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Huang H, Wu Q. Pushing the TAD boundary: Decoding insulator codes of clustered CTCF sites in 3D genomes. Bioessays 2024:e2400121. [PMID: 39169755 DOI: 10.1002/bies.202400121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
Topologically associating domain (TAD) boundaries are the flanking edges of TADs, also known as insulated neighborhoods, within the 3D structure of genomes. A prominent feature of TAD boundaries in mammalian genomes is the enrichment of clustered CTCF sites often with mixed orientations, which can either block or facilitate enhancer-promoter (E-P) interactions within or across distinct TADs, respectively. We will discuss recent progress in the understanding of fundamental organizing principles of the clustered CTCF insulator codes at TAD boundaries. Specifically, both inward- and outward-oriented CTCF sites function as topological chromatin insulators by asymmetrically blocking improper TAD-boundary-crossing cohesin loop extrusion. In addition, boundary stacking and enhancer clustering facilitate long-distance E-P interactions across multiple TADs. Finally, we provide a unified mechanism for RNA-mediated TAD boundary function via R-loop formation for both insulation and facilitation. This mechanism of TAD boundary formation and insulation has interesting implications not only on how the 3D genome folds in the Euclidean nuclear space but also on how the specificity of E-P interactions is developmentally regulated.
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Affiliation(s)
- Haiyan Huang
- Center for Comparative Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Wu
- Center for Comparative Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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2
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Chang LH, Noordermeer D. Permeable TAD boundaries and their impact on genome-associated functions. Bioessays 2024:e2400137. [PMID: 39093600 DOI: 10.1002/bies.202400137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin-mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter-TAD loop formation. Based on the reanalysis of Nano-C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read-through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter-TAD loops is restricted though. We speculate that the DNA-encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer-promoter loop formation and other genomic processes.
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Affiliation(s)
- Li-Hsin Chang
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Blood and Transplant Research Unit in Precision Cellular Therapeutics, National Institute of Health Research, Oxford, UK
| | - Daan Noordermeer
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
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3
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Grothusen GP, Chang R, Cao Z, Zhou N, Mittal M, Datta A, Wulfridge P, Beer T, Wang B, Zheng N, Tang HY, Sarma K, Greenberg RA, Shi J, Busino L. DCAF15 control of cohesin dynamics sustains acute myeloid leukemia. Nat Commun 2024; 15:5604. [PMID: 38961054 PMCID: PMC11222469 DOI: 10.1038/s41467-024-49882-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/21/2024] [Indexed: 07/05/2024] Open
Abstract
The CRL4-DCAF15 E3 ubiquitin ligase complex is targeted by the aryl-sulfonamide molecular glues, leading to neo-substrate recruitment, ubiquitination, and proteasomal degradation. However, the physiological function of DCAF15 remains unknown. Using a domain-focused genetic screening approach, we reveal DCAF15 as an acute myeloid leukemia (AML)-biased dependency. Loss of DCAF15 results in suppression of AML through compromised replication fork integrity and consequent accumulation of DNA damage. Accordingly, DCAF15 loss sensitizes AML to replication stress-inducing therapeutics. Mechanistically, we discover that DCAF15 directly interacts with the SMC1A protein of the cohesin complex and destabilizes the cohesin regulatory factors PDS5A and CDCA5. Loss of PDS5A and CDCA5 removal precludes cohesin acetylation on chromatin, resulting in uncontrolled chromatin loop extrusion, defective DNA replication, and apoptosis. Collectively, our findings uncover an endogenous, cell autonomous function of DCAF15 in sustaining AML proliferation through post-translational control of cohesin dynamics.
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Affiliation(s)
- Grant P Grothusen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Renxu Chang
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhendong Cao
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nan Zhou
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Monika Mittal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arindam Datta
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phillip Wulfridge
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Thomas Beer
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Baiyun Wang
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Kavitha Sarma
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luca Busino
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Chiu K, Berrada Y, Eskndir N, Song D, Fong C, Naughton S, Chen T, Moy S, Gyurmey S, James L, Ezeiruaku C, Capistran C, Lowey D, Diwanji V, Peterson S, Parakh H, Burgess AR, Probert C, Zhu A, Anderson B, Levi N, Gerlitz G, Packard MC, Dorfman KA, Bahiru MS, Stephens AD. CTCF is essential for proper mitotic spindle structure and anaphase segregation. Chromosoma 2024; 133:183-194. [PMID: 37728741 DOI: 10.1007/s00412-023-00810-w] [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: 01/11/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
Mitosis is an essential process in which the duplicated genome is segregated equally into two daughter cells. CTCF has been reported to be present in mitosis and has a role in localizing CENP-E, but its importance for mitotic fidelity remains to be determined. To evaluate the importance of CTCF in mitosis, we tracked mitotic behaviors in wild-type and two different CTCF CRISPR-based genetic knockdowns. We find that knockdown of CTCF results in prolonged mitoses and failed anaphase segregation via time-lapse imaging of SiR-DNA. CTCF knockdown did not alter cell cycling or the mitotic checkpoint, which was activated upon nocodazole treatment. Immunofluorescence imaging of the mitotic spindle in CTCF knockdowns revealed disorganization via tri/tetrapolar spindles and chromosomes behind the spindle pole. Imaging of interphase nuclei showed that nuclear size increased drastically, consistent with failure to divide the duplicated genome in anaphase. Long-term inhibition of CNEP-E via GSK923295 recapitulates CTCF knockdown abnormal mitotic spindles with polar chromosomes and increased nuclear sizes. Population measurements of nuclear shape in CTCF knockdowns do not display decreased circularity or increased nuclear blebbing relative to wild-type. However, failed mitoses do display abnormal nuclear morphologies relative to successful mitoses, suggesting that population images do not capture individual behaviors. Thus, CTCF is important for both proper metaphase organization and anaphase segregation which impacts the size and shape of the interphase nucleus likely through its known role in recruiting CENP-E.
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Affiliation(s)
- Katherine Chiu
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Yasmin Berrada
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Nebiyat Eskndir
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Dasol Song
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Claire Fong
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Sarah Naughton
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Tina Chen
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Savanna Moy
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Sarah Gyurmey
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Liam James
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Chimere Ezeiruaku
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Caroline Capistran
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Daniel Lowey
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Vedang Diwanji
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Samantha Peterson
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Harshini Parakh
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Ayanna R Burgess
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Cassandra Probert
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Annie Zhu
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Bryn Anderson
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Nehora Levi
- Biology Department of Molecular Biology, Faculty of Life Sciences, Ariel University, 40700, Ariel, Israel
| | - Gabi Gerlitz
- Biology Department of Molecular Biology, Faculty of Life Sciences, Ariel University, 40700, Ariel, Israel
| | - Mary C Packard
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Katherine A Dorfman
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Michael Seifu Bahiru
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Andrew D Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
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5
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Crewe M, Segev A, Rueda R, Madabhushi R. Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States. Mol Neurobiol 2024; 61:3240-3257. [PMID: 37979036 DOI: 10.1007/s12035-023-03762-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
Multivalent binding of CTCF to variable DNA sequences is thought to underlie its ability to mediate diverse cellular functions. CTCF typically binds a 20 base-pair consensus DNA sequence, but the full diversity of CTCF binding sites (CBS) within the genome has not been interrogated. We assessed CTCF occupancy in cultured cortical neurons and observed surprisingly that ~ 22% of CBS lack the consensus CTCF motif. We report here that sequence diversity at most of these atypical CBS involves degeneracy at specific nucleotide positions within the consensus CTCF motif, which likely affect the binding of CTCF zinc fingers 6 and 7. This mode of atypical CTCF binding defines most CBS at gene promoters, as well as CBS that are dynamically altered during neural differentiation and following neuronal stimulation, revealing how atypical CTCF binding could influence gene activity. Dynamic CBS are distributed both within and outside loop anchors and TAD boundaries, suggesting both looping-dependent and independent roles for CTCF. Finally, we describe a second mode of atypical CTCF binding to DNA sequences that are completely unrelated to the consensus CTCF motif, which are enriched within the bodies of tissue-specific genes. These tissue-specific atypical CBS are also enriched in H3K27ac, which marks cis-regulatory elements within chromatin, including enhancers. Overall, these results indicate how atypical CBS could dynamically regulate gene activity patterns during differentiation, development, and in response to environmental cues.
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Affiliation(s)
- Morgan Crewe
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amir Segev
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Richard Rueda
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ram Madabhushi
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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6
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Kong IY, Giulino-Roth L. Targeting latent viral infection in EBV-associated lymphomas. Front Immunol 2024; 15:1342455. [PMID: 38464537 PMCID: PMC10920267 DOI: 10.3389/fimmu.2024.1342455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Epstein-Barr virus (EBV) contributes to the development of a significant subset of human lymphomas. As a herpes virus, EBV can transition between a lytic state which is required to establish infection and a latent state where a limited number of viral antigens are expressed which allows infected cells to escape immune surveillance. Three broad latency programs have been described which are defined by the expression of viral proteins RNA, with latency I being the most restrictive expressing only EBV nuclear antigen 1 (EBNA1) and EBV-encoded small RNAs (EBERs) and latency III expressing the full panel of latent viral genes including the latent membrane proteins 1 and 2 (LMP1/2), and EBNA 2, 3, and leader protein (LP) which induce a robust T-cell response. The therapeutic use of EBV-specific T-cells has advanced the treatment of EBV-associated lymphoma, however this approach is only effective against EBV-associated lymphomas that express the latency II or III program. Latency I tumors such as Burkitt lymphoma (BL) and a subset of diffuse large B-cell lymphomas (DLBCL) evade the host immune response to EBV and are resistant to EBV-specific T-cell therapies. Thus, strategies for inducing a switch from the latency I to the latency II or III program in EBV+ tumors are being investigated as mechanisms to sensitize tumors to T-cell mediated killing. Here, we review what is known about the establishment and regulation of latency in EBV infected B-cells, the role of EBV-specific T-cells in lymphoma, and strategies to convert latency I tumors to latency II/III.
