, STAG1 and STAG2. Using CRISPR/Cas9 genome editing to generate individual stable knockout lines for PDS5A and PDS5B, we find that loss of one PDS5 subunit does not alter the distribution of the other PDS5 subunit, nor the core cohesin complex. Both PDS5A and PDS5B are required for proper gene expression, yet they display only partially overlapping effects on gene targets. Remarkably, gene expression following dual depletion of the PDS5 HEAT repeat proteins does not completely overlap the gene expression changes caused by dual depletion of the STAG HEAT repeat proteins, despite the overlapping genomic distribution of all four proteins. Furthermore, dual loss of PDS5A and PDS5B decreases cohesin association with NIPBL and WAPL, reduces SMC3 acetylation, and does not alter overall levels of cohesin on the genome. CONCLUSIONS This work reveals the importance of PDS5A and PDS5B for proper cohesin function. Loss of either subunit has little effect on cohesin localization across the genome yet PDS5A and PDS5B are differentially required for gene expression.
Collapse
Affiliation(s)
- Nicole L Arruda
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Audra F Bryan
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jill M Dowen
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| |
Collapse
|
8
|
Macdonald L, Taylor GC, Brisbane JM, Christodoulou E, Scott L, von Kriegsheim A, Rossant J, Gu B, Wood AJ. Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons. eLife 2022; 11:e77987. [PMID: 35736539 PMCID: PMC9273210 DOI: 10.7554/elife.77987] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Auxin-inducible degrons are a chemical genetic tool for targeted protein degradation and are widely used to study protein function in cultured mammalian cells. Here, we develop CRISPR-engineered mouse lines that enable rapid and highly specific degradation of tagged endogenous proteins in vivo. Most but not all cell types are competent for degradation. By combining ligand titrations with genetic crosses to generate animals with different allelic combinations, we show that degradation kinetics depend upon the dose of the tagged protein, ligand, and the E3 ligase substrate receptor TIR1. Rapid degradation of condensin I and II - two essential regulators of mitotic chromosome structure - revealed that both complexes are individually required for cell division in precursor lymphocytes, but not in their differentiated peripheral lymphocyte derivatives. This generalisable approach provides unprecedented temporal control over the dose of endogenous proteins in mouse models, with implications for studying essential biological pathways and modelling drug activity in mammalian tissues.
Collapse
Affiliation(s)
- Lewis Macdonald
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Gillian C Taylor
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Jennifer Margaret Brisbane
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Ersi Christodoulou
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Lucy Scott
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick ChildrenTorontoCanada
| | - Bin Gu
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State UniversityEast LansingUnited States
- Department of Biomedical Engineering; Michigan State UniversityEast LansingUnited States
- Institute for Quantitative Health Science and Engineering, Michigan State UniversityEast LansingUnited States
| | - Andrew J Wood
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| |
Collapse
|
9
|
Haase J, Chen R, Parker WM, Bonner MK, Jenkins LM, Kelly AE. The TFIIH complex is required to establish and maintain mitotic chromosome structure. eLife 2022; 11:75475. [PMID: 35293859 PMCID: PMC8956287 DOI: 10.7554/elife.75475] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Condensins compact chromosomes to promote their equal segregation during mitosis, but the mechanism of condensin engagement with and action on chromatin is incompletely understood. Here, we show that the general transcription factor TFIIH complex is continuously required to establish and maintain a compacted chromosome structure in transcriptionally silent Xenopus egg extracts. Inhibiting the DNA-dependent ATPase activity of the TFIIH complex subunit XPB rapidly and reversibly induces a complete loss of chromosome structure and prevents the enrichment of condensins I and II, but not topoisomerase II, on chromatin. In addition, inhibiting TFIIH prevents condensation of both mouse and Xenopus nuclei in Xenopus egg extracts, which suggests an evolutionarily conserved mechanism of TFIIH action. Reducing nucleosome density through partial histone depletion restores chromosome structure and condensin enrichment in the absence of TFIIH activity. We propose that the TFIIH complex promotes mitotic chromosome condensation by dynamically altering the chromatin environment to facilitate condensin loading and condensin-dependent loop extrusion.
Collapse
Affiliation(s)
- Julian Haase
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Richard Chen
- Graduate School of Biomedical Sciences, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Wesley M Parker
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Mary Kate Bonner
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Lisa M Jenkins
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Alexander E Kelly
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| |
Collapse
|
10
|
Di Nardo M, Pallotta MM, Musio A. The multifaceted roles of cohesin in cancer. J Exp Clin Cancer Res 2022; 41:96. [PMID: 35287703 PMCID: PMC8919599 DOI: 10.1186/s13046-022-02321-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
The cohesin complex controls faithful chromosome segregation by pairing sister chromatids after DNA replication until mitosis. In addition, it is crucial for hierarchal three-dimensional organization of the genome, transcription regulation and maintaining DNA integrity. The core complex subunits SMC1A, SMC3, STAG1/2, and RAD21 as well as its modulators, have been found to be recurrently mutated in human cancers. The mechanisms by which cohesin mutations trigger cancer development and disease progression are still poorly understood. Since cohesin is involved in a range of chromosome-related processes, the outcome of cohesin mutations in cancer is complex. Herein, we discuss recent discoveries regarding cohesin that provide new insight into its role in tumorigenesis.
Collapse
Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Maria M. Pallotta
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| |
Collapse
|
11
|
Choi EH, Yoon S, Koh YE, Hong TK, Do JT, Lee BK, Hahn Y, Kim KP. Meiosis-specific cohesin complexes display essential and distinct roles in mitotic embryonic stem cell chromosomes. Genome Biol 2022; 23:70. [PMID: 35241136 PMCID: PMC8892811 DOI: 10.1186/s13059-022-02632-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cohesin is a chromosome-associated SMC-kleisin complex that mediates sister chromatid cohesion, recombination, and most chromosomal processes during mitosis and meiosis. However, it remains unclear whether meiosis-specific cohesin complexes are functionally active in mitotic chromosomes. RESULTS Through high-resolution 3D-structured illumination microscopy (3D-SIM) and functional analyses, we report multiple biological processes associated with the meiosis-specific cohesin components, α-kleisin REC8 and STAG3, and the distinct loss of function of meiotic cohesin during the cell cycle of embryonic stem cells (ESCs). First, we show that STAG3 is required for the efficient localization of REC8 to the nucleus by interacting with REC8. REC8-STAG3-containing cohesin regulates topological properties of chromosomes and maintains sister chromatid cohesion. Second, REC8-cohesin has additional sister chromatid cohesion roles in concert with mitotic RAD21-cohesin on ESC chromosomes. SIM imaging of REC8 and RAD21 co-staining revealed that the two types of α-kleisin subunits exhibited distinct loading patterns along ESC chromosomes. Third, knockdown of REC8 or RAD21-cohesin not only leads to higher rates of premature sister chromatid separation and delayed replication fork progression, which can cause proliferation and developmental defects, but also enhances chromosome compaction by hyperloading of retinoblastoma protein-condensin complexes from the prophase onward. CONCLUSIONS Our findings indicate that the delicate balance between mitotic and meiotic cohesins may regulate ESC-specific chromosomal organization and the mitotic program.
Collapse
Affiliation(s)
- Eui-Hwan Choi
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Seobin Yoon
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Young Eun Koh
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Tae Kyung Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, South Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, South Korea
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University of Albany-State University of New York, Rensselaer, NY, USA
| | - Yoonsoo Hahn
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Keun P Kim
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea.
| |
Collapse
|
12
|
Mfarej MG, Skibbens RV. Genetically induced redox stress occurs in a yeast model for Roberts syndrome. G3 (BETHESDA, MD.) 2022; 12:6460337. [PMID: 34897432 PMCID: PMC9210317 DOI: 10.1093/g3journal/jkab426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 12/31/2022]
Abstract
Roberts syndrome (RBS) is a multispectrum developmental disorder characterized by severe limb, craniofacial, and organ abnormalities and often intellectual disabilities. The genetic basis of RBS is rooted in loss-of-function mutations in the essential N-acetyltransferase ESCO2 which is conserved from yeast (Eco1/Ctf7) to humans. ESCO2/Eco1 regulate many cellular processes that impact chromatin structure, chromosome transmission, gene expression, and repair of the genome. The etiology of RBS remains contentious with current models that include transcriptional dysregulation or mitotic failure. Here, we report evidence that supports an emerging model rooted in defective DNA damage responses. First, the results reveal that redox stress is elevated in both eco1 and cohesion factor Saccharomyces cerevisiae mutant cells. Second, we provide evidence that Eco1 and cohesion factors are required for the repair of oxidative DNA damage such that ECO1 and cohesin gene mutations result in reduced cell viability and hyperactivation of DNA damage checkpoints that occur in response to oxidative stress. Moreover, we show that mutation of ECO1 is solely sufficient to induce endogenous redox stress and sensitizes mutant cells to exogenous genotoxic challenges. Remarkably, antioxidant treatment desensitizes eco1 mutant cells to a range of DNA damaging agents, raising the possibility that modulating the cellular redox state may represent an important avenue of treatment for RBS and tumors that bear ESCO2 mutations.
