1
|
Ma F, Cao Y, Du H, Braikia FZ, Zong L, Ollikainen N, Bayer M, Qiu X, Park B, Roy R, Nandi S, Sarantopoulou D, Ziman A, Bianchi AH, Beerman I, Zhao K, Grosschedl R, Sen R. Three-dimensional chromatin reorganization regulates B cell development during ageing. Nat Cell Biol 2024; 26:991-1002. [PMID: 38866970 PMCID: PMC11178499 DOI: 10.1038/s41556-024-01424-9] [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: 11/01/2022] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
The contribution of three-dimensional genome organization to physiological ageing is not well known. Here we show that large-scale chromatin reorganization distinguishes young and old bone marrow progenitor (pro-) B cells. These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs). The gene encoding Ebf1, a key B cell regulator, switches from compartment A to B with age. Genetically reducing Ebf1 recapitulates some features of old pro-B cells. TADs that are most reduced with age contain genes important for B cell development, including the immunoglobulin heavy chain (Igh) locus. Weaker intra-TAD interactions at Igh correlate with altered variable (V), diversity (D) and joining (J) gene recombination. Our observations implicate three-dimensional chromatin reorganization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age.
Collapse
Affiliation(s)
- Fei Ma
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Hansen Du
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Fatima Zohra Braikia
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Le Zong
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Noah Ollikainen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Marc Bayer
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Xiang Qiu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Bongsoo Park
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Satabdi Nandi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Dimitra Sarantopoulou
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | | | - Aisha Haley Bianchi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Isabel Beerman
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA.
| |
Collapse
|
2
|
Chen B, Ren C, Ouyang Z, Xu J, Xu K, Li Y, Guo H, Bai X, Tian M, Xu X, Wang Y, Li H, Bo X, Chen H. Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair. Brief Bioinform 2024; 25:bbae306. [PMID: 38935071 PMCID: PMC11210073 DOI: 10.1093/bib/bbae306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/01/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Advances in chromatin mapping have exposed the complex chromatin hierarchical organization in mammals, including topologically associating domains (TADs) and their substructures, yet the functional implications of this hierarchy in gene regulation and disease progression are not fully elucidated. Our study delves into the phenomenon of shared TAD boundaries, which are pivotal in maintaining the hierarchical chromatin structure and regulating gene activity. By integrating high-resolution Hi-C data, chromatin accessibility, and DNA double-strand breaks (DSBs) data from various cell lines, we systematically explore the complex regulatory landscape at high-level TAD boundaries. Our findings indicate that these boundaries are not only key architectural elements but also vibrant hubs, enriched with functionally crucial genes and complex transcription factor binding site-clustered regions. Moreover, they exhibit a pronounced enrichment of DSBs, suggesting a nuanced interplay between transcriptional regulation and genomic stability. Our research provides novel insights into the intricate relationship between the 3D genome structure, gene regulation, and DNA repair mechanisms, highlighting the role of shared TAD boundaries in maintaining genomic integrity and resilience against perturbations. The implications of our findings extend to understanding the complexities of genomic diseases and open new avenues for therapeutic interventions targeting the structural and functional integrity of TAD boundaries.
Collapse
Affiliation(s)
- Bijia Chen
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Chao Ren
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Zhangyi Ouyang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Jingxuan Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Kang Xu
- School of Software, Shandong University, Jinan 250101, China
| | - Yaru Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hejiang Guo
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xuemei Bai
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Mengge Tian
- The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Xiang Xu
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yuyang Wang
- College of Computer and Data Science, Fuzhou University, Fuzhou 350108, China
| | - Hao Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiaochen Bo
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hebing Chen
- Academy of Military Medical Sciences, Beijing 100850, China
| |
Collapse
|
3
|
Liu C, Nagashima H, Fernando N, Bass V, Gopalakrishnan J, Signorella S, Montgomery W, Lim AI, Harrison O, Reich L, Yao C, Sun HW, Brooks SR, Jiang K, Nagarajan V, Zhao Y, Jung S, Phillips R, Mikami Y, Lareau CA, Kanno Y, Jankovic D, Aryee MJ, Pękowska A, Belkaid Y, O'Shea J, Shih HY. A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification. Immunity 2024; 57:1005-1018.e7. [PMID: 38697116 PMCID: PMC11108081 DOI: 10.1016/j.immuni.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/12/2023] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Cytokine expression during T cell differentiation is a highly regulated process that involves long-range promoter-enhancer and CTCF-CTCF contacts at cytokine loci. Here, we investigated the impact of dynamic chromatin loop formation within the topologically associating domain (TAD) in regulating the expression of interferon gamma (IFN-γ) and interleukin-22 (IL-22); these cytokine loci are closely located in the genome and are associated with complex enhancer landscapes, which are selectively active in type 1 and type 3 lymphocytes. In situ Hi-C analyses revealed inducible TADs that insulated Ifng and Il22 enhancers during Th1 cell differentiation. Targeted deletion of a 17 bp boundary motif of these TADs imbalanced Th1- and Th17-associated immunity, both in vitro and in vivo, upon Toxoplasma gondii infection. In contrast, this boundary element was dispensable for cytokine regulation in natural killer cells. Our findings suggest that precise cytokine regulation relies on lineage- and developmental stage-specific interactions of 3D chromatin architectures and enhancer landscapes.