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7
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Zeng Y, Jain R, Lam M, Ahmed M, Guo H, Xu W, Zhong Y, Wei GH, Xu W, He HH. DNA methylation modulated genetic variant effect on gene transcriptional regulation. Genome Biol 2023; 24:285. [PMID: 38066556 PMCID: PMC10709945 DOI: 10.1186/s13059-023-03130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Expression quantitative trait locus (eQTL) analysis has emerged as an important tool in elucidating the link between genetic variants and gene expression, thereby bridging the gap between risk SNPs and associated diseases. We recently identified and validated a specific case where the methylation of a CpG site influences the relationship between the genetic variant and gene expression. RESULTS Here, to systematically evaluate this regulatory mechanism, we develop an extended eQTL mapping method, termed DNA methylation modulated eQTL (memo-eQTL). Applying this memo-eQTL mapping method to 128 normal prostate samples enables identification of 1063 memo-eQTLs, the majority of which are not recognized as conventional eQTLs in the same cohort. We observe that the methylation of the memo-eQTL CpG sites can either enhance or insulate the interaction between SNP and gene expression by altering CTCF-based chromatin 3D structure. CONCLUSIONS This study demonstrates the prevalence of memo-eQTLs paving the way to identify novel causal genes for traits or diseases associated with genetic variations.
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Affiliation(s)
- Yong Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
| | - Rahi Jain
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Magnus Lam
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Haiyang Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
| | - Wenjie Xu
- MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yuan Zhong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Gong-Hong Wei
- MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
- Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
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8
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Bose S, Saha S, Goswami H, Shanmugam G, Sarkar K. Involvement of CCCTC-binding factor in epigenetic regulation of cancer. Mol Biol Rep 2023; 50:10383-10398. [PMID: 37840067 DOI: 10.1007/s11033-023-08879-3] [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: 09/13/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
A major global health burden continues to be borne by the complex and multifaceted disease of cancer. Epigenetic changes, which are essential for the emergence and spread of cancer, have drawn a huge amount of attention recently. The CCCTC-binding factor (CTCF), which takes part in a wide range of cellular processes including genomic imprinting, X chromosome inactivation, 3D chromatin architecture, local modifications of histone, and RNA polymerase II-mediated gene transcription, stands out among the diverse array of epigenetic regulators. CTCF not only functions as an architectural protein but also modulates DNA methylation and histone modifications. Epigenetic regulation of cancer has already been the focus of plenty of studies. Understanding the role of CTCF in the cancer epigenetic landscape may lead to the development of novel targeted therapeutic strategies for cancer. CTCF has already earned its status as a tumor suppressor gene by acting like a homeostatic regulator of genome integrity and function. Moreover, CTCF has a direct effect on many important transcriptional regulators that control the cell cycle, apoptosis, senescence, and differentiation. As we learn more about CTCF-mediated epigenetic modifications and transcriptional regulations, the possibility of utilizing CTCF as a diagnostic marker and therapeutic target for cancer will also increase. Thus, the current review intends to promote personalized and precision-based therapeutics for cancer patients by shedding light on the complex interplay between CTCF and epigenetic processes.
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Affiliation(s)
- Sayani Bose
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Srawsta Saha
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Harsita Goswami
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Geetha Shanmugam
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Koustav Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India.
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Chen J, Floyd EN, Dawson DS, Rankin S. Cornelia de Lange Syndrome mutations in SMC1A cause cohesion defects in yeast. Genetics 2023; 225:iyad159. [PMID: 37650609 PMCID: PMC10550314 DOI: 10.1093/genetics/iyad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a developmental disorder characterized by limb truncations, craniofacial abnormalities, and cognitive delays. CdLS is caused mainly by mutations in genes encoding subunits or regulators of the cohesin complex. Cohesin plays 2 distinct roles in chromosome dynamics as follows: it promotes looping, organization, and compaction of individual chromosomes, and it holds newly replicated sister chromatids together until cell division. CdLS-associated mutations result in altered gene expression likely by affecting chromosome architecture. Whether CdLS mutations cause phenotypes through impact on sister chromatid cohesion is less clear. Here, we show that CdLS-associated mutations introduced into the SMC1A gene of budding yeast had measurable impacts on sister chromatid cohesion, mitotic progression, and DNA damage sensitivity. These data suggest that sister chromatid cohesion-related defects may contribute to phenotypes seen in CdLS affected individuals.
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Affiliation(s)
- Jingrong Chen
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th St. Oklahoma City, OK 73104, USA
| | - Erin N Floyd
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th St. Oklahoma City, OK 73104, USA
| | - Dean S Dawson
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th St. Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Susannah Rankin
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, 825 NE 13th St. Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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10
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Hu X, Wu J, Feng Y, Ma H, Zhang E, Zhang C, Sun Q, Wang T, Ge Y, Zong D, Chen W, He X. METTL3-stabilized super enhancers-lncRNA SUCLG2-AS1 mediates the formation of a long-range chromatin loop between enhancers and promoters of SOX2 in metastasis and radiosensitivity of nasopharyngeal carcinoma. Clin Transl Med 2023; 13:e1361. [PMID: 37658588 PMCID: PMC10474317 DOI: 10.1002/ctm2.1361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/23/2023] [Accepted: 07/28/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Super enhancers (SE) play pivotal roles in cell identity and diseases occur including tumorigenesis. The depletion of SE-associated lncRNA transcripts, also known as super-lncRNA, causes the activity of SE to be dysregulated. METHODS We screened and identified an elevated metastasis-associated SE-lncRNA SUCLG2-AS1 in nasopharyngeal carcinoma (NPC) using RNA-sequencing, real-time quantitative polymerase chain reaction (RT-qPCR) and bioinformatics. Western blotting, RT-qPCR, methylated RNA immunoprecipitation (MeRIP), RNA immunoprecipitation, chromatin immunoprecipitation, RNA pull-down and 3C (chromosome conformation capture assays) were used for mechanistic studies. RESULTS SUCLG2-AS1 was correlated with a poor prognosis. SUCLG2-AS1 promotes NPC cell invasion and metastasis while repressing apoptosis and radiosensitivity in vitro and in vivo. Mechanistically, high SUCLG2-AS1 expression occurred in an m6A-dependent manner. SUCLG2-AS1 was found to be located in the SE region of SOX2, and it regulated the expression of SOX2 via long-range chromatin loop formation, which via mediating CTCF (transcription factor) occupied the SE and promoter region of SOX2, thus regulating the metastasis and radiosensitivity of NPC. CONCLUSIONS Taken together, our data suggest that SUCLG2-AS1 may serve as a novel intervention target for the clinical treatment of NPC.
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Affiliation(s)
- Xinyu Hu
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Jianfeng Wu
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Yong Feng
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Hongxia Ma
- Department of Epidemiology and BiostatisticsInternational Joint Research Center On Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical UniversityNanjingChina
| | - Erbao Zhang
- Department of Epidemiology and BiostatisticsInternational Joint Research Center On Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical UniversityNanjingChina
| | - Chang Zhang
- Department of Epidemiology and BiostatisticsInternational Joint Research Center On Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical UniversityNanjingChina
| | - Qi Sun
- Department of Epidemiology and BiostatisticsInternational Joint Research Center On Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical UniversityNanjingChina
| | - Tingting Wang
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Yizhi Ge
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Dan Zong
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Wei Chen
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Xia He
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
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Tan B, Liu S, Feng X, Pan X, Qian G, Liu L, Zhang X, Yao H, Dong X. Expanding the mutational and clinical spectrum of Chinese intellectual disability patients with two novel CTCF variants. Front Pediatr 2023; 11:1195862. [PMID: 37664546 PMCID: PMC10469948 DOI: 10.3389/fped.2023.1195862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
CCCTC-Binding Factor (CTCF) is a protein-coding gene involved in transcriptional regulation, insulator activity, and regulation of chromatin structure, and is closely associated with intellectual developmental disorders. In this study, we report two unrelated Chinese patients with intellectual disability (ID). According to variant interpretation results from exome sequencing data and RNA-seq data, we present two novel heterozygous CTCF variants, NM_006565.3:c.1519_2184del (p. Glu507_Arg727delins47) and NM_006565.3:c.1838_1852del (p.Glu613_Pro617del), found in two distinct unrelated patients, respectively. Moreover, RNA-seq data of patient 1 indicated the absence of the mutant transcript, while in patient 2, the RNA-seq data revealed a CTCF mRNA transcript with a deletion of 15 nucleotides. Notably, the RNA sequencing data revealed 507 differentially expressed genes shared between these two patients. Specifically, among them, 194 were down-regulated, and 313 were up-regulated, primarily involved in gene regulation and cellular response. Our study expands the genetic and clinical spectrum of CTCF and advances our understanding of the pathogenesis of CTCF in vivo.
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Affiliation(s)
- Bo Tan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Sihan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xin Pan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guanhua Qian
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xu Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Yao
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojing Dong
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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12
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Biswas U, Deb Mallik T, Pschirer J, Lesche M, Sameith K, Jessberger R. Cohesin SMC1β promotes closed chromatin and controls TERRA expression at spermatocyte telomeres. Life Sci Alliance 2023; 6:e202201798. [PMID: 37160312 PMCID: PMC10172765 DOI: 10.26508/lsa.202201798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/11/2023] Open
Abstract
Previous data showed that meiotic cohesin SMC1β protects spermatocyte telomeres from damage. The underlying reason, however, remained unknown as the expressions of telomerase and shelterin components were normal in Smc1β -/- spermatocytes. Here. we report that SMC1β restricts expression of the long noncoding RNA TERRA (telomeric repeat containing RNA) in spermatocytes. In somatic cell lines increased TERRA was reported to cause telomere damage through altering telomere chromatin structure. In Smc1β -/- spermatocytes, we observed strongly increased levels of TERRA which accumulate on damaged chromosomal ends, where enhanced R-loop formation was found. This suggested a more open chromatin configuration near telomeres in Smc1β -/- spermatocytes, which was confirmed by ATAC-seq. Telomere-distal regions were not affected by the absence of SMC1β but RNA-seq revealed increased transcriptional activity in telomere-proximal regions. Thus, SMC1β promotes closed chromatin specifically near telomeres and limits TERRA expression in spermatocytes.