Collapse
Affiliation(s)
- Michael G Mfarej
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Robert V Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| |
Collapse
|
13
|
Vos ESM, Valdes-Quezada C, Huang Y, Allahyar A, Verstegen MJAM, Felder AK, van der Vegt F, Uijttewaal ECH, Krijger PHL, de Laat W. Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression. Mol Cell 2021; 81:3082-3095.e6. [PMID: 34197738 DOI: 10.1016/j.molcel.2021.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 04/28/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022]
Abstract
To understand how chromatin domains coordinate gene expression, we dissected select genetic elements organizing topology and transcription around the Prdm14 super enhancer in mouse embryonic stem cells. Taking advantage of allelic polymorphisms, we developed methods to sensitively analyze changes in chromatin topology, gene expression, and protein recruitment. We show that enhancer insulation does not rely strictly on loop formation between its flanking boundaries, that the enhancer activates the Slco5a1 gene beyond its prominent domain boundary, and that it recruits cohesin for loop extrusion. Upon boundary inversion, we find that oppositely oriented CTCF terminates extrusion trajectories but does not stall cohesin, while deleted or mutated CTCF sites allow cohesin to extend its trajectory. Enhancer-mediated gene activation occurs independent of paused loop extrusion near the gene promoter. We expand upon the loop extrusion model to propose that cohesin loading and extrusion trajectories originating at an enhancer contribute to gene activation.
Collapse
Affiliation(s)
- Erica S M Vos
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Christian Valdes-Quezada
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Yike Huang
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Amin Allahyar
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Anna-Karina Felder
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Floor van der Vegt
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Esther C H Uijttewaal
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
| |
Collapse
|
14
|
García-Gutiérrez P, García-Domínguez M. BETting on a Transcriptional Deficit as the Main Cause for Cornelia de Lange Syndrome. Front Mol Biosci 2021; 8:709232. [PMID: 34386522 PMCID: PMC8353280 DOI: 10.3389/fmolb.2021.709232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a human developmental syndrome with complex multisystem phenotypic features. It has been traditionally considered a cohesinopathy together with other phenotypically related diseases because of their association with mutations in subunits of the cohesin complex. Despite some overlap, the clinical manifestations of cohesinopathies vary considerably and, although their precise molecular mechanisms are not well defined yet, the potential pathomechanisms underlying these diverse developmental defects have been theoretically linked to alterations of the cohesin complex function. The cohesin complex plays a critical role in sister chromatid cohesion, but this function is not affected in CdLS. In the last decades, a non-cohesion-related function of this complex on transcriptional regulation has been well established and CdLS pathoetiology has been recently associated to gene expression deregulation. Up to 70% of CdLS cases are linked to mutations in the cohesin-loading factor NIPBL, which has been shown to play a prominent function on chromatin architecture and transcriptional regulation. Therefore, it has been suggested that CdLS can be considered a transcriptomopathy. Actually, CdLS-like phenotypes have been associated to mutations in chromatin-associated proteins, as KMT2A, AFF4, EP300, TAF6, SETD5, SMARCB1, MAU2, ZMYND11, MED13L, PHIP, ARID1B, NAA10, BRD4 or ANKRD11, most of which have no known direct association with cohesin. In the case of BRD4, a critical highly investigated transcriptional coregulator, an interaction with NIPBL has been recently revealed, providing evidence on their cooperation in transcriptional regulation of developmentally important genes. This new finding reinforces the notion of an altered gene expression program during development as the major etiological basis for CdLS. In this review, we intend to integrate the recent available evidence on the molecular mechanisms underlying the clinical manifestations of CdLS, highlighting data that favors a transcription-centered framework, which support the idea that CdLS could be conceptualized as a transcriptomopathy.
Collapse
Affiliation(s)
- Pablo García-Gutiérrez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| | - Mario García-Domínguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| |
Collapse
|
15
|
Municio C, Antosz W, Grasser KD, Kornobis E, Van Bel M, Eguinoa I, Coppens F, Bräutigam A, Lermontova I, Bruckmann A, Zelkowska K, Houben A, Schubert V. The Arabidopsis condensin CAP-D subunits arrange interphase chromatin. THE NEW PHYTOLOGIST 2021; 230:972-987. [PMID: 33475158 DOI: 10.1111/nph.17221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Condensins are best known for their role in shaping chromosomes. Other functions such as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals, but little is known about their function in plants. To elucidate the specific composition of condensin complexes and the expression of CAP-D2 (condensin I) and CAP-D3 (condensin II), we performed biochemical analyses in Arabidopsis. The role of CAP-D3 in interphase chromatin organization and function was evaluated using cytogenetic and transcriptome analysis in cap-d3 T-DNA insertion mutants. CAP-D2 and CAP-D3 are highly expressed in mitotically active tissues. In silico and pull-down experiments indicate that both CAP-D proteins interact with the other condensin I and II subunits. In cap-d3 mutants, an association of heterochromatic sequences occurs, but the nuclear size and the general histone and DNA methylation patterns remain unchanged. Also, CAP-D3 influences the expression of genes affecting the response to water, chemicals, and stress. The expression and composition of the condensin complexes in Arabidopsis are similar to those in other higher eukaryotes. We propose a model for the CAP-D3 function during interphase in which CAP-D3 localizes in euchromatin loops to stiffen them and consequently separates centromeric regions and 45S rDNA repeats.
Collapse
Affiliation(s)
- Celia Municio
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Wojciech Antosz
- Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Etienne Kornobis
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, 75015, Paris, France
- Hub de Bioinformatique et Biostatistique -Département Biologie Computationnelle, Institut Pasteur, 75015, Paris, France
| | - Michiel Van Bel
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, 9052, Gent, Belgium
| | - Ignacio Eguinoa
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, 9052, Gent, Belgium
| | - Frederik Coppens
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, 9052, Gent, Belgium
| | - Andrea Bräutigam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Center, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Katarzyna Zelkowska
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| |
Collapse
|
16
|
Paulson JR, Hudson DF, Cisneros-Soberanis F, Earnshaw WC. Mitotic chromosomes. Semin Cell Dev Biol 2021; 117:7-29. [PMID: 33836947 PMCID: PMC8406421 DOI: 10.1016/j.semcdb.2021.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 01/25/2023]
Abstract
Our understanding of the structure and function of mitotic chromosomes has come a long way since these iconic objects were first recognized more than 140 years ago, though many details remain to be elucidated. In this chapter, we start with the early history of chromosome studies and then describe the path that led to our current understanding of the formation and structure of mitotic chromosomes. We also discuss some of the remaining questions. It is now well established that each mitotic chromatid consists of a central organizing region containing a so-called "chromosome scaffold" from which loops of DNA project radially. Only a few key non-histone proteins and protein complexes are required to form the chromosome: topoisomerase IIα, cohesin, condensin I and condensin II, and the chromokinesin KIF4A. These proteins are concentrated along the axis of the chromatid. Condensins I and II are primarily responsible for shaping the chromosome and the scaffold, and they produce the loops of DNA by an ATP-dependent process known as loop extrusion. Modelling of Hi-C data suggests that condensin II adopts a spiral staircase arrangement with an extruded loop extending out from each step in a roughly helical pattern. Condensin I then forms loops nested within these larger condensin II loops, thereby giving rise to the final compaction of the mitotic chromosome in a process that requires Topo IIα.
Collapse
Affiliation(s)
- James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA.
| | - Damien F Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Fernanda Cisneros-Soberanis
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
| |
Collapse
|
17
|
Rivosecchi J, Jost D, Vachez L, Gautier FD, Bernard P, Vanoosthuyse V. RNA polymerase backtracking results in the accumulation of fission yeast condensin at active genes. Life Sci Alliance 2021; 4:4/6/e202101046. [PMID: 33771877 PMCID: PMC8046420 DOI: 10.26508/lsa.202101046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 12/23/2022] Open
Abstract
Using both experiments and mathematical modelling, the authors show that RNA polymerase backtracking contributes to the accumulation of condensin in the termination zone of active genes. The mechanisms leading to the accumulation of the SMC complexes condensins around specific transcription units remain unclear. Observations made in bacteria suggested that RNA polymerases (RNAPs) constitute an obstacle to SMC translocation, particularly when RNAP and SMC travel in opposite directions. Here we show in fission yeast that gene termini harbour intrinsic condensin-accumulating features whatever the orientation of transcription, which we attribute to the frequent backtracking of RNAP at gene ends. Consistent with this, to relocate backtracked RNAP2 from gene termini to gene bodies was sufficient to cancel the accumulation of condensin at gene ends and to redistribute it evenly within transcription units, indicating that RNAP backtracking may play a key role in positioning condensin. Formalization of this hypothesis in a mathematical model suggests that the inclusion of a sub-population of RNAP with longer dwell-times is essential to fully recapitulate the distribution profiles of condensin around active genes. Taken together, our data strengthen the idea that dense arrays of proteins tightly bound to DNA alter the distribution of condensin on chromosomes.