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Affiliation(s)
- Uddipta Biswas
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Tanaya Deb Mallik
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Johannes Pschirer
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Matthias Lesche
- Center for Molecular and Cellular Bioengineering, Genome Center Technology Platform, Dresden, Germany
| | - Katrin Sameith
- Center for Molecular and Cellular Bioengineering, Genome Center Technology Platform, Dresden, Germany
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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13
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Pandupuspitasari NS, Khan FA, Huang C, Ali A, Yousaf MR, Shakeel F, Putri EM, Negara W, Muktiani A, Prasetiyono BWHE, Kustiawan L, Wahyuni DS. Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease. Funct Integr Genomics 2023; 23:214. [PMID: 37386239 DOI: 10.1007/s10142-023-01146-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.
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Affiliation(s)
- Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia.
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Azhar Ali
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Rizwan Yousaf
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Farwa Shakeel
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Ezi Masdia Putri
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Anis Muktiani
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Bambang Waluyo Hadi Eko Prasetiyono
- Laboratory of Feed Technology, Animal Science Department, Faculty of Animal and Agricultural Sciences Universitas Diponegoro, Semarang, Indonesia
| | - Limbang Kustiawan
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Dimar Sari Wahyuni
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
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14
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Bobbitt JR, Seachrist DD, Keri RA. Chromatin Organization and Transcriptional Programming of Breast Cancer Cell Identity. Endocrinology 2023; 164:bqad100. [PMID: 37394919 PMCID: PMC10370366 DOI: 10.1210/endocr/bqad100] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
Abstract
The advent of sequencing technologies for assessing chromosome conformations has provided a wealth of information on the organization of the 3-dimensional genome and its role in cancer progression. It is now known that changes in chromatin folding and accessibility can promote aberrant activation or repression of transcriptional programs that can drive tumorigenesis and progression in diverse cancers. This includes breast cancer, which comprises several distinct subtypes defined by their unique transcriptomes that dictate treatment response and patient outcomes. Of these, basal-like breast cancer is an aggressive subtype controlled by a pluripotency-enforcing transcriptome. Meanwhile, the more differentiated luminal subtype of breast cancer is driven by an estrogen receptor-dominated transcriptome that underlies its responsiveness to antihormone therapies and conveys improved patient outcomes. Despite the clear differences in molecular signatures, the genesis of each subtype from normal mammary epithelial cells remains unclear. Recent technical advances have revealed key distinctions in chromatin folding and organization between subtypes that could underlie their transcriptomic and, hence, phenotypic differences. These studies also suggest that proteins controlling particular chromatin states may be useful targets for treating aggressive disease. In this review, we explore the current state of understanding of chromatin architecture in breast cancer subtypes and its potential role in defining their phenotypic characteristics.
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Affiliation(s)
- Jessica R Bobbitt
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Ruth A Keri
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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15
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Smits WK, Vermeulen C, Hagelaar R, Kimura S, Vroegindeweij EM, Buijs-Gladdines JGCAM, van de Geer E, Verstegen MJAM, Splinter E, van Reijmersdal SV, Buijs A, Galjart N, van Eyndhoven W, van Min M, Kuiper R, Kemmeren P, Mullighan CG, de Laat W, Meijerink JPP. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia. Cell Rep 2023; 42:112373. [PMID: 37060567 PMCID: PMC10750298 DOI: 10.1016/j.celrep.2023.112373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023] Open
Abstract
Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In patients with T cell acute lymphoblastic leukemia (T-ALL), we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5; 14) (q35; q32.2) rearranged patients, especially when CTCF-binding sites are preserved in between the BCL11B enhancer and the TLX3 oncogene. These solitary intervening sites insulate TLX3 from the enhancer by inducing competitive looping to multiple binding sites near the TLX3 promoter. Reduced CTCF levels or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3 promoter to BCL11B enhancer looping, which elevates oncogene expression levels and leukemia burden.
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Affiliation(s)
- Willem K Smits
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Carlo Vermeulen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Shunsuke Kimura
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | | | | | - Ellen van de Geer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
| | | | | | - Arjan Buijs
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niels Galjart
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | - Roland Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Charles G Mullighan
- Laboratory of Pathology, St. Jude's Children's Research Hospital, Memphis TN, USA
| | - Wouter de Laat
- Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute-KNAW, Utrecht, the Netherlands
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16
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Wei Z, Wang S, Xu Y, Wang W, Soares F, Ahmed M, Su P, Wang T, Orouji E, Xu X, Zeng Y, Chen S, Liu X, Jia T, Liu Z, Du L, Wang Y, Chen S, Wang C, He HH, Guo H. MYC reshapes CTCF-mediated chromatin architecture in prostate cancer. Nat Commun 2023; 14:1787. [PMID: 36997534 PMCID: PMC10063626 DOI: 10.1038/s41467-023-37544-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
MYC is a well characterized oncogenic transcription factor in prostate cancer, and CTCF is the main architectural protein of three-dimensional genome organization. However, the functional link between the two master regulators has not been reported. In this study, we find that MYC rewires prostate cancer chromatin architecture by interacting with CTCF protein. Through combining the H3K27ac, AR and CTCF HiChIP profiles with CRISPR deletion of a CTCF site upstream of MYC gene, we show that MYC activation leads to profound changes of CTCF-mediated chromatin looping. Mechanistically, MYC colocalizes with CTCF at a subset of genomic sites, and enhances CTCF occupancy at these loci. Consequently, the CTCF-mediated chromatin looping is potentiated by MYC activation, resulting in the disruption of enhancer-promoter looping at neuroendocrine lineage plasticity genes. Collectively, our findings define the function of MYC as a CTCF co-factor in three-dimensional genome organization.
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Affiliation(s)
- Zhao Wei
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China
| | - Song Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Yaning Xu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Wenzheng Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Fraser Soares
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Ping Su
- National Administration of Health Data, Jinan, 250000, China
| | - Tingting Wang
- Institute of Medical Sciences, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
| | - Elias Orouji
- Epigenetics Initiative, Princess Margaret Genomics Centre, Toronto, ON, Canada
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Xu
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Yong Zeng
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Sujun Chen
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Xiaoyu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Tianwei Jia
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Zhaojian Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Lutao Du
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Yunshan Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Shaoyong Chen
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Chuanxin Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China
| | - Housheng Hansen He
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 2M9, Canada.
| | - Haiyang Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, China.
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, Shandong, China.
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, Shandong, China.
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17
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Banigan EJ, Tang W, van den Berg AA, Stocsits RR, Wutz G, Brandão HB, Busslinger GA, Peters JM, Mirny LA. Transcription shapes 3D chromatin organization by interacting with loop extrusion. Proc Natl Acad Sci U S A 2023; 120:e2210480120. [PMID: 36897969 PMCID: PMC10089175 DOI: 10.1073/pnas.2210480120] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/03/2022] [Indexed: 03/12/2023] Open
Abstract
Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. "Loop extrusion" can be impeded by chromatin-bound factors, such as CTCF, which generates characteristic and functional chromatin organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin and that active promoters are cohesin loading sites. However, the effects of transcription on cohesin have not been reconciled with observations of active extrusion by cohesin. To determine how transcription modulates extrusion, we studied mouse cells in which we could alter cohesin abundance, dynamics, and localization by genetic "knockouts" of the cohesin regulators CTCF and Wapl. Through Hi-C experiments, we discovered intricate, cohesin-dependent contact patterns near active genes. Chromatin organization around active genes exhibited hallmarks of interactions between transcribing RNA polymerases (RNAPs) and extruding cohesins. These observations could be reproduced by polymer simulations in which RNAPs were moving barriers to extrusion that obstructed, slowed, and pushed cohesins. The simulations predicted that preferential loading of cohesin at promoters is inconsistent with our experimental data. Additional ChIP-seq experiments showed that the putative cohesin loader Nipbl is not predominantly enriched at promoters. Therefore, we propose that cohesin is not preferentially loaded at promoters and that the barrier function of RNAP accounts for cohesin accumulation at active promoters. Altogether, we find that RNAP is an extrusion barrier that is not stationary, but rather, translocates and relocalizes cohesin. Loop extrusion and transcription might interact to dynamically generate and maintain gene interactions with regulatory elements and shape functional genomic organization.
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Affiliation(s)
- Edward J. Banigan
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Wen Tang
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
| | - Aafke A. van den Berg
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Roman R. Stocsits
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
| | - Hugo B. Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA02138
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- The Broad Institute of MIT and Harvard, Cambridge, MA02142
| | - Georg A. Busslinger
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna1090, Austria
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna1090, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
| | - Leonid A. Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
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18
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Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis. Nat Struct Mol Biol 2023; 30:463-474. [PMID: 36914797 DOI: 10.1038/s41594-023-00939-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/08/2023] [Indexed: 03/16/2023]
Abstract
Mammalian erythropoiesis involves progressive chromatin compaction and subsequent enucleation in terminal differentiation, but the mechanisms underlying the three-dimensional chromatin reorganization remain obscure. Here, we systematically analyze the higher-order chromatin in purified populations of primary human erythroblasts. Our results reveal that heterochromatin regions undergo substantial compression, with H3K9me3 markers relocalizing to the nuclear periphery and forming a significant number of long-range interactions, and that ~58% of the topologically associating domain (TAD) boundaries are disrupted, while certain TADs enriched for markers of the active transcription state and erythroid master regulators, GATA1 and KLF1, are selectively maintained during terminal erythropoiesis. Finally, we demonstrate that GATA1 is involved in safeguarding selected essential chromatin domains during terminal erythropoiesis. Our study therefore delineates the molecular characteristics of a development-driven chromatin compaction process, which reveals transcription competence as a key indicator of the selected domain maintenance to ensure appropriate gene expression during the extreme compaction of chromatin.