Collapse
Affiliation(s)
- Julieta Rivosecchi
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - Laetitia Vachez
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - François Dr Gautier
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - Pascal Bernard
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - Vincent Vanoosthuyse
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| |
Collapse
|
18
|
Carico ZM, Stefan HC, Justice M, Yimit A, Dowen JM. A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression. PLoS Genet 2021; 17:e1009435. [PMID: 33760811 PMCID: PMC7990204 DOI: 10.1371/journal.pgen.1009435] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/20/2021] [Indexed: 12/21/2022] Open
Abstract
The cohesin complex spatially organizes interphase chromatin by bringing distal genomic loci into close physical proximity, looping out the intervening DNA. Mutation of cohesin complex subunits is observed in cancer and developmental disorders, but the mechanisms through which these mutations may contribute to disease remain poorly understood. Here, we investigate a recurrent missense mutation to the hinge domain of the cohesin subunit SMC1A, observed in acute myeloid leukemia. Engineering this mutation into murine embryonic stem cells caused widespread changes in gene expression, including dysregulation of the pluripotency gene expression program. This mutation reduced cohesin levels at promoters and enhancers, decreased DNA loops and interactions across short genomic distances, and weakened insulation at CTCF-mediated DNA loops. These findings provide insight into how altered cohesin function contributes to disease and identify a requirement for the cohesin hinge domain in three-dimensional chromatin structure.
Collapse
Affiliation(s)
- Zachary M. Carico
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Holden C. Stefan
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Megan Justice
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Askar Yimit
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jill M. Dowen
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| |
Collapse
|
19
|
Spreafico M, Mangano E, Mazzola M, Consolandi C, Bordoni R, Battaglia C, Bicciato S, Marozzi A, Pistocchi A. The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression. Int J Mol Sci 2020; 21:E9719. [PMID: 33352756 PMCID: PMC7766774 DOI: 10.3390/ijms21249719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity, such as the cohesin genes and their regulator NIPBL. In our previous studies, using a zebrafish model for nipblb knockdown, we described the effect of nipblb loss-of-function in specific contexts, such as central nervous system development and hematopoiesis. However, the genome-wide transcriptional impact of nipblb loss-of-function in zebrafish embryos at diverse developmental stages remains under investigation. By RNA-seq analyses in zebrafish embryos at 24 h post-fertilization, we examined genome-wide effects of nipblb knockdown on transcriptional programs. Differential gene expression analysis revealed that nipblb loss-of-function has an impact on gene expression at 24 h post fertilization, mainly resulting in gene inactivation. A similar transcriptional effect has also been reported in other organisms, supporting the use of zebrafish as a model to understand the role of Nipbl in gene regulation during early vertebrate development. Moreover, we unraveled a connection between nipblb-dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes, enforcing our previous evidence on the involvement of NIPBL-related transcriptional dysregulation in hematological malignancies.
Collapse
Affiliation(s)
- Marco Spreafico
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Eleonora Mangano
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Mara Mazzola
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Roberta Bordoni
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Cristina Battaglia
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio-Emilia, Via G. Campi 287, 41125 Modena, Italy;
| | - Anna Marozzi
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Anna Pistocchi
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| |
Collapse
|
20
|
Weyburne E, Bosco G. Cancer-associated mutations in the condensin II subunit CAPH2 cause genomic instability through telomere dysfunction and anaphase chromosome bridges. J Cell Physiol 2020; 236:3579-3598. [PMID: 33078399 PMCID: PMC7983937 DOI: 10.1002/jcp.30113] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 01/10/2023]
Abstract
Genome instability in cancer drives tumor heterogeneity, undermines the success of therapies, and leads to metastasis and recurrence. Condensins are conserved chromatin‐binding proteins that promote genomic stability, mainly by ensuring proper condensation of chromatin and mitotic chromosome segregation. Condensin mutations are found in human tumors, but it is not known how or even if such mutations promote cancer progression. In this study, we focus on condensin II subunit CAPH2 and specific CAPH2 mutations reported to be enriched in human cancer patients, and we test how CAPH2 cancer‐specific mutations may lead to condensin II complex dysfunction and contribute to genome instability. We find that R551P, R551S, and S556F mutations in CAPH2 cause genomic instability by causing DNA damage, anaphase defects, micronuclei, and chromosomal instability. DNA damage and anaphase defects are caused primarily by ataxia telangiectasia and Rad3‐related‐dependent telomere dysfunction, as anaphase bridges are enriched for telomeric repeat sequences. We also show that these mutations decrease the binding of CAPH2 to the ATPase subunit SMC4 as well as the rest of the condensin II complex, and decrease the amount of CAPH2 protein bound to chromatin. Thus, in vivo the R551P, R551S, and S556F cancer‐specific CAPH2 mutant proteins are likely to impair condensin II complex formation, impede condensin II activity during mitosis and interphase, and promote genetic heterogeneity in cell populations that can lead to clonal outgrowth of cancer cells with highly diverse genotypes.
Collapse
Affiliation(s)
- Emily Weyburne
- Department of Molecular and Systems Biology, Dartmouth College, Hanover, New Hampshire, USA
| | - Giovanni Bosco
- Department of Molecular and Systems Biology, Dartmouth College, Hanover, New Hampshire, USA
| |
Collapse
|
21
|
Senigl F, Maman Y, Dinesh RK, Alinikula J, Seth RB, Pecnova L, Omer AD, Rao SSP, Weisz D, Buerstedde JM, Aiden EL, Casellas R, Hejnar J, Schatz DG. Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. Cell Rep 2020; 29:3902-3915.e8. [PMID: 31851922 PMCID: PMC6980758 DOI: 10.1016/j.celrep.2019.11.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/26/2019] [Accepted: 11/08/2019] [Indexed: 12/26/2022] Open
Abstract
Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes but also causes mutations in other parts of the genome. We have used lentiviral SHM reporter vectors to identify regions of the genome that are susceptible (“hot”) and resistant (“cold”) to SHM, revealing that SHM susceptibility and resistance are often properties of entire topologically associated domains (TADs). Comparison of hot and cold TADs reveals that while levels of transcription are equivalent, hot TADs are enriched for the cohesin loader NIPBL, super-enhancers, markers of paused/stalled RNA polymerase 2, and multiple important B cell transcription factors. We demonstrate that at least some hot TADs contain enhancers that possess SHM targeting activity and that insertion of a strong Ig SHM-targeting element into a cold TAD renders it hot. Our findings lead to a model for SHM susceptibility involving the cooperative action of cis-acting SHM targeting elements and the dynamic and architectural properties of TADs. Senigl et al. show that genome susceptibility to somatic hypermutation (SHM) is confined within topologically associated domains (TADs) and is linked to markers of strong enhancers and stalled transcription and high levels of the cohesin loader NIPBL. Insertion of an ectopic SHM targeting element renders an entire TAD susceptible to SHM.
Collapse
Affiliation(s)
- Filip Senigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic.
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Jukka Alinikula
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Rashu B Seth
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Lubomira Pecnova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Arina D Omer
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Erez Lieberman Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jiri Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA.
| |
Collapse
|
22
|
Jiang Y, Huang J, Lun K, Li B, Zheng H, Li Y, Zhou R, Duan W, Wang C, Feng Y, Yao H, Li C, Ji X. Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III. Genome Biol 2020; 21:158. [PMID: 32616013 PMCID: PMC7331254 DOI: 10.1186/s13059-020-02067-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/08/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The relationship between transcription and the 3D chromatin structure is debated. Multiple studies have shown that transcription affects global Cohesin binding and 3D genome structures. However, several other studies have indicated that inhibited transcription does not alter chromatin conformations. RESULTS We provide the most comprehensive evidence to date to demonstrate that transcription plays a relatively modest role in organizing the local, small-scale chromatin structures in mammalian cells. We show degraded Pol I, Pol II, and Pol III proteins in mESCs cause few or no changes in large-scale 3D chromatin structures, selected RNA polymerases with a high abundance of binding sites or active promoter-associated interactions appear to be relatively more affected after the degradation, transcription inhibition alters local, small loop domains, as indicated by high-resolution chromatin interaction maps, and loops with bound Pol II but without Cohesin or CTCF are identified and found to be largely unchanged after transcription inhibition. Interestingly, Pol II depletion for a longer time significantly affects the chromatin accessibility and Cohesin occupancy, suggesting that RNA polymerases are capable of affecting the 3D genome indirectly. These direct and indirect effects explain the previous inconsistent findings on the influence of transcription inhibition on the 3D genome. CONCLUSIONS We conclude that Pol I, Pol II, and Pol III loss alters local, small-scale chromatin interactions in mammalian cells, suggesting that the 3D chromatin structures are pre-established and relatively stable.
Collapse
Affiliation(s)
- Yongpeng Jiang
- 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
| | - Jie Huang
- 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
| | - Kehuan Lun
- 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
| | - Boyuan Li
- 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
| | - Haonan Zheng
- 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
| | - Yuanjun Li
- 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
| | - Rong Zhou
- 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
| | - Wenjia Duan
- 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
| | - Yuanqing Feng
- 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
| | - Hong Yao
- 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
| | - Cheng Li
- Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Center for Statistical Science, Center for Bioinformatics, 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.
| |
Collapse
|
23
|
Sarogni P, Pallotta MM, Musio A. Cornelia de Lange syndrome: from molecular diagnosis to therapeutic approach. J Med Genet 2020; 57:289-295. [PMID: 31704779 PMCID: PMC7231464 DOI: 10.1136/jmedgenet-2019-106277] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/08/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a severe genetic disorder characterised by multisystemic malformations. CdLS is due to pathogenetic variants in NIPBL, SMC1A, SMC3, RAD21 and HDAC8 genes which belong to the cohesin pathway. Cohesin plays a pivotal role in chromatid cohesion, gene expression, and DNA repair. In this review, we will discuss how perturbations in those biological processes contribute to CdLS phenotype and will emphasise the state-of-art of CdLS therapeutic approaches.
Collapse
Affiliation(s)
- Patrizia Sarogni
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Maria M Pallotta
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| |
Collapse
|
24
|
Justice M, Carico ZM, Stefan HC, Dowen JM. A WIZ/Cohesin/CTCF Complex Anchors DNA Loops to Define Gene Expression and Cell Identity. Cell Rep 2020; 31:107503. [PMID: 32294452 PMCID: PMC7212317 DOI: 10.1016/j.celrep.2020.03.067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/14/2020] [Accepted: 03/20/2020] [Indexed: 12/31/2022] Open
Abstract
Chromosome structure is a key regulator of gene expression. CTCF and cohesin play critical roles in structuring chromosomes by mediating physical interactions between distant genomic sites. The resulting DNA loops often contain genes and their cis-regulatory elements. Despite the importance of DNA loops in maintaining proper transcriptional regulation and cell identity, there is limited understanding of the molecular mechanisms that regulate their dynamics and function. We report a previously unrecognized role for WIZ (widely interspaced zinc finger-containing protein) in DNA loop architecture and regulation of gene expression. WIZ forms a complex with cohesin and CTCF that occupies enhancers, promoters, insulators, and anchors of DNA loops. Aberrant WIZ function alters cohesin occupancy and increases the number of DNA loop structures in the genome. WIZ is required for proper gene expression and transcriptional insulation. Our results uncover an unexpected role for WIZ in DNA loop architecture, transcriptional control, and maintenance of cell identity.
Collapse
Affiliation(s)
- Megan Justice
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zachary M Carico
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Holden C Stefan
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jill M Dowen
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
25
|
Avagliano L, Parenti I, Grazioli P, Di Fede E, Parodi C, Mariani M, Kaiser FJ, Selicorni A, Gervasini C, Massa V. Chromatinopathies: A focus on Cornelia de Lange syndrome. Clin Genet 2020; 97:3-11. [PMID: 31721174 DOI: 10.1111/cge.13674] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 01/01/2023]
Abstract
In recent years, many genes have been associated with chromatinopathies classified as "Cornelia de Lange Syndrome-like." It is known that the phenotype of these patients becomes less recognizable, overlapping to features characteristic of other syndromes caused by genetic variants affecting different regulators of chromatin structure and function. Therefore, Cornelia de Lange syndrome diagnosis might be arduous due to the seldom discordance between unexpected molecular diagnosis and clinical evaluation. Here, we review the molecular features of Cornelia de Lange syndrome, supporting the hypothesis that "CdLS-like syndromes" are part of a larger "rare disease family" sharing multiple clinical features and common disrupted molecular pathways.
Collapse
Affiliation(s)
- Laura Avagliano
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Ilaria Parenti
- Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, Lübeck, Germany
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Paolo Grazioli
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Elisabetta Di Fede
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Chiara Parodi
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | | | - Frank J Kaiser
- Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, Lübeck, Germany
- DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | | | - Cristina Gervasini
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Valentina Massa
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| |
Collapse
|
26
|
Iwasaki O, Tanizawa H, Kim KD, Kossenkov A, Nacarelli T, Tashiro S, Majumdar S, Showe LC, Zhang R, Noma KI. Involvement of condensin in cellular senescence through gene regulation and compartmental reorganization. Nat Commun 2019; 10:5688. [PMID: 31831736 PMCID: PMC6908677 DOI: 10.1038/s41467-019-13604-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/11/2019] [Indexed: 01/21/2023] Open
Abstract
Senescence is induced by various stimuli such as oncogene expression and telomere shortening, referred to as oncogene-induced senescence (OIS) and replicative senescence (RS), respectively, and accompanied by global transcriptional alterations and 3D genome reorganization. Here, we demonstrate that the human condensin II complex participates in senescence via gene regulation and reorganization of euchromatic A and heterochromatic B compartments. Both OIS and RS are accompanied by A-to-B and B-to-A compartmental transitions, the latter of which occur more frequently and are undergone by 14% (430 Mb) of the human genome. Mechanistically, condensin is enriched in A compartments and implicated in B-to-A transitions. The full activation of senescence genes (SASP genes and p53 targets) requires condensin; its depletion impairs senescence markers. This study describes that condensin reinforces euchromatic A compartments and promotes B-to-A transitions, both of which are coupled to optimal expression of senescence genes, thereby allowing condensin to contribute to senescent processes.
Collapse
Affiliation(s)
- Osamu Iwasaki
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Hideki Tanizawa
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17456, Republic of Korea
| | | | | | - Sanki Tashiro
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | | | | | - Rugang Zhang
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Ken-Ichi Noma
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA.
| |
Collapse
|
27
|
Deutschman E, Ward JR, Kumar A, Ray G, Welch N, Lemieux ME, Dasarathy S, Longworth MS. Condensin II protein dysfunction impacts mitochondrial respiration and mitochondrial oxidative stress responses. J Cell Sci 2019; 132:jcs233783. [PMID: 31653782 PMCID: PMC6899004 DOI: 10.1242/jcs.233783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/21/2019] [Indexed: 12/28/2022] Open
Abstract
The maintenance of mitochondrial respiratory function and homeostasis is essential to human health. Here, we identify condensin II subunits as novel regulators of mitochondrial respiration and mitochondrial stress responses. Condensin II is present in the nucleus and cytoplasm. While the effects of condensin II depletion on nuclear genome organization are well studied, the effects on essential cytoplasmic and metabolic processes are not as well understood. Excitingly, we observe that condensin II chromosome-associated protein (CAP) subunits individually localize to different regions of mitochondria, suggesting possible mitochondrial-specific functions independent from those mediated by the canonical condensin II holocomplex. Changes in cellular ATP levels and mitochondrial respiration are observed in condensin II CAP subunit-deficient cells. Surprisingly, we find that loss of NCAPD3 also sensitizes cells to oxidative stress. Together, these studies identify new, and possibly independent, roles for condensin II CAP subunits in preventing mitochondrial damage and dysfunction. These findings reveal a new area of condensin protein research that could contribute to the identification of targets to treat diseases where aberrant function of condensin II proteins is implicated.
Collapse
Affiliation(s)
- Emily Deutschman
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland, OH 44106, USA
| | - Jacqueline R Ward
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Avinash Kumar
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Greeshma Ray
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Nicole Welch
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | | | - Srinivisan Dasarathy
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Michelle S Longworth
- Department of Inflammation and Immunity, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| |
Collapse
|
28
|
Huang B, Wang B, Yuk-Wai Lee W, Pong U K, Leung KT, Li X, Liu Z, Chen R, Lin JC, Tsang LL, Liu B, Ruan YC, Chan HC, Li G, Jiang X. KDM3A and KDM4C Regulate Mesenchymal Stromal Cell Senescence and Bone Aging via Condensin-mediated Heterochromatin Reorganization. iScience 2019; 21:375-390. [PMID: 31704649 PMCID: PMC6888768 DOI: 10.1016/j.isci.2019.10.041] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/30/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022] Open
Abstract
Epigenomic changes and stem cell deterioration are two hallmarks of aging. Accumulating evidence suggest that senescence of mesenchymal stromal cells (MSCs) perpetuates aging or age-related diseases. Here we report that two H3K9 demethylases, KDM3A and KDM4C, regulate heterochromatin reorganization via transcriptionally activating condensin components NCAPD2 and NCAPG2 during MSC senescence. Suppression of KDM3A or KDM4C by either genetic or biochemical approach leads to robust DNA damage response and aggravates cellular senescence, whereas overexpression of KDM3A/KDM4C or NCAPD2 promotes heterochromatin reorganization and blunts DNA damage response. Moreover, MSCs derived from Kdm3a−/− mice exhibit defective chromosome organization and exacerbated DNA damage response, which are associated with accelerated bone aging. Consistently, analysis of human bone marrow MSCs and transcriptome database reveals inverse correlation of KDM3A/KDM4C and/or NCAPD2/NCAPG2 with aging. Taken together, the present finding unveils that H3K9 demethylases function as a surveillance mechanism to restrain DNA damage accumulation in stem cells during aging. KDM3A and KDM4C restrain DNA damage response during MSC senescence KDM3A and KDM4C promote heterochromatin reorganization via induction of condensin Loss of Kdm3a exacerbates MSC senescence and bone aging in mice Chronological aging of human MSCs is associated with reduced expression of KDM3A and KDM4C
Collapse
Affiliation(s)
- Biao Huang
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Room 409A, Lo Kwee Seong Integrated Biomedical Sciences Building, Area 39, Shatin, Hong Kong SAR, PR China; The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China
| | - Bin Wang
- The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China; Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Wayne Yuk-Wai Lee
- The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China; Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Kin Pong U
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Room 409A, Lo Kwee Seong Integrated Biomedical Sciences Building, Area 39, Shatin, Hong Kong SAR, PR China; The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China
| | - Kam Tong Leung
- Department of Pediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Xican Li
- School of Chinese Herbal Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China; Innovative Research & Development Laboratory of TCM, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Zhenqing Liu
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Room 409A, Lo Kwee Seong Integrated Biomedical Sciences Building, Area 39, Shatin, Hong Kong SAR, PR China
| | - Rui Chen
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Room 409A, Lo Kwee Seong Integrated Biomedical Sciences Building, Area 39, Shatin, Hong Kong SAR, PR China
| | - Jia Cheng Lin
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Room 409A, Lo Kwee Seong Integrated Biomedical Sciences Building, Area 39, Shatin, Hong Kong SAR, PR China; The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China
| | - Lai Ling Tsang
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Room 409A, Lo Kwee Seong Integrated Biomedical Sciences Building, Area 39, Shatin, Hong Kong SAR, PR China; The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China
| | - Baohua Liu
- Shenzhen University Health Science Center, Shenzhen University, Shenzhen, PR China
| | - Ye Chun Ruan
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong, PR China
| | - Hsiao Chang Chan
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Room 409A, Lo Kwee Seong Integrated Biomedical Sciences Building, Area 39, Shatin, Hong Kong SAR, PR China; The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China
| | - Gang Li
- The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China; Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Xiaohua Jiang
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Room 409A, Lo Kwee Seong Integrated Biomedical Sciences Building, Area 39, Shatin, Hong Kong SAR, PR China; The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China.