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19
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Babushkina NP, Kucher AN. Regulatory Potential of SNP Markers in Genes of DNA Repair Systems. Mol Biol 2023. [DOI: 10.1134/s002689332301003x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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20
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Dotts AJ, Reiman D, Yin P, Kujawa S, Grobman WA, Dai Y, Bulun SE. In Vivo Genome-Wide PGR Binding in Pregnant Human Myometrium Identifies Potential Regulators of Labor. Reprod Sci 2023; 30:544-559. [PMID: 35732928 PMCID: PMC9988762 DOI: 10.1007/s43032-022-01002-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/03/2022] [Indexed: 12/22/2022]
Abstract
The alterations in myometrial biology during labor are not well understood. The myometrium is the contractile portion of the uterus and contributes to labor, a process that may be regulated by the steroid hormone progesterone. Thus, human myometrial tissues from term pregnant in-active-labor (TIL) and term pregnant not-in-labor (TNIL) subjects were used for genome-wide analyses to elucidate potential future preventive or therapeutic targets involved in the regulation of labor. Using myometrial tissues directly subjected to RNA sequencing (RNA-seq), progesterone receptor (PGR) chromatin immunoprecipitation sequencing (ChIP-seq), and histone modification ChIP-seq, we profiled genome-wide changes associated with gene expression in myometrial smooth muscle tissue in vivo. In TIL myometrium, PGR predominantly occupied promoter regions, including the classical progesterone response element, whereas it bound mainly to intergenic regions in TNIL myometrial tissue. Differential binding analysis uncovered over 1700 differential PGR-bound sites between TIL and TNIL, with 1361 sites gained and 428 lost in labor. Functional analysis identified multiple pathways involved in cAMP-mediated signaling enriched in labor. A three-way integration of the data for ChIP-seq, RNA-seq, and active histone marks uncovered the following genes associated with PGR binding, transcriptional activation, and altered mRNA levels: ATP11A, CBX7, and TNS1. In vitro studies showed that ATP11A, CBX7, and TNS1 are progesterone responsive. We speculate that these genes may contribute to the contractile phenotype of the myometrium during various stages of labor. In conclusion, we provide novel labor-associated genome-wide events and PGR-target genes that can serve as targets for future mechanistic studies.
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Affiliation(s)
- Ariel J Dotts
- Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Derek Reiman
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Ping Yin
- Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Stacy Kujawa
- Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - William A Grobman
- Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Yang Dai
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Serdar E Bulun
- Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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21
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Chiu K, Berrada Y, Eskndir N, Song D, Fong C, Naughton S, Chen T, Moy S, Gyurmey S, James L, Ezeiruaku C, Capistran C, Lowey D, Diwanji V, Peterson S, Parakh H, Burgess AR, Probert C, Zhu A, Anderson B, Levi N, Gerlitz G, Packard MC, Dorfman KA, Bahiru MS, Stephens AD. CTCF is essential for proper mitotic spindle structure and anaphase segregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523293. [PMID: 36712070 PMCID: PMC9881978 DOI: 10.1101/2023.01.09.523293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mitosis is an essential process in which the duplicated genome is segregated equally into two daughter cells. CTCF has been reported to be present in mitosis but its importance for mitotic fidelity remains to be determined. To evaluate the importance of CTCF in mitosis, we tracked mitotic behaviors in wild type and two different CTCF CRISPR-based genetic knockdowns. We find that knockdown of CTCF results in prolonged mitoses and failed anaphase segregation via time lapse imaging of SiR-DNA. CTCF knockdown did not alter cell cycling or the mitotic checkpoint, which was activated upon nocodazole treatment. Immunofluorescence imaging of the mitotic spindle in CTCF knockdowns revealed disorganization via tri/tetrapolar spindles and chromosomes behind the spindle pole. Imaging of interphase nuclei showed that nuclear size increased drastically, consistent with failure to divide the duplicated genome in anaphase. Population measurements of nuclear shape in CTCF knockdowns do not display decreased circularity or increased nuclear blebbing relative to wild type. However, failed mitoses do display abnormal nuclear morphologies relative to successful mitoses, suggesting population images do not capture individual behaviors. Thus, CTCF is important for both proper metaphase organization and anaphase segregation which impacts the size and shape of the interphase nucleus.
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Affiliation(s)
- Katherine Chiu
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Yasmin Berrada
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Nebiyat Eskndir
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Dasol Song
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Claire Fong
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sarah Naughton
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Tina Chen
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Savanna Moy
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sarah Gyurmey
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Liam James
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Chimere Ezeiruaku
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Caroline Capistran
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Daniel Lowey
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Vedang Diwanji
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Samantha Peterson
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Harshini Parakh
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ayanna R. Burgess
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Cassandra Probert
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Annie Zhu
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Bryn Anderson
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Nehora Levi
- Biology Department of Molecular Biology, Faculty of Life Sciences, Ariel University, Ariel 40700, Israel
| | - Gabi Gerlitz
- Biology Department of Molecular Biology, Faculty of Life Sciences, Ariel University, Ariel 40700, Israel
| | - Mary C. Packard
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | | | | | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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22
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Davis O. Abnormal Chromatin Folding in the Molecular Pathogenesis of Epilepsy and Autism Spectrum Disorder: a Meta-synthesis with Systematic Searching. Mol Neurobiol 2023; 60:768-779. [PMID: 36367658 PMCID: PMC9849311 DOI: 10.1007/s12035-022-03106-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]
Abstract
How DNA is folded and packaged in nucleosomes is an essential regulator of gene expression. Abnormal patterns of chromatin folding are implicated in a wide range of diseases and disorders, including epilepsy and autism spectrum disorder (ASD). These disorders are thought to have a shared pathogenesis involving an imbalance in the number of excitatory-inhibitory neurons formed during neurodevelopment; however, the underlying pathological mechanism behind this imbalance is poorly understood. Studies are increasingly implicating abnormal chromatin folding in neural stem cells as one of the candidate pathological mechanisms, but no review has yet attempted to summarise the knowledge in this field. This meta-synthesis is a systematic search of all the articles on epilepsy, ASD, and chromatin folding. Its two main objectives were to determine to what extent abnormal chromatin folding is implicated in the pathogenesis of epilepsy and ASD, and secondly how abnormal chromatin folding leads to pathological disease processes. This search produced 22 relevant articles, which together strongly implicate abnormal chromatin folding in the pathogenesis of epilepsy and ASD. A range of mutations and chromosomal structural abnormalities lead to this effect, including single nucleotide polymorphisms, copy number variants, translocations and mutations in chromatin modifying. However, knowledge is much more limited into how abnormal chromatin organisation subsequently causes pathological disease processes, not yet showing, for example, whether it leads to abnormal excitation-inhibitory neuron imbalance in human brain organoids.
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Affiliation(s)
- Oliver Davis
- grid.5335.00000000121885934Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
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23
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Lee SH, Kim KD, Cho M, Huh S, An SH, Seo D, Kang K, Lee M, Tanizawa H, Jung I, Cho H, Kang H. Characterization of a new CCCTC-binding factor binding site as a dual regulator of Epstein-Barr virus latent infection. PLoS Pathog 2023; 19:e1011078. [PMID: 36696451 PMCID: PMC9876287 DOI: 10.1371/journal.ppat.1011078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/15/2022] [Indexed: 01/26/2023] Open
Abstract
Distinct viral gene expression characterizes Epstein-Barr virus (EBV) infection in EBV-producing marmoset B-cell (B95-8) and EBV-associated gastric carcinoma (SNU719) cell lines. CCCTC-binding factor (CTCF) is a structural chromatin factor that coordinates chromatin interactions in the EBV genome. Chromatin immunoprecipitation followed by sequencing against CTCF revealed 16 CTCF binding sites in the B95-8 and SNU719 EBV genomes. The biological function of one CTCF binding site (S13 locus) located on the BamHI A right transcript (BART) miRNA promoter was elucidated experimentally. Microscale thermophoresis assay showed that CTCF binds more readily to the stable form than the mutant form of the S13 locus. EBV BART miRNA clusters encode 22 miRNAs, whose roles are implicated in EBV-related cancer pathogenesis. The B95-8 EBV genome lacks a 11.8-kb EcoRI C fragment, whereas the SNU719 EBV genome is full-length. ChIP-PCR assay revealed that CTCF, RNA polymerase II, H3K4me3 histone, and H3K9me3 histone were more enriched at S13 and S16 (167-kb) loci in B95-8 than in the SNU719 EBV genome. 4C-Seq and 3C-PCR assays using B95-8 and SNU719 cells showed that the S13 locus was associated with overall EBV genomic loci including 3-kb and 167-kb region in both EBV genomes. We generated mutations in the S13 locus in bacmids with or without the 11.8-kb BART transcript unit (BART(+/-)). The S13 mutation upregulated BART miRNA expression, weakened EBV latency, and reduced EBV infectivity in the presence of EcoRI C fragment. Another 3C-PCR assay using four types of BART(+/-)·S13(wild-type(Wt)/mutant(Mt)) HEK293-EBV cells revealed that the S13 mutation decreased DNA associations between the 167-kb region and 3-kb in the EBV genome. Based on these results, CTCF bound to the S13 locus along with the 11.8-kb EcoRI C fragment is suggested to form an EBV 3-dimensional DNA loop for coordinated EBV BART miRNA expression and infectivity.