| |
Collapse
|
29
|
Nakazawa N, Arakawa O, Yanagida M. Condensin locates at transcriptional termination sites in mitosis, possibly releasing mitotic transcripts. Open Biol 2019; 9:190125. [PMID: 31615333 PMCID: PMC6833218 DOI: 10.1098/rsob.190125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Condensin is an essential component of chromosome dynamics, including mitotic chromosome condensation and segregation, DNA repair, and development. Genome-wide localization of condensin is known to correlate with transcriptional activity. The functional relationship between condensin accumulation and transcription sites remains unclear, however. By constructing the auxin-inducible degron strain of condensin, herein we demonstrate that condensin does not affect transcription itself. Instead, RNA processing at transcriptional termination appears to define condensin accumulation sites during mitosis, in the fission yeast Schizosaccharomyces pombe. Combining the auxin-degron strain with the nda3 β-tubulin cold-sensitive (cs) mutant enabled us to inactivate condensin in mitotically arrested cells, without releasing the cells into anaphase. Transcriptional activation and termination were not affected by condensin's degron-mediated depletion, at heat-shock inducible genes or mitotically activated genes. On the other hand, condensin accumulation sites shifted approximately 500 bp downstream in the auxin-degron of 5′-3′ exoribonuclease Dhp1, in which transcripts became aberrantly elongated, suggesting that condensin accumulates at transcriptionally terminated DNA regions. Growth defects in mutant strains of 3′-processing ribonuclease and polyA cleavage factors were additive in condensin temperature-sensitive (ts) mutants. Considering condensin's in vitro activity to form double-stranded DNAs from unwound, single-stranded DNAs or DNA-RNA hybrids, condensin-mediated processing of mitotic transcripts at the 3′-end may be a prerequisite for faithful chromosome segregation.
Collapse
Affiliation(s)
- Norihiko Nakazawa
- Okinawa Institute of Science and Technology Graduate University, G0 Cell Unit, Onna-son, Okinawa 904-0495, Japan
| | - Orie Arakawa
- Okinawa Institute of Science and Technology Graduate University, G0 Cell Unit, Onna-son, Okinawa 904-0495, Japan
| | - Mitsuhiro Yanagida
- Okinawa Institute of Science and Technology Graduate University, G0 Cell Unit, Onna-son, Okinawa 904-0495, Japan
| |
Collapse
|
30
|
The Cornelia de Lange Syndrome-associated factor NIPBL interacts with BRD4 ET domain for transcription control of a common set of genes. Cell Death Dis 2019; 10:548. [PMID: 31320616 PMCID: PMC6639259 DOI: 10.1038/s41419-019-1792-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/17/2019] [Accepted: 07/02/2019] [Indexed: 01/19/2023]
Abstract
Mutations in NIPBL are the major cause of Cornelia de Lange Syndrome (CdLS). NIPBL is the cohesin-loading factor and has recently been associated with the BET (bromodomains and extra-terminal (ET) domain) proteins BRD2 and BRD4. Related to this, a CdLS-like phenotype has been described associated to BRD4 mutations. Here, we show direct interaction of NIPBL with different BET members in yeast, and selective interaction with BRD4 in cells, being the ET domain involved in the interaction. To understand the relationship between NIPBL and BET proteins, we have performed RNA-Seq expression analysis following depletion of the different proteins. Results indicate that genes regulated by NIPBL largely overlap with those regulated by BRD4 but not with those regulated by BRD2. ChIP-Seq analysis indicates preferential NIPBL occupancy at promoters, and knockdown experiments show mutual stabilization of NIPBL and BRD4 on co-regulated promoters. Moreover, human fibroblasts from CdLS probands with mutations in NIPBL show reduced BRD4 at co-occupied promoters. Functional analysis in vivo, using mutants of Drosophila melanogaster, confirmed the genetic interaction between Nipped-B and fs(1)h, the orthologs of human NIPBL and BRD4, respectively. Thus, we provide evidence for NIPBL and BRD4 cooperation in transcriptional regulation, which should contribute to explain the recently observed CdLS-like phenotype associated with BRD4 mutations.
Collapse
|
31
|
Wu S, Fatkhutdinov N, Rosin L, Luppino JM, Iwasaki O, Tanizawa H, Tang HY, Kossenkov AV, Gardini A, Noma KI, Speicher DW, Joyce EF, Zhang R. ARID1A spatially partitions interphase chromosomes. SCIENCE ADVANCES 2019; 5:eaaw5294. [PMID: 31131328 PMCID: PMC6531001 DOI: 10.1126/sciadv.aaw5294] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/12/2019] [Indexed: 05/12/2023]
Abstract
ARID1A, a subunit of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex, localizes to both promoters and enhancers to influence transcription. However, the role of ARID1A in higher-order spatial chromosome partitioning and genome organization is unknown. Here, we show that ARID1A spatially partitions interphase chromosomes and regulates higher-order genome organization. The SWI/SNF complex interacts with condensin II, and they display significant colocalizations at enhancers. ARID1A knockout drives the redistribution of condensin II preferentially at enhancers, which positively correlates with changes in transcription. ARID1A and condensin II contribute to transcriptionally inactive B-compartment formation, while ARID1A weakens the border strength of topologically associated domains. Condensin II redistribution induced by ARID1A knockout positively correlates with chromosome sizes, which negatively correlates with interchromosomal interactions. ARID1A loss increases the trans interactions of small chromosomes, which was validated by three-dimensional interphase chromosome painting. These results demonstrate that ARID1A is important for large-scale genome folding and spatially partitions interphase chromosomes.
Collapse
Affiliation(s)
- Shuai Wu
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Nail Fatkhutdinov
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
- Kazan Federal University, Kazan, Russia
| | - Leah Rosin
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer M. Luppino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Osamu Iwasaki
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Hideki Tanizawa
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Andrew V. Kossenkov
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Ken-ichi Noma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - David W. Speicher
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Eric F. Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
- Corresponding author.
| |
Collapse
|
32
|
Sarogni P, Palumbo O, Servadio A, Astigiano S, D'Alessio B, Gatti V, Cukrov D, Baldari S, Pallotta MM, Aretini P, Dell'Orletta F, Soddu S, Carella M, Toietta G, Barbieri O, Fontanini G, Musio A. Overexpression of the cohesin-core subunit SMC1A contributes to colorectal cancer development. J Exp Clin Cancer Res 2019; 38:108. [PMID: 30823889 PMCID: PMC6397456 DOI: 10.1186/s13046-019-1116-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/21/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cancer cells are characterized by chromosomal instability (CIN) and it is thought that errors in pathways involved in faithful chromosome segregation play a pivotal role in the genesis of CIN. Cohesin forms a large protein ring that binds DNA strands by encircling them. In addition to this central role in chromosome segregation, cohesin is also needed for DNA repair, gene transcription regulation and chromatin architecture. Though mutations in both cohesin and cohesin-regulator genes have been identified in many human cancers, the contribution of cohesin to cancer development is still under debate. METHODS Normal mucosa, early adenoma, and carcinoma samples deriving from 16 subjects affected by colorectal cancer (CRC) were analyzed by OncoScan for scoring both chromosome gains and losses (CNVs) and loss of heterozygosity (LOH). Then the expression of SMC1A was analyzed by immunochemistry in 66 subjects affected by CRC. The effects of SMC1A overexpression and mutated SMC1A were analyzed in vivo using immunocompromised mouse models. Finally, we measured global gene expression profiles in induced-tumors by RNA-seq. RESULTS Here we showed that SMC1A cohesin core gene was present as extra-copies, mutated, and overexpressed in human colorectal carcinomas. We then demonstrated that cohesin overexpression led to the development of aggressive cancers in immunocompromised mice through gene expression dysregulation. CONCLUSION Collectively, these results support a role of defective cohesin in the development of human colorectal cancer.
Collapse
Affiliation(s)
- Patrizia Sarogni
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Orazio Palumbo
- Division of Medical Genetics, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Adele Servadio
- Division of Pathology, Department of Surgery, University of Pisa, Pisa, Italy
| | - Simonetta Astigiano
- IRCCS Ospedale Policlinico San Martino, Department of Translational Oncology, Genoa, Italy
| | - Barbara D'Alessio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Veronica Gatti
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy.,Present address: Institute of Cell Biology and Neurobiology, National Research Council (CNR), Monterotondo, Italy
| | - Dubravka Cukrov
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Silvia Baldari
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy
| | - Maria Michela Pallotta
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Paolo Aretini
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, Italy
| | - Felice Dell'Orletta
- Institute for Computational Linguistics (ILC) "A. Zampolli", National Research Council (CNR), Pisa, Italy
| | - Silvia Soddu
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy
| | - Massimo Carella
- Division of Medical Genetics, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Gabriele Toietta
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy
| | - Ottavia Barbieri
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Gabriella Fontanini
- Division of Pathology, Department of Surgery, University of Pisa, Pisa, Italy
| | - Antonio Musio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy.
| |
Collapse
|
33
|
Oomen ME, Hansen AS, Liu Y, Darzacq X, Dekker J. CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning. Genome Res 2019; 29:236-249. [PMID: 30655336 PMCID: PMC6360813 DOI: 10.1101/gr.241547.118] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/15/2018] [Indexed: 12/28/2022]
Abstract
CCCTC-binding factor (CTCF) plays a key role in the formation of topologically associating domains (TADs) and loops in interphase. During mitosis TADs are absent, but how TAD formation is dynamically controlled during the cell cycle is not known. Several contradicting observations have been made regarding CTCF binding to mitotic chromatin using both genomics- and microscopy-based techniques. Here, we have used four different assays to address this debate. First, using 5C, we confirmed that TADs and CTCF loops are readily detected in interphase, but absent during prometaphase. Second, ATAC-seq analysis showed that CTCF sites display greatly reduced accessibility and lose the CTCF footprint in prometaphase, suggesting loss of CTCF binding and rearrangement of the nucleosomal array around the binding motif. In contrast, transcription start sites remain accessible in prometaphase, although adjacent nucleosomes can also become repositioned and occupy at least a subset of start sites during mitosis. Third, loss of site-specific CTCF binding was directly demonstrated using CUT&RUN. Histone modifications and histone variants are maintained in mitosis, suggesting a role in bookmarking of active CTCF sites. Finally, live-cell imaging, fluorescence recovery after photobleaching, and single molecule tracking showed that almost all CTCF chromatin binding is lost in prometaphase. Combined, our results demonstrate loss of CTCF binding to CTCF sites during prometaphase and rearrangement of the chromatin landscape around CTCF motifs. This, combined with loss of cohesin, would contribute to the observed loss of TADs and CTCF loops during mitosis and reveals that CTCF sites, key architectural cis-elements, display cell cycle stage–dependent dynamics in factor binding and nucleosome positioning.
Collapse
Affiliation(s)
- Marlies E Oomen
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Anders S Hansen
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, California 94720, USA
| | - Yu Liu
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, California 94720, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| |
Collapse
|
34
|
Condensin action and compaction. Curr Genet 2018; 65:407-415. [PMID: 30361853 DOI: 10.1007/s00294-018-0899-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 10/18/2018] [Accepted: 10/20/2018] [Indexed: 12/20/2022]
Abstract
Condensin is a multi-subunit protein complex that belongs to the family of structural maintenance of chromosomes (SMC) complexes. Condensins regulate chromosome structure in a wide range of processes including chromosome segregation, gene regulation, DNA repair and recombination. Recent research defined the structural features and molecular activities of condensins, but it is unclear how these activities are connected to the multitude of phenotypes and functions attributed to condensins. In this review, we briefly discuss the different molecular mechanisms by which condensins may regulate global chromosome compaction, organization of topologically associated domains, clustering of specific loci such as tRNA genes, rDNA segregation, and gene regulation.
Collapse
|
35
|
Hocquet C, Robellet X, Modolo L, Sun XM, Burny C, Cuylen-Haering S, Toselli E, Clauder-Münster S, Steinmetz L, Haering CH, Marguerat S, Bernard P. Condensin controls cellular RNA levels through the accurate segregation of chromosomes instead of directly regulating transcription. eLife 2018; 7:38517. [PMID: 30230473 PMCID: PMC6173581 DOI: 10.7554/elife.38517] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 09/18/2018] [Indexed: 12/15/2022] Open
Abstract
Condensins are genome organisers that shape chromosomes and promote their accurate transmission. Several studies have also implicated condensins in gene expression, although any mechanisms have remained enigmatic. Here, we report on the role of condensin in gene expression in fission and budding yeasts. In contrast to previous studies, we provide compelling evidence that condensin plays no direct role in the maintenance of the transcriptome, neither during interphase nor during mitosis. We further show that the changes in gene expression in post-mitotic fission yeast cells that result from condensin inactivation are largely a consequence of chromosome missegregation during anaphase, which notably depletes the RNA-exosome from daughter cells. Crucially, preventing karyotype abnormalities in daughter cells restores a normal transcriptome despite condensin inactivation. Thus, chromosome instability, rather than a direct role of condensin in the transcription process, changes gene expression. This knowledge challenges the concept of gene regulation by canonical condensin complexes.
Collapse
Affiliation(s)
- Clémence Hocquet
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | - Xavier Robellet
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | - Laurent Modolo
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Claire Burny
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | - Sara Cuylen-Haering
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Esther Toselli
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | | | - Lars Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian H Haering
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Samuel Marguerat
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pascal Bernard
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| |
Collapse
|
36
|
Comparing and Contrasting the Effects of Drosophila Condensin II Subunit dCAP-D3 Overexpression and Depletion in Vivo. Genetics 2018; 210:531-546. [PMID: 30068527 PMCID: PMC6216582 DOI: 10.1534/genetics.118.301344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/31/2018] [Indexed: 11/18/2022] Open
Abstract
The Condensin II complex plays important, conserved roles in genome organization throughout the cell cycle and in the regulation of gene expression. Previous studies have linked decreased Condensin II subunit expression with a variety of diseases. Here, we show that elevated levels of Condensin II subunits are detected in somatic cancers. To evaluate potential biological effects of elevated Condensin II levels, we overexpressed the Condensin II subunit, dCAP-D3 in Drosophila melanogaster larval tissues and examined the effects on the mitotic- and interphase-specific functions of Condensin II. Interestingly, while ubiquitous overexpression resulted in pupal lethality, tissue specific overexpression of dCAP-D3 caused formation of nucleoplasmic protein aggregates which slowed mitotic prophase progression, mimicking results observed when dCAP-D3 levels are depleted. Surprisingly, dCAP-D3 aggregate formation resulted in faster transitions from metaphase to anaphase. Overexpressed dCAP-D3 protein failed to precipitate other Condensin II subunits in nondividing tissues, but did cause changes to gene expression which occurred in a manner opposite of what was observed when dCAP-D3 levels were depleted in both dividing and nondividing tissues. Our findings show that altering dCAP-D3 levels in either direction has detrimental effects on mitotic timing, the regulation of gene expression, and organism development. Taken together, these data suggest that the different roles for Condensin II throughout the cell cycle may be independent of each other and/or that dCAP-D3 may possess functions that are separate from those involving its association with the Condensin II complex. If conserved, these findings could have implications for tumors harboring elevated CAP-D3 levels.
Collapse
|
37
|
Jassinskaja M, Johansson E, Kristiansen TA, Åkerstrand H, Sjöholm K, Hauri S, Malmström J, Yuan J, Hansson J. Comprehensive Proteomic Characterization of Ontogenic Changes in Hematopoietic Stem and Progenitor Cells. Cell Rep 2018; 21:3285-3297. [PMID: 29241553 DOI: 10.1016/j.celrep.2017.11.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/27/2017] [Accepted: 11/19/2017] [Indexed: 12/22/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) in the fetus and adult possess distinct molecular landscapes that regulate cell fate and change their susceptibility to initiation and progression of hematopoietic malignancies. Here, we applied in-depth quantitative proteomics to comprehensively describe and compare the proteome of fetal and adult HSPCs. Our data uncover a striking difference in complexity of the cellular proteomes, with more diverse adult-specific HSPC proteomic signatures. The differential protein content in fetal and adult HSPCs indicate distinct metabolic profiles and protein complex stoichiometries. Additionally, adult characteristics include an arsenal of proteins linked to viral and bacterial defense, as well as protection against ROS-induced protein oxidation. Further analyses show that interferon α, as well as Neutrophil elastase, has distinct functional effects in fetal and adult HSPCs. This study provides a rich resource aimed toward an enhanced mechanistic understanding of normal and malignant hematopoiesis during fetal and adult life.