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Affiliation(s)
- Sun Hee Lee
- College of Pharmacy, Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, Kyungpook National University, Daegu, Korea
| | - Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Miyeon Cho
- College of Pharmacy, Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, Kyungpook National University, Daegu, Korea
| | - Sora Huh
- College of Pharmacy, Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, Kyungpook National University, Daegu, Korea
| | - Seong Ho An
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Donghyun Seo
- College of Pharmacy, Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, Kyungpook National University, Daegu, Korea
| | - Kyuhyun Kang
- College of Pharmacy, Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, Kyungpook National University, Daegu, Korea
| | - Minhee Lee
- College of Pharmacy, Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, Kyungpook National University, Daegu, Korea
| | - Hideki Tanizawa
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Inuk Jung
- Department of Computer Science and Engineering, Kyungpook National University, Daegu, Korea
| | - Hyosun Cho
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
- * E-mail: (HC); (HK)
| | - Hyojeung Kang
- College of Pharmacy, Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, Kyungpook National University, Daegu, Korea
- * E-mail: (HC); (HK)
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24
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Ito S, Das ND, Umehara T, Koseki H. Factors and Mechanisms That Influence Chromatin-Mediated Enhancer-Promoter Interactions and Transcriptional Regulation. Cancers (Basel) 2022; 14:5404. [PMID: 36358822 PMCID: PMC9659172 DOI: 10.3390/cancers14215404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic gene expression is regulated through chromatin conformation, in which enhancers and promoters physically interact (E-P interactions). How such chromatin-mediated E-P interactions affect gene expression is not yet fully understood, but the roles of histone acetylation and methylation, pioneer transcription factors, and architectural proteins such as CCCTC binding factor (CTCF) and cohesin have recently attracted attention. Moreover, accumulated data suggest that E-P interactions are mechanistically involved in biophysical events, including liquid-liquid phase separation, and in biological events, including cancers. In this review, we discuss various mechanisms that regulate eukaryotic gene expression, focusing on emerging views regarding chromatin conformations that are involved in E-P interactions and factors that establish and maintain them.
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Affiliation(s)
- Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Nando Dulal Das
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Immune Regulation, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
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25
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Interruption of aberrant chromatin looping is required for regenerating RB1 function and suppressing tumorigenesis. Commun Biol 2022; 5:1036. [PMID: 36175480 PMCID: PMC9522773 DOI: 10.1038/s42003-022-04007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
RB transcriptional corepressor 1 (RB1) is a critical regulatory gene in physiological and pathological processes. Genetic mutation is considered to be the main cause of RB1 inactivation. However, accumulating evidence has shown that not all RB1 dysfunction is triggered by gene mutations, and the additional mechanism underlying RB1 dysfunction remains unclear. Here, we firstly reveal that a CCCTC binding factor (CTCF) mediated intrachromosomal looping served as a regulatory inducer to inactivate RB1. Once the core genomic fragment was deleted by Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 (CRISPR/Cas9), this intrachromosomal looping was disrupted. After the open of chromatin, Enhancer of Zeste Homolog 2 (EZH2) was released and decreased the level of Tri-Methyl-Histone H3 Lys27 (H3K27me3) at the RB1 promoter, which substantially restored the expression of RB protein (pRB) and inhibited tumorigenesis. In addition, targeted correction of abnormal RB1 looping using the small-molecule compound GSK503 efficiently restored RB1 transcription and suppressed tumorigenesis. Our study reveals an alternative transcriptional mechanism underlying RB1 dysfunction independent of gene mutation, and advancing the discovery of potential therapeutic chemicals based on aberrant chromatin looping. A CTCF mediated intrachromosomal looping of RB1 promoter and its downstream silencer served as a regulatory inducer to inactivate RB1, revealing a novel transcriptional mechanism underlying RB1 dysfunction independent of gene mutation.
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26
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Dehingia B, Milewska M, Janowski M, Pękowska A. CTCF shapes chromatin structure and gene expression in health and disease. EMBO Rep 2022; 23:e55146. [PMID: 35993175 PMCID: PMC9442299 DOI: 10.15252/embr.202255146] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/31/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
CCCTC-binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations of its ZFs. The great majority of the ~50,000 genomic locations bound by the CTCF protein in a given cell type is intergenic, and a fraction of these sites overlaps with transcriptional enhancers. Furthermore, a proportion of the regions bound by CTCF intersect genes and promoters. This suggests multiple ways in which CTCF may impact gene expression. At promoters, CTCF can directly affect transcription. At more distal sites, CTCF may orchestrate interactions between regulatory elements and help separate eu- and heterochromatic areas in the genome, exerting a chromatin barrier function. In this review, we outline how CTCF contributes to the regulation of the three-dimensional structure of chromatin and the formation of chromatin domains. We discuss how CTCF binding and architectural functions are regulated. We examine the literature implicating CTCF in controlling gene expression in development and disease both by acting as an insulator and a factor facilitating regulatory elements to efficiently interact with each other in the nuclear space.
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Affiliation(s)
- Bondita Dehingia
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental BiologyPolish Academy of SciencesWarsawPoland
| | - Małgorzata Milewska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental BiologyPolish Academy of SciencesWarsawPoland
| | - Marcin Janowski
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental BiologyPolish Academy of SciencesWarsawPoland
| | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental BiologyPolish Academy of SciencesWarsawPoland
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27
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Sun X, Zhang J, Cao C. CTCF and Its Partners: Shaper of 3D Genome during Development. Genes (Basel) 2022; 13:genes13081383. [PMID: 36011294 PMCID: PMC9407368 DOI: 10.3390/genes13081383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes.
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Affiliation(s)
- Xiaoyue Sun
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Zhang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chunwei Cao
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Guangzhou Laboratory, Guangzhou 510320, China
- Correspondence:
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28
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Stefanucci L, Frontini M. Non-coding genetic variation in regulatory elements determines thrombosis and hemostasis phenotypes. J Thromb Haemost 2022; 20:1759-1765. [PMID: 35514262 PMCID: PMC9540108 DOI: 10.1111/jth.15754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 11/26/2022]
Abstract
Since the early inception of genome-wide association studies (GWAS), it became clear that, in all diseases or traits studied, most genetic variants are likely to exert their effect on gene expression mainly by altering the function of regulatory elements. At the same time, the regulation of the gene expression field broadened its boundaries, from the univocal relationship between regulatory elements and genes to include genome organization, long-range DNA interactions, and epigenetics. Next-generation sequencing has introduced genome-wide approaches that have greatly improved our understanding of the general principles of gene expression. However, elucidating how these apply in every single genomic locus still requires painstaking experimental work, in which several independent lines of evidence are required, and often this is helped by rare genetic variants in individuals with rare diseases. This review will focus on the non-coding features of the genome involved in transcriptional regulation, that when altered, leads to known cases of inherited (familial) thrombotic and hemostatic phenotypes, emphasizing the role of enhancers and super-enhancers.
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Affiliation(s)
- Luca Stefanucci
- Department of HaematologyUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- National Health Service (NHS) Blood and TransplantCambridge Biomedical CampusCambridgeUK
- British Heart Foundation, Cambridge Centre for Research ExcellenceUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
| | - Mattia Frontini
- Department of HaematologyUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- National Health Service (NHS) Blood and TransplantCambridge Biomedical CampusCambridgeUK
- British Heart Foundation, Cambridge Centre for Research ExcellenceUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- Institute of Biomedical & Clinical Science, College of Medicine and HealthUniversity of Exeter Medical SchoolExeterUK
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29
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Schmidbaur H, Kawaguchi A, Clarence T, Fu X, Hoang OP, Zimmermann B, Ritschard EA, Weissenbacher A, Foster JS, Nyholm SV, Bates PA, Albertin CB, Tanaka E, Simakov O. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nat Commun 2022; 13:2172. [PMID: 35449136 PMCID: PMC9023564 DOI: 10.1038/s41467-022-29694-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/28/2022] [Indexed: 12/17/2022] Open
Abstract
Coleoid cephalopods (squid, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that coleoid cephalopod genomes have been extensively restructured compared to other animals, leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identify a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understanding cephalopod innovations.
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Affiliation(s)
- Hannah Schmidbaur
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | | | - Tereza Clarence
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Xiao Fu
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Oi Pui Hoang
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Elena A Ritschard
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | | | - Jamie S Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab, Merritt Island, FL, USA
| | - Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Caroline B Albertin
- Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA.
| | - Elly Tanaka
- Institute for Molecular Pathology, Vienna, Austria.
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria.
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30
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Sefer E. A comparison of topologically associating domain callers over mammals at high resolution. BMC Bioinformatics 2022; 23:127. [PMID: 35413815 PMCID: PMC9006547 DOI: 10.1186/s12859-022-04674-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Topologically associating domains (TADs) are locally highly-interacting genome regions, which also play a critical role in regulating gene expression in the cell. TADs have been first identified while investigating the 3D genome structure over High-throughput Chromosome Conformation Capture (Hi-C) interaction dataset. Substantial degree of efforts have been devoted to develop techniques for inferring TADs from Hi-C interaction dataset. Many TAD-calling methods have been developed which differ in their criteria and assumptions in TAD inference. Correspondingly, TADs inferred via these callers vary in terms of both similarities and biological features they are enriched in. RESULT We have carried out a systematic comparison of 27 TAD-calling methods over mammals. We use Micro-C, a recent high-resolution variant of Hi-C, to compare TADs at a very high resolution, and classify the methods into 3 categories: feature-based methods, Clustering methods, Graph-partitioning methods. We have evaluated TAD boundaries, gaps between adjacent TADs, and quality of TADs across various criteria. We also found particularly CTCF and Cohesin proteins to be effective in formation of TADs with corner dots. We have also assessed the callers performance on simulated datasets since a gold standard for TADs is missing. TAD sizes and numbers change remarkably between TAD callers and dataset resolutions, indicating that TADs are hierarchically-organized domains, instead of disjoint regions. A core subset of feature-based TAD callers regularly perform the best while inferring reproducible domains, which are also enriched for TAD related biological properties. CONCLUSION We have analyzed the fundamental principles of TAD-calling methods, and identified the existing situation in TAD inference across high resolution Micro-C interaction datasets over mammals. We come up with a systematic, comprehensive, and concise framework to evaluate the TAD-calling methods performance across Micro-C datasets. Our research will be useful in selecting appropriate methods for TAD inference and evaluation based on available data, experimental design, and biological question of interest. We also introduce our analysis as a benchmarking tool with publicly available source code.