Collapse
Affiliation(s)
- Maria Jassinskaja
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden
| | - Emil Johansson
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden
| | - Trine Ahn Kristiansen
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden
| | - Hugo Åkerstrand
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden
| | - Kristoffer Sjöholm
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, 221 84 Lund, Sweden
| | - Simon Hauri
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, 221 84 Lund, Sweden
| | - Johan Malmström
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, 221 84 Lund, Sweden
| | - Joan Yuan
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden
| | - Jenny Hansson
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden.
| |
Collapse
|
38
|
Wang Q, Wang C, Li N, Liu X, Ren W, Wang Q, Cao X. Condensin Smc4 promotes inflammatory innate immune response by epigenetically enhancing NEMO transcription. J Autoimmun 2018; 92:67-76. [PMID: 29803706 DOI: 10.1016/j.jaut.2018.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/01/2018] [Accepted: 05/08/2018] [Indexed: 01/13/2023]
Abstract
Structural maintenance of chromosome (Smc) protein complex (condensin) plays a central role in organizing and compacting chromosomes, which determines DNA-binding activity and gene expression; however, the role of condensin Smc in innate immunity and inflammation remains largely unknown. Through a high-throughput screening of the epigenetic modifiers, we identified Smc4, a core subunit of condensin, to potentially promote inflammatory innate immune response. Knockdown or deficiency of Smc4 inhibited TLR- or virus-triggered production of proinflammatory cytokines IL-6, TNF-α and IFN-β in macrophages. Mice with Smc4 knockdown were less susceptible to sepsis. Mechanistically, Smc4 enhanced NEMO transcription by recruiting H4K5ac to and increasing H4K5 acetylation of nemo promoter, leading to innate signals-triggered more potent activation of NF-κB and IRF3 pathways. Therefore, Smc4 promotes inflammatory innate immune responses by enhancing NEMO transcription, and our data add insight to epigenetic regulation of innate immunity and inflammation, and outline potential target for controlling inflammatory diseases.
Collapse
Affiliation(s)
- Qinlan Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chunmei Wang
- Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Nan Li
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
| | - Xingguang Liu
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
| | - Wenhui Ren
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
| | - Qingqing Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xuetao Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China.
| |
Collapse
|
39
|
Loguercio S, Barajas-Mora EM, Shih HY, Krangel MS, Feeney AJ. Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci. Front Immunol 2018; 9:425. [PMID: 29593713 PMCID: PMC5859386 DOI: 10.3389/fimmu.2018.00425] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/16/2018] [Indexed: 12/19/2022] Open
Abstract
CCCTC-binding factor (CTCF) is largely responsible for the 3D architecture of the genome, in concert with the action of cohesin, through the creation of long-range chromatin loops. Cohesin is hypothesized to be the main driver of these long-range chromatin interactions by the process of loop extrusion. Here, we performed ChIP-seq for CTCF and cohesin in two stages each of T and B cell differentiation and examined the binding pattern in all six antigen receptor (AgR) loci in these lymphocyte progenitors and in mature T and B cells, ES cells, and fibroblasts. The four large AgR loci have many bound CTCF sites, most of which are only occupied in lymphocytes, while only the CTCF sites at the end of each locus near the enhancers or J genes tend to be bound in non-lymphoid cells also. However, despite the generalized lymphocyte restriction of CTCF binding in AgR loci, the Igκ locus is the only locus that also shows significant lineage-specificity (T vs. B cells) and developmental stage-specificity (pre-B vs. pro-B) in CTCF binding. We show that cohesin binding shows greater lineage- and stage-specificity than CTCF at most AgR loci, providing more specificity to the loops. We also show that the culture of pro-B cells in IL7, a common practice to expand the number of cells before ChIP-seq, results in a CTCF-binding pattern resembling pre-B cells, as well as other epigenetic and transcriptional characteristics of pre-B cells. Analysis of the orientation of the CTCF sites show that all sites within the large V portions of the Igh and TCRβ loci have the same orientation. This suggests either a lack of requirement for convergent CTCF sites creating loops, or indicates an absence of any loops between CTCF sites within the V region portion of those loci but only loops to the convergent sites at the D-J-enhancer end of each locus. The V region portions of the Igκ and TCRα/δ loci, by contrast, have CTCF sites in both orientations, providing many options for creating CTCF-mediated convergent loops throughout the loci. CTCF/cohesin loops, along with transcription factors, drives contraction of AgR loci to facilitate the creation of a diverse repertoire of antibodies and T cell receptors.
Collapse
Affiliation(s)
- Salvatore Loguercio
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - E. Mauricio Barajas-Mora
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Han-Yu Shih
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Michael S. Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Ann J. Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| |
Collapse
|
40
|
Hnisz D, Schuijers J, Li CH, Young RA. Regulation and Dysregulation of Chromosome Structure in Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2018. [DOI: 10.1146/annurev-cancerbio-030617-050134] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancer arises from genetic alterations that produce dysregulated gene expression programs. Normal gene regulation occurs in the context of chromosome loop structures called insulated neighborhoods, and recent studies have shown that these structures are altered and can contribute to oncogene dysregulation in various cancer cells. We review the types of genetic and epigenetic alterations that influence neighborhood structures and contribute to gene dysregulation in cancer, present models for insulated neighborhoods associated with the most prominent human oncogenes, and discuss how such models may lead to further advances in cancer diagnosis and therapy.
Collapse
Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
| | - Charles H. Li
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
41
|
Nesprin-2 Interacts with Condensin Component SMC2. Int J Cell Biol 2018; 2017:8607532. [PMID: 29445399 PMCID: PMC5763115 DOI: 10.1155/2017/8607532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/17/2017] [Accepted: 12/07/2017] [Indexed: 01/24/2023] Open
Abstract
The nuclear envelope proteins, Nesprins, have been primarily studied during interphase where they function in maintaining nuclear shape, size, and positioning. We analyze here the function of Nesprin-2 in chromatin interactions in interphase and dividing cells. We characterize a region in the rod domain of Nesprin-2 that is predicted as SMC domain (aa 1436-1766). We show that this domain can interact with itself. It furthermore has the capacity to bind to SMC2 and SMC4, the core subunits of condensin. The interaction was observed during all phases of the cell cycle; it was particularly strong during S phase and persisted also during mitosis. Nesprin-2 knockdown did not affect condensin distribution; however we noticed significantly higher numbers of chromatin bridges in Nesprin-2 knockdown cells in anaphase. Thus, Nesprin-2 may have an impact on chromosomes which might be due to its interaction with condensins or to indirect mechanisms provided by its interactions at the nuclear envelope.
Collapse
|
42
|
Abstract
Structural maintenance of chromosome (SMC) protein complexes, including cohesin and condensin, are increasingly being recognized for their important role in cancer and development, making it critical that we understand how these evolutionarily conserved multi-subunit protein complexes associate with and organize the genome. We review adaptor proteins for SMC complexes and how these adaptors may capture SMC complexes following loop extrusion to provide a framework for chromosome organization.
Collapse
Affiliation(s)
- Kobe C. Yuen
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Oncology Biomarker Development, Genentech, Inc., South San Francisco, California, United States of America
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, Kansas, United States of America
- University of Kansas Cancer Center, Kansas City, Kansas, United States of America
| |
Collapse
|
43
|
Abstract
The three-dimensional (3D) genome structure is highly ordered by a hierarchy of organizing events ranging from enhancer-promoter or gene-gene contacts to chromosomal territorial arrangement. It is becoming clear that the cohesin and condensin complexes are key molecular machines that organize the 3D genome structure. These complexes are highly conserved from simple systems, e.g., yeast cells, to the much more complex human system. Therefore, knowledge from the budding and fission yeast systems illuminates highly conserved molecular mechanisms of how cohesin and condensin establish the functional 3D genome structures. Here I discuss how these complexes are recruited across the yeast genomes, mediate distinct genome-organizing events such as gene contacts and topological domain formation, and participate in important nuclear activities including transcriptional regulation and chromosomal dynamics.
Collapse
Affiliation(s)
- Ken-Ichi Noma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA;
| |
Collapse
|
44
|
Festuccia N, Gonzalez I, Owens N, Navarro P. Mitotic bookmarking in development and stem cells. Development 2017; 144:3633-3645. [DOI: 10.1242/dev.146522] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The changes imposed on the nucleus, chromatin and its regulators during mitosis lead to the dismantlement of most gene regulatory processes. However, an increasing number of transcriptional regulators are being identified as capable of binding their genomic targets during mitosis. These so-called ‘mitotic bookmarking factors’ encompass transcription factors and chromatin modifiers that are believed to convey gene regulatory information from mother to daughter cells. In this Primer, we review mitotic bookmarking processes in development and stem cells and discuss the interest and potential importance of this concept with regard to epigenetic regulation and cell fate transitions involving cellular proliferation.