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Affiliation(s)
- Emre Sefer
- Department of Computer Science, Ozyegin University, Istanbul, Turkey.
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31
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Chandrasekaran V, Oparina N, Garcia-Bonete MJ, Wasén C, Erlandsson MC, Malmhäll-Bah E, Andersson KME, Jensen M, Silfverswärd ST, Katona G, Bokarewa MI. Cohesin-Mediated Chromatin Interactions and Autoimmunity. Front Immunol 2022; 13:840002. [PMID: 35222432 PMCID: PMC8866859 DOI: 10.3389/fimmu.2022.840002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 11/23/2022] Open
Abstract
Proper physiological functioning of any cell type requires ordered chromatin organization. In this context, cohesin complex performs important functions preventing premature separation of sister chromatids after DNA replication. In partnership with CCCTC-binding factor, it ensures insulator activity to organize enhancers and promoters within regulatory chromatin. Homozygous mutations and dysfunction of individual cohesin proteins are embryonically lethal in humans and mice, which limits in vivo research work to embryonic stem cells and progenitors. Conditional alleles of cohesin complex proteins have been generated to investigate their functional roles in greater detail at later developmental stages. Thus, genome regulation enabled by action of cohesin proteins is potentially crucial in lineage cell development, including immune homeostasis. In this review, we provide current knowledge on the role of cohesin complex in leukocyte maturation and adaptive immunity. Conditional knockout and shRNA-mediated inhibition of individual cohesin proteins in mice demonstrated their importance in haematopoiesis, adipogenesis and inflammation. Notably, these effects occur rather through changes in transcriptional gene regulation than through expected cell cycle defects. This positions cohesin at the crossroad of immune pathways including NF-kB, IL-6, and IFNγ signaling. Cohesin proteins emerged as vital regulators at early developmental stages of thymocytes and B cells and after antigen challenge. Human genome-wide association studies are remarkably concordant with these findings and present associations between cohesin and rheumatoid arthritis, multiple sclerosis and HLA-B27 related chronic inflammatory conditions. Furthermore, bioinformatic prediction based on protein-protein interactions reveal a tight connection between the cohesin complex and immune relevant processes supporting the notion that cohesin will unearth new clues in regulation of autoimmunity.
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Affiliation(s)
- Venkataragavan Chandrasekaran
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Nina Oparina
- Rheumatology Clinic, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria-Jose Garcia-Bonete
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Caroline Wasén
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Malin C. Erlandsson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Eric Malmhäll-Bah
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Karin M. E. Andersson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Maja Jensen
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| | - Sofia T. Silfverswärd
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| | - Maria I. Bokarewa
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Rheumatology Clinic, Sahlgrenska University Hospital, Gothenburg, Sweden
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Ortabozkoyun H, Huang PY, Cho H, Narendra V, LeRoy G, Gonzalez-Buendia E, Skok JA, Tsirigos A, Mazzoni EO, Reinberg D. CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters. Nat Genet 2022; 54:202-212. [PMID: 35145304 PMCID: PMC8837555 DOI: 10.1038/s41588-021-01008-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022]
Abstract
CCCTC-binding factor (CTCF) is critical to three-dimensional genome organization. Upon differentiation, CTCF insulates active and repressed genes within Hox gene clusters. We conducted a genome-wide CRISPR knockout (KO) screen to identify genes required for CTCF-boundary activity at the HoxA cluster, complemented by biochemical approaches. Among the candidates, we identified Myc-associated zinc-finger protein (MAZ) as a cofactor in CTCF insulation. MAZ colocalizes with CTCF at chromatin borders and, similar to CTCF, interacts with the cohesin subunit RAD21. MAZ KO disrupts gene expression and local contacts within topologically associating domains. Similar to CTCF motif deletions, MAZ motif deletions lead to derepression of posterior Hox genes immediately after CTCF boundaries upon differentiation, giving rise to homeotic transformations in mouse. Thus, MAZ is a factor contributing to appropriate insulation, gene expression and genomic architecture during development.
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Affiliation(s)
- Havva Ortabozkoyun
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Pin-Yao Huang
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Hyunwoo Cho
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA
| | - Varun Narendra
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Edgar Gonzalez-Buendia
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jane A Skok
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Danny Reinberg
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA. .,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
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33
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Tang R, Li Y, Han F, Li Z, Lin X, Sun H, Zhang X, Jiang Q, Nie H, Li Y. A CTCF-Binding Element and Histone Deacetylation Cooperatively Maintain Chromatin Loops, Linking to Long-Range Gene Regulation in Cancer Genomes. Front Oncol 2022; 11:821495. [PMID: 35127534 PMCID: PMC8813737 DOI: 10.3389/fonc.2021.821495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022] Open
Abstract
Background Genes spanning long chromosomal domains are coordinately regulated in human genome, which contribute to global gene dysregulation and carcinogenesis in cancer. It has been noticed that epigenetic modification and chromatin architecture may participate in the regulation process. However, the regulation patterns and functional elements of long-range gene regulation are unclear. Methods Based on the clinical transcriptome data from different tumor sets, a novel expressional correlation analysis pipeline was performed to classify the co-regulated regions and subsets of intercorrelated regions. The GLAM2 program was used to predict conserved DNA elements that enriched in regions. Two conserved elements were selected to delete in Ishikawa and HeLa cells by CRISPR-Cas9. SAHA treatment and HDAC knockdown were used to change the histone acetylation status. Using qPCR, MTT, and scratch healing assay, we evaluate the effect on gene expression and cancer cell phenotype. By DNA pull-down and ChIP, the element-binding proteins were testified. 3C and 3D-FISH were performed to depict the alteration in chromatin architecture. Results In multiple cancer genomes, we classified subsets of coordinately regulated regions (sub-CRRs) that possibly shared the same regulatory mechanisms and exhibited similar expression patterns. A new conserved DNA element (CRE30) was enriched in sub-CRRs and associated with cancer patient survival. CRE30 could restrict gene regulation in sub-CRRs and affect cancer cell phenotypes. DNA pull-down showed that multiple proteins including CTCF were recruited on the CRE30 locus, and ChIP assay confirmed the CTCF-binding signals. Subsequent results uncovered that as an essential element, CRE30 maintained chromatin loops and mediated a compact chromatin architecture. Moreover, we found that blocking global histone deacetylation induced chromatin loop disruption and CTCF dropping in the region containing CRE30, linked to promoted gene regulation. Additionally, similar effects were observed with CRE30 deletion in another locus of chromosome 8. Conclusions Our research clarified a new functional element that recruits CTCF and collaborates with histone deacetylation to maintain high-order chromatin organizations, linking to long-range gene regulation in cancer genomes. The findings highlight a close relationship among conserved DNA element, epigenetic modification, and chromatin architecture in long-range gene regulation process.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Huan Nie
- *Correspondence: Yu Li, ; Huan Nie,
| | - Yu Li
- *Correspondence: Yu Li, ; Huan Nie,
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Pileggi S, La Vecchia M, Colombo EA, Fontana L, Colapietro P, Rovina D, Morotti A, Tabano S, Porta G, Alcalay M, Gervasini C, Miozzo M, Sirchia SM. Cohesin Mutations Induce Chromatin Conformation Perturbation of the H19/ IGF2 Imprinted Region and Gene Expression Dysregulation in Cornelia de Lange Syndrome Cell Lines. Biomolecules 2021; 11:1622. [PMID: 34827619 PMCID: PMC8615450 DOI: 10.3390/biom11111622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023] Open
Abstract
Traditionally, Cornelia de Lange Syndrome (CdLS) is considered a cohesinopathy caused by constitutive mutations in cohesin complex genes. Cohesin is a major regulator of chromatin architecture, including the formation of chromatin loops at the imprinted IGF2/H19 domain. We used 3C analysis on lymphoblastoid cells from CdLS patients carrying mutations in NIPBL and SMC1A genes to explore 3D chromatin structure of the IGF2/H19 locus and evaluate the influence of cohesin alterations in chromatin architecture. We also assessed quantitative expression of imprinted loci and WNT pathway genes, together with DMR methylation status of the imprinted genes. A general impairment of chromatin architecture and the emergence of new interactions were found. Moreover, imprinting alterations also involved the expression and methylation levels of imprinted genes, suggesting an association among cohesin genetic defects, chromatin architecture impairment, and imprinting network alteration. The WNT pathway resulted dysregulated: canonical WNT, cell cycle, and WNT signal negative regulation were the most significantly affected subpathways. Among the deregulated pathway nodes, the key node of the frizzled receptors was repressed. Our study provides new evidence that mutations in genes of the cohesin complex have effects on the chromatin architecture and epigenetic stability of genes commonly regulated by high order chromatin structure.
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Affiliation(s)
- Silvana Pileggi
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Marta La Vecchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Elisa Adele Colombo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Laura Fontana
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Patrizia Colapietro
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
| | - Davide Rovina
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Annamaria Morotti
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Silvia Tabano
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
- Laboratory of Medical Genetics, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giovanni Porta
- Centro di Medicina Genomica, Department of Medicine and Surgery, Università degli Studi dell’Insubria, 21100 Varese, Italy;
| | - Myriam Alcalay
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Monica Miozzo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Silvia Maria Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
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Bailey ML, Tieu D, Habsid A, Tong AHY, Chan K, Moffat J, Hieter P. Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2. Life Sci Alliance 2021; 4:e202101083. [PMID: 34462321 PMCID: PMC8408347 DOI: 10.26508/lsa.202101083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 12/14/2022] Open
Abstract
STAG2, a component of the mitotically essential cohesin complex, is highly mutated in several different tumour types, including glioblastoma and bladder cancer. Whereas cohesin has roles in many cancer-related pathways, such as chromosome instability, DNA repair and gene expression, the complex nature of cohesin function has made it difficult to determine how STAG2 loss might either promote tumorigenesis or be leveraged therapeutically across divergent cancer types. Here, we have performed whole-genome CRISPR-Cas9 screens for STAG2-dependent genetic interactions in three distinct cellular backgrounds. Surprisingly, STAG1, the paralog of STAG2, was the only negative genetic interaction that was shared across all three backgrounds. We also uncovered a paralogous synthetic lethal mechanism behind a genetic interaction between STAG2 and the iron regulatory gene IREB2 Finally, investigation of an unusually strong context-dependent genetic interaction in HAP1 cells revealed factors that could be important for alleviating cohesin loading stress. Together, our results reveal new facets of STAG2 and cohesin function across a variety of genetic contexts.
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Affiliation(s)
- Melanie L Bailey
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - David Tieu
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Andrea Habsid
- Donnelly Centre, University of Toronto, Toronto, Canada
| | | | | | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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36
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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37
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Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer. Proc Natl Acad Sci U S A 2021; 118:2025647118. [PMID: 34426493 PMCID: PMC8536346 DOI: 10.1073/pnas.2025647118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cellular senescence causes a dramatic alteration of chromatin organization and changes the gene expression profile of proinflammatory factors, thereby contributing to various age-related pathologies through the senescence-associated secretory phenotype (SASP). Chromatin organization and global gene expression are maintained by the CCCTC-binding factor (CTCF); however, the molecular mechanism underlying CTCF regulation and its association with SASP gene expression remains unclear. We discovered that noncoding RNA (ncRNA) derived from normally silenced pericentromeric repetitive sequences directly impairs the DNA binding of CTCF. This CTCF disturbance increases the accessibility of chromatin and activates the transcription of SASP-like inflammatory genes, promoting malignant transformation. Notably, pericentromeric ncRNA was transferred into surrounding cells via small extracellular vesicles acting as a tumorigenic SASP factor. Because CTCF blocks the expression of pericentromeric ncRNA in young cells, the down-regulation of CTCF during cellular senescence triggers the up-regulation of this ncRNA and SASP-related inflammatory gene expression. In this study, we show that pericentromeric ncRNA provokes chromosomal alteration by inhibiting CTCF, leading to a SASP-like inflammatory response in a cell-autonomous and non-cell-autonomous manner and thus may contribute to the risk of tumorigenesis during aging.
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Liu N, Low WY, Alinejad-Rokny H, Pederson S, Sadlon T, Barry S, Breen J. Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenetics Chromatin 2021; 14:41. [PMID: 34454581 PMCID: PMC8399707 DOI: 10.1186/s13072-021-00417-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Eukaryotic genomes are highly organised within the nucleus of a cell, allowing widely dispersed regulatory elements such as enhancers to interact with gene promoters through physical contacts in three-dimensional space. Recent chromosome conformation capture methodologies such as Hi-C have enabled the analysis of interacting regions of the genome providing a valuable insight into the three-dimensional organisation of the chromatin in the nucleus, including chromosome compartmentalisation and gene expression. Complicating the analysis of Hi-C data, however, is the massive amount of identified interactions, many of which do not directly drive gene function, thus hindering the identification of potentially biologically functional 3D interactions. In this review, we collate and examine the downstream analysis of Hi-C data with particular focus on methods that prioritise potentially functional interactions. We classify three groups of approaches: structural-based discovery methods, e.g. A/B compartments and topologically associated domains, detection of statistically significant chromatin interactions, and the use of epigenomic data integration to narrow down useful interaction information. Careful use of these three approaches is crucial to successfully identifying potentially functional interactions within the genome.
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Affiliation(s)
- Ning Liu
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab, The Graduate School of Biomedical Engineering, The University of New South Wales, NSW, 2052, Sydney, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
| | - Stephen Pederson
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
- Dame Roma Mitchell Cancer Research Laboratories (DRMCRL), Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - Simon Barry
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - James Breen
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia.
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia.
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia.
- South Australian Genomics Centre (SAGC), South Australian Health & Medical Research Institute (SAHMRI), SA, 5000, Adelaide, Australia.
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Alharbi AB, Schmitz U, Bailey CG, Rasko JEJ. CTCF as a regulator of alternative splicing: new tricks for an old player. Nucleic Acids Res 2021; 49:7825-7838. [PMID: 34181707 PMCID: PMC8373115 DOI: 10.1093/nar/gkab520] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
Three decades of research have established the CCCTC-binding factor (CTCF) as a ubiquitously expressed chromatin organizing factor and master regulator of gene expression. A new role for CTCF as a regulator of alternative splicing (AS) has now emerged. CTCF has been directly and indirectly linked to the modulation of AS at the individual transcript and at the transcriptome-wide level. The emerging role of CTCF-mediated regulation of AS involves diverse mechanisms; including transcriptional elongation, DNA methylation, chromatin architecture, histone modifications, and regulation of splicing factor expression and assembly. CTCF thereby appears to not only co-ordinate gene expression regulation but contributes to the modulation of transcriptomic complexity. In this review, we highlight previous discoveries regarding the role of CTCF in AS. In addition, we summarize detailed mechanisms by which CTCF mediates AS regulation. We propose opportunities for further research designed to examine the possible fate of CTCF-mediated alternatively spliced genes and associated biological consequences. CTCF has been widely acknowledged as the 'master weaver of the genome'. Given its multiple connections, further characterization of CTCF's emerging role in splicing regulation might extend its functional repertoire towards a 'conductor of the splicing orchestra'.
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Affiliation(s)
- Adel B Alharbi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E J Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
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40
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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: 9] [Impact Index Per Article: 3.0] [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.
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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
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41
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Long Q, Liu Z, Gullerova M. Sweet Melody or Jazz? Transcription Around DNA Double-Strand Breaks. Front Mol Biosci 2021; 8:655786. [PMID: 33959637 PMCID: PMC8096065 DOI: 10.3389/fmolb.2021.655786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/22/2021] [Indexed: 12/23/2022] Open
Abstract
Genomic integrity is continuously threatened by thousands of endogenous and exogenous damaging factors. To preserve genome stability, cells developed comprehensive DNA damage response (DDR) pathways that mediate the recognition of damaged DNA lesions, the activation of signaling cascades, and the execution of DNA repair. Transcription has been understood to pose a threat to genome stability in the presence of DNA breaks. Interestingly, accumulating evidence in recent years shows that the transient transcriptional activation at DNA double-strand break (DSB) sites is required for efficient repair, while the rest of the genome exhibits temporary transcription silencing. This genomic shut down is a result of multiple signaling cascades involved in the maintenance of DNA/RNA homeostasis, chromatin stability, and genome fidelity. The regulation of transcription of protein-coding genes and non-coding RNAs has been extensively studied; however, the exact regulatory mechanisms of transcription at DSBs remain enigmatic. These complex processes involve many players such as transcription-associated protein complexes, including kinases, transcription factors, chromatin remodeling complexes, and helicases. The damage-derived transcripts themselves also play an essential role in DDR regulation. In this review, we summarize the current findings on the regulation of transcription at DSBs and discussed the roles of various accessory proteins in these processes and consequently in DDR.
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Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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42
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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.
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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.
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43
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Lou S, Li T, Kong X, Zhang J, Liu J, Lee D, Gerstein M. TopicNet: a framework for measuring transcriptional regulatory network change. Bioinformatics 2021; 36:i474-i481. [PMID: 32657410 PMCID: PMC7355251 DOI: 10.1093/bioinformatics/btaa403] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Motivation Recently, many chromatin immunoprecipitation sequencing experiments have been carried out for a diverse group of transcription factors (TFs) in many different types of human cells. These experiments manifest large-scale and dynamic changes in regulatory network connectivity (i.e. network ‘rewiring’), highlighting the different regulatory programs operating in disparate cellular states. However, due to the dense and noisy nature of current regulatory networks, directly comparing the gains and losses of targets of key TFs across cell states is often not informative. Thus, here, we seek an abstracted, low-dimensional representation to understand the main features of network change. Results We propose a method called TopicNet that applies latent Dirichlet allocation to extract functional topics for a collection of genes regulated by a given TF. We then define a rewiring score to quantify regulatory-network changes in terms of the topic changes for this TF. Using this framework, we can pinpoint particular TFs that change greatly in network connectivity between different cellular states (such as observed in oncogenesis). Also, incorporating gene expression data, we define a topic activity score that measures the degree to which a given topic is active in a particular cellular state. And we show how activity differences can indicate differential survival in various cancers. Availability and Implementation The TopicNet framework and related analysis were implemented using R and all codes are available at https://github.com/gersteinlab/topicnet. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shaoke Lou
- Department of Molecular Biophysics and Biochemistry
| | - Tianxiao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | | | - Jing Zhang
- Department of Molecular Biophysics and Biochemistry
| | - Jason Liu
- Department of Molecular Biophysics and Biochemistry
| | - Donghoon Lee
- Department of Molecular Biophysics and Biochemistry
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry
- To whom correspondence should be addressed. E-mail:
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44
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Labudina A, Horsfield JA. The three-dimensional genome in zebrafish development. Brief Funct Genomics 2021:elab008. [PMID: 33675363 DOI: 10.1093/bfgp/elab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/05/2021] [Accepted: 01/29/2021] [Indexed: 01/01/2023] Open
Abstract
In recent years, remarkable progress has been made toward understanding the three-dimensional (3D) organisation of genomes and the influence of genome organisation on gene regulation. Although 3D genome organisation probably plays a crucial role in embryo development, animal studies addressing the developmental roles of chromosome topology are only just starting to emerge. Zebrafish, an important model system for early development, have already contributed important advances in understanding the developmental consequences of perturbation in 3D genome organisation. Zebrafish have been used to determine the effects of mutations in proteins responsible for 3D genome organisation: cohesin and CTCF. In this review, we highlight research to date from zebrafish that has provided insight into how 3D genome organisation contributes to tissue-specific gene regulation and embryo development.