Collapse
Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Nick Owens
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| |
Collapse
|
45
|
Huang L, Liu P, Yuan Z, Zhou T, Yu J. The free-energy cost of interaction between DNA loops. Sci Rep 2017; 7:12610. [PMID: 28974770 PMCID: PMC5626758 DOI: 10.1038/s41598-017-12765-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/14/2017] [Indexed: 12/03/2022] Open
Abstract
From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.
Collapse
Affiliation(s)
- Lifang Huang
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Peijiang Liu
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Zhanjiang Yuan
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China.
| | - Jianshe Yu
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China.
| |
Collapse
|
46
|
Yuen KC, Slaughter BD, Gerton JL. Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters. SCIENCE ADVANCES 2017; 3:e1700191. [PMID: 28691095 PMCID: PMC5479651 DOI: 10.1126/sciadv.1700191] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/05/2017] [Indexed: 05/26/2023]
Abstract
Structural maintenance of chromosome complexes, such as cohesin, have been implicated in a wide variety of chromatin-dependent functions such as genome organization, replication, and gene expression. How these complexes find their sites of association and affect local chromosomal processes is not well understood. We report that condensin II, a complex distinct from cohesin, physically interacts with TFIIIC, and they both colocalize at active gene promoters in the mouse and human genomes, facilitated by interaction between NCAPD3 and the epigenetic mark H3K4me3. Condensin II is important for maintaining high levels of expression of the histone gene clusters as well as the interaction between these clusters in the mouse genome. Our findings suggest that condensin II is anchored to the mammalian genome by a combination of H3K4me3 and the sequence-specific binding of TFIIIC, and that condensin supports the expression of active gene-dense regions found at the boundaries of topological domains. Together, our results support a working model in which condensin II contributes to topological domain boundary-associated gene activity in the mammalian genome.
Collapse
Affiliation(s)
- Kobe C. Yuen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| |
Collapse
|
47
|
Albritton SE, Kranz AL, Winterkorn LH, Street LA, Ercan S. Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation. eLife 2017; 6. [PMID: 28562241 PMCID: PMC5451215 DOI: 10.7554/elife.23645] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/02/2017] [Indexed: 12/17/2022] Open
Abstract
In many organisms, it remains unclear how X chromosomes are specified for dosage compensation, since DNA sequence motifs shown to be important for dosage compensation complex (DCC) recruitment are themselves not X-specific. Here, we addressed this problem in C. elegans. We found that the DCC recruiter, SDC-2, is required to maintain open chromatin at a small number of primary DCC recruitment sites, whose sequence and genomic context are X-specific. Along the X, primary recruitment sites are interspersed with secondary sites, whose function is X-dependent. A secondary site can ectopically recruit the DCC when additional recruitment sites are inserted either in tandem or at a distance (>30 kb). Deletion of a recruitment site on the X results in reduced DCC binding across several megabases surrounded by topologically associating domain (TAD) boundaries. Our work elucidates that hierarchy and long-distance cooperativity between gene-regulatory elements target a single chromosome for regulation. DOI:http://dx.doi.org/10.7554/eLife.23645.001 The DNA inside living cells is organized in structures called chromosomes. In many animals, females have two X chromosomes, whereas males have only one. To ensure that females do not end up with a double dose of the proteins encoded by the genes on the X chromosome, animals use a process called dosage compensation to correct this imbalance. The mechanisms underlying this process vary between species, but they typically involve a regulatory complex that binds to the X chromosomes of one sex to modify gene expression. Caenorhabditis elegans, for example, is a species of nematode worm in which individuals with two X chromosomes are hermaphrodites and those with one X chromosome are males. In C. elegans, a regulatory complex, called the dosage compensation complex, attaches to both X chromosomes of a hermaphrodite, and reduces the expression of the genes on each by half to match the level seen in the males. Previous research has shown that short DNA sequences, known as motifs, recruit the dosage compensation complex to the X chromosomes. However, these sequences are also found on the other chromosomes and, until now, it was not known why the complex was only recruited to the X chromosomes. Albritton et al. now show the X chromosomes have a ‘hierarchical’ recruitment system. A few sites on the X chromosomes contain clusters of a specific DNA motif, which initiate the process and attract the dosage compensation complex more strongly than other sites. These ‘strong’ recruitment sites are placed across the length of the X chromosomes and cooperate with several ‘weaker’ ones located in between. This way, multiple recruitment sites can cooperate over a long distance, while non-sex chromosomes, which have only one or two stronger recruitment sites, do not have thisadvantage. Hierarchy and cooperativity may be general features of gene expression, in which proteins are targeted to chromosomes without the need for having specific motifs at every recruitment site. The way DNA sequences are distributed across the genome may give us clues about their role. Thus, knowing how genomes are structured will help us identify disrupted areas in diseases such as cancer. DOI:http://dx.doi.org/10.7554/eLife.23645.002
Collapse
Affiliation(s)
- Sarah Elizabeth Albritton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| | - Anna-Lena Kranz
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| | - Lara Heermans Winterkorn
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| | - Lena Annika Street
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| | - Sevinc Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| |
Collapse
|
48
|
Urbanek MO, Michalak M, Krzyzosiak WJ. 2D and 3D FISH of expanded repeat RNAs in human lymphoblasts. Methods 2017; 120:49-57. [PMID: 28404480 DOI: 10.1016/j.ymeth.2017.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/09/2017] [Accepted: 04/05/2017] [Indexed: 12/18/2022] Open
Abstract
The first methods for visualizing RNAs within cells were designed for simple imaging of specific transcripts in cells or tissues and since then significant technical advances have been made in this field. Today, high-resolution images can be obtained, enabling visualization of single transcript molecules, quantitative analyses of images, and precise localization of RNAs within cells as well as co-localization of transcripts with specific proteins or other molecules. In addition, tracking of RNA dynamics within single cell has become possible. RNA imaging techniques have been utilized for investigating the role of mutant RNAs in a number of human disorders caused by simple microsatellite expansions. These diseases include myotonic dystrophy type 1 and 2, amyotrophic lateral sclerosis/frontotemporal dementia, fragile X-associated tremor/ataxia syndrome, and Huntington's disease. Mutant RNAs with expanded repeats tend to aggregate predominantly within cell nuclei, forming structures called RNA foci. In this study, we demonstrate methods for fluorescent visualization of RNAs in both fixed and living cells using the example of RNAs containing various expanded repeat tracts (CUG, CCUG, GGGGCC, CGG, and CAG) from experiment design to image analysis. We describe in detail 2D and 3D fluorescence in situ hybridization (FISH) protocols for imaging expanded repeats RNAs, and we review briefly live imaging techniques used to characterize RNA foci formed by mutant RNAs. These methods could be used to image the entire cellular pathway of RNAs, from transcription to degradation.
Collapse
Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Michal Michalak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
| |
Collapse
|
49
|
Condensin, master organizer of the genome. Chromosome Res 2017; 25:61-76. [PMID: 28181049 DOI: 10.1007/s10577-017-9553-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/19/2016] [Accepted: 01/23/2017] [Indexed: 02/06/2023]
Abstract
A fundamental requirement in nature is for a cell to correctly package and divide its replicated genome. Condensin is a mechanical multisubunit complex critical to this process. Condensin uses ATP to power conformational changes in DNA to enable to correct DNA compaction, organization, and segregation of DNA from the simplest bacteria to humans. The highly conserved nature of the condensin complex and the structural similarities it shares with the related cohesin complex have provided important clues as to how it functions in cells. The fundamental requirement for condensin in mitosis and meiosis is well established, yet the precise mechanism of action is still an open question. Mutation or removal of condensin subunits across a range of species disrupts orderly chromosome condensation leading to errors in chromosome segregation and likely death of the cell. There are divergences in function across species for condensin. Once considered to function solely in mitosis and meiosis, an accumulating body of evidence suggests that condensin has key roles in also regulating the interphase genome. This review will examine how condensin organizes our genomes, explain where and how it binds the genome at a mechanical level, and highlight controversies and future directions as the complex continues to fascinate and baffle biologists.
Collapse
|
50
|
Rana V, Bosco G. Condensin Regulation of Genome Architecture. J Cell Physiol 2017; 232:1617-1625. [PMID: 27888504 DOI: 10.1002/jcp.25702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 02/06/2023]
Abstract
Condensin complexes exist across all domains of life and are central to the structure and organization of chromatin. As architectural proteins, condensins control chromatin compaction during interphase and mitosis. Condensin activity has been well studied in mitosis but have recently emerged as important regulators of genome organization and gene expression during interphase. Here, we focus our discussion on recent findings on the molecular mechanism and how condensins are used to shape chromosomes during interphase. These findings suggest condensin activity during interphase is required for proper chromosome organization. J. Cell. Physiol. 232: 1617-1625, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Vibhuti Rana
- Department of Molecular Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Giovanni Bosco
- Department of Molecular Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| |
Collapse
|