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45
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Luan J, Xiang G, Gómez-García PA, Tome JM, Zhang Z, Vermunt MW, Zhang H, Huang A, Keller CA, Giardine BM, Zhang Y, Lan Y, Lis JT, Lakadamyali M, Hardison RC, Blobel GA. Distinct properties and functions of CTCF revealed by a rapidly inducible degron system. Cell Rep 2021; 34:108783. [PMID: 33626344 PMCID: PMC7999233 DOI: 10.1016/j.celrep.2021.108783] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/25/2020] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
CCCTC-binding factor (CTCF) is a conserved zinc finger transcription factor implicated in a wide range of functions, including genome organization, transcription activation, and elongation. To explore the basis for CTCF functional diversity, we coupled an auxin-induced degron system with precision nuclear run-on. Unexpectedly, oriented CTCF motifs in gene bodies are associated with transcriptional stalling in a manner independent of bound CTCF. Moreover, CTCF at different binding sites (CBSs) displays highly variable resistance to degradation. Motif sequence does not significantly predict degradation behavior, but location at chromatin boundaries and chromatin loop anchors, as well as co-occupancy with cohesin, are associated with delayed degradation. Single-molecule tracking experiments link chromatin residence time to CTCF degradation kinetics, which has ramifications regarding architectural CTCF functions. Our study highlights the heterogeneity of CBSs, uncovers properties specific to architecturally important CBSs, and provides insights into the basic processes of genome organization and transcription regulation.
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Affiliation(s)
- Jing Luan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guanjue Xiang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Pablo Aurelio Gómez-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jacob M Tome
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Marit W Vermunt
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Haoyue Zhang
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yu Zhang
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Yemin Lan
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA.
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46
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VonHandorf A, Zablon HA, Biesiada J, Zhang X, Medvedovic M, Puga A. Hexavalent chromium promotes differential binding of CTCF to its cognate sites in Euchromatin. Epigenetics 2021; 16:1361-1376. [PMID: 33319643 DOI: 10.1080/15592294.2020.1864168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Hexavalent chromium compounds are well-established respiratory carcinogens to which humans are commonly exposed in industrial and occupational settings. In addition, natural and anthropogenic sources of these compounds contribute to the exposure of global populations through multiple routes, including dermal, ingestion and inhalation that elevate the risk of cancer by largely unresolved mechanisms. Cr(VI) has genotoxic properties that include ternary adduct formation with DNA, increases in DNA damage, mostly by double-strand break formation, and altered transcriptional responses. Our previous work using ATAC-seq showed that CTCF motifs were enriched in Cr(VI)-dependent differentially accessible chromatin, suggesting that CTCF, a key transcription factor responsible for the regulation of the transcriptome, might be a chromium target. To test this hypothesis, we investigated the effect of Cr(VI) treatment on the binding of CTCF to its cognate sites and ensuing changes in transcription-related histone modifications. Differentially bound CTCF sites were enriched by Cr(VI) treatment within transcription-related regions, specifically transcription start sites and upstream genic regions. Functional annotation of the affected genes highlighted biological processes previously associated with Cr(VI) exposure. Notably, we found that differentially bound CTCF sites proximal to the promoters of this subset of genes were frequently associated with the active histone marks H3K27ac, H3K4me3, and H3K36me3, in agreement with the concept that Cr(VI) targets CTCF in euchromatic regions of the genome. Our results support the conclusion that Cr(VI) treatment promotes the differential binding of CTCF to its cognate sites in genes near transcription-active boundaries, targeting these genes for dysregulation.
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Affiliation(s)
- Andrew VonHandorf
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Hesbon A Zablon
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jacek Biesiada
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Alvaro Puga
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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47
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Regulation and dysregulation of spatial chromatin structure in the central nervous system. Anat Sci Int 2021; 96:179-186. [PMID: 33392926 DOI: 10.1007/s12565-020-00567-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
Chromatin exists as a non-linear, "three-dimensional" structure in the nuclear space. The dynamic alteration of the chromatin structure leads to transcriptional changes during the formation of the neuronal network. Several studies providing evidence for the link between the dysregulation of spatial chromatin architecture and developmental disorders have accumulated. Therefore, we studied and reviewed the regulation and dysregulation of 3D genome organization in the central nervous system, with a special focus on the cohesin complex that is crucial for the formation of the chromatin loop structure. This review summarizes the function and mechanisms of spatial chromatin architecture during the development of the central nervous system. We discuss the link between the disturbances in the 3D chromatin structure and the diseases of the central nervous system. Finally, we discuss how the knowledge of 3D genome organization may lead to further advances in diagnosis and therapy for the diseases of the central nervous system.
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48
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Hansen AS. CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism. Nucleus 2020; 11:132-148. [PMID: 32631111 PMCID: PMC7566886 DOI: 10.1080/19491034.2020.1782024] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 01/10/2023] Open
Abstract
Mammalian genome structure is closely linked to function. At the scale of kilobases to megabases, CTCF and cohesin organize the genome into chromatin loops. Mechanistically, cohesin is proposed to extrude chromatin loops bidirectionally until it encounters occupied CTCF DNA-binding sites. Curiously, loops form predominantly between CTCF binding sites in a convergent orientation. How CTCF interacts with and blocks cohesin extrusion in an orientation-specific manner has remained a mechanistic mystery. Here, we review recent papers that have shed light on these processes and suggest a multi-step interaction between CTCF and cohesin. This interaction may first involve a pausing step, where CTCF halts cohesin extrusion, followed by a stabilization step of the CTCF-cohesin complex, resulting in a chromatin loop. Finally, we discuss our own recent studies on an internal RNA-Binding Region (RBRi) in CTCF to elucidate its role in regulating CTCF clustering, target search mechanisms and chromatin loop formation and future challenges.
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Affiliation(s)
- Anders S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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49
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Raizis AM, Racher HM, Foucal A, Dimaras H, Gallie BL, George PM. DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the RB1 gene promoter. Epigenetics 2020; 16:940-954. [PMID: 33258708 DOI: 10.1080/15592294.2020.1834911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA hypermethylation events occur frequently in human cancers, but less is known of the mechanisms leading to their initiation. Retinoblastoma, an intraocular cancer affecting young children, involves bi-allelic inactivation of the RB1 gene (RB-/-). RB1 encodes a tumour suppressing, cell cycle regulating transcription factor (pRB) that binds and regulates the RB1 core and other E2F responsive promoters with epigenetic functions that include recruitment of histone deacetylases (HDACs). Evidence suggests that bi-allelic epigenetic inactivation/hypermethylation of the RB1 core promoter (PrE-/E-), is specific to sporadic retinoblastomas (frequency~10%), whereas heritable RB1 promoter variants (Pr-/+, frequency~1-2%) are not associated with known epigenetic phenomena. We report heritable Pr-/- retinoblastomas with the expected loss of pRB expression, in which hypermethylation consistent with distal boundary displacement (BD) relative to normal peripheral blood DNAs was detected in 4/4 cases. In contrast, proximal BD was identified in 16/16 RB-/- retinoblastomas while multiple boundaries distal of the core promoter was further identified in PrE-/E-and PrE-/E+ retinoblastomas. However, weak or no DNA hypermethylation/BD in peripheral blood DNA was detected in 8/9 Pr-/+ patients, with the exception, a carrier of a microdeletion encompassing several RB1 promoter elements. These findings suggest that loss of boundary control may be a critical step leading to epigenetic inactivation of the RB1 gene and that novel DNA methylation boundaries/profiles identified in the RB1 promoter of Pr-/- retinoblastomas, may be the result of epigenetic phenomena associated with epimutation in conjunction with loss of pRB expression/binding and/or RB1 promoter interactions with boundary control elements.
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Affiliation(s)
- A M Raizis
- C/o Dept. of Molecular Pathology, Canterbury Health Laboratories, Christchurch, New Zealand
| | - H M Racher
- Department of Genetics, c/o Impact Genetics, Bowmanville, Ontario, Canada
| | - A Foucal
- Universit#xE9; de Nantes, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - H Dimaras
- Departments of Ophthalmology & Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology & Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, Canada.,Division of Clinical Public Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.,Child Health Evaluative Sciences, SickKids Research Institute, Toronto, Canada
| | - B L Gallie
- Departments of Ophthalmology & Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology & Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, Canada.,Department of Pediatrics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Departments of Molecular Genetics and Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - P M George
- Department of Pathology, University of Otago, Christchurch, New Zealand
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50
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Oudelaar AM, Higgs DR. The relationship between genome structure and function. Nat Rev Genet 2020; 22:154-168. [PMID: 33235358 DOI: 10.1038/s41576-020-00303-x] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 02/06/2023]
Abstract
Precise patterns of gene expression in metazoans are controlled by three classes of regulatory elements: promoters, enhancers and boundary elements. During differentiation and development, these elements form specific interactions in dynamic higher-order chromatin structures. However, the relationship between genome structure and its function in gene regulation is not completely understood. Here we review recent progress in this field and discuss whether genome structure plays an instructive role in regulating gene expression or is a reflection of the activity of the regulatory elements of the genome.
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Affiliation(s)
| | - Douglas R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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