Collapse
Affiliation(s)
- Chunhong Liu
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hiroyuki Nagashima
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nilisha Fernando
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victor Bass
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jaanam Gopalakrishnan
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sadie Signorella
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Will Montgomery
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Oliver Harrison
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Reich
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chen Yao
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kan Jiang
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vijayaraj Nagarajan
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yongbing Zhao
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seolkyoung Jung
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rachael Phillips
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yohei Mikami
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Caleb A Lareau
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dragana Jankovic
- Immunoparasitology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aleksandra Pękowska
- Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
4
|
Liu H, Pan Z, Lin X, Chen L, Yang Q, Zhang W, Dai L, Zhang Y, Li W, Chen Y, Peng K, Wanggou S, Zeng F, Li X. A potassium-chloride co-transporter with altered genome architecture functions as a suppressor in glioma. J Cell Mol Med 2024; 28:e18352. [PMID: 38685685 PMCID: PMC11058328 DOI: 10.1111/jcmm.18352] [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: 01/04/2024] [Revised: 03/28/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Gliomas, the most lethal tumours in brain, have a poor prognosis despite accepting standard treatment. Limited benefits from current therapies can be attributed to genetic, epigenetic and microenvironmental cues that affect cell programming and drive tumour heterogeneity. Through the analysis of Hi-C data, we identified a potassium-chloride co-transporter SLC12A5 associated with disrupted topologically associating domain which was downregulated in tumour tissues. Multiple independent glioma cohorts were included to analyse the characterization of SLC12A5 and found it was significantly associated with pathological features, prognostic value, genomic alterations, transcriptional landscape and drug response. We constructed two SLC12A5 overexpression cell lines to verify the function of SLC12A5 that suppressed tumour cell proliferation and migration in vitro. In addition, SLC12A5 was also positively associated with GABAA receptor activity and negatively associated with pro-tumour immune signatures and immunotherapy response. Collectively, our study provides a comprehensive characterization of SLC12A5 in glioma and supports SLC12A5 as a potential suppressor of disease progression.
Collapse
Affiliation(s)
- Hongwei Liu
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Zhouyang Pan
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xuelei Lin
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Long Chen
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Qi Yang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Wei Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Luohuan Dai
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Yihao Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Wang Li
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Yinhua Chen
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Kang Peng
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
- Department of Radiology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Siyi Wanggou
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| | - Feiyue Zeng
- Department of Radiology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xuejun Li
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya HospitalCentral South UniversityChangshaChina
| |
Collapse
|
5
|
Gillani R, Collins RL, Crowdis J, Garza A, Jones JK, Walker M, Sanchis-Juan A, Whelan C, Pierce-Hoffman E, Talkowski M, Brand H, Haigis K, LoPiccolo J, AlDubayan SH, Gusev A, Crompton BD, Janeway KA, Van Allen EM. Rare germline structural variants increase risk for pediatric solid tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591484. [PMID: 38746320 PMCID: PMC11092455 DOI: 10.1101/2024.04.27.591484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Pediatric solid tumors are rare malignancies that represent a leading cause of death by disease among children in developed countries. The early age-of-onset of these tumors suggests that germline genetic factors are involved, yet conventional germline testing for short coding variants in established predisposition genes only identifies pathogenic events in 10-15% of patients. Here, we examined the role of germline structural variants (SVs)-an underexplored form of germline variation-in pediatric extracranial solid tumors using germline genome sequencing of 1,766 affected children, their 943 unaffected relatives, and 6,665 adult controls. We discovered a sex-biased association between very large (>1 megabase) germline chromosomal abnormalities and a four-fold increased risk of solid tumors in male children. The overall impact of germline SVs was greatest in neuroblastoma, where we revealed burdens of ultra-rare SVs that cause loss-of-function of highly expressed, mutationally intolerant, neurodevelopmental genes, as well as noncoding SVs predicted to disrupt three-dimensional chromatin domains in neural crest-derived tissues. Collectively, our results implicate rare germline SVs as a predisposing factor to pediatric solid tumors that may guide future studies and clinical practice.
Collapse
Affiliation(s)
- Riaz Gillani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Ryan L. Collins
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Amanda Garza
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jill K. Jones
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Mark Walker
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alba Sanchis-Juan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Chris Whelan
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Talkowski
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Harrison Brand
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin Haigis
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jaclyn LoPiccolo
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Saud H. AlDubayan
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA
- College of Medicine, King Saudi bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alexander Gusev
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brian D. Crompton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Katie A. Janeway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Eliezer M. Van Allen
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| |
Collapse
|
6
|
Friedman MJ, Wagner T, Lee H, Rosenfeld MG, Oh S. Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations. Exp Mol Med 2024; 56:772-787. [PMID: 38658702 PMCID: PMC11058250 DOI: 10.1038/s12276-024-01233-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
Collapse
Affiliation(s)
- Meyer J Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Wagner
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haram Lee
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Michael G Rosenfeld
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Soohwan Oh
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
| |
Collapse
|
7
|
Liu R, Xu R, Yan S, Li P, Jia C, Sun H, Sheng K, Wang Y, Zhang Q, Guo J, Xin X, Li X, Guo D. Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells. Front Genet 2024; 15:1377238. [PMID: 38586584 PMCID: PMC10995239 DOI: 10.3389/fgene.2024.1377238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition and significance of the three-dimensional chromatin structure, summarize the technologies available for studying it, and describe the research progress on the chromatin spatial structure of dendritic cells, macrophages, T cells, B cells, and neutrophils.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Dianhao Guo
- School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| |
Collapse
|
8
|
Liu E, Lyu H, Liu Y, Fu L, Cheng X, Yin X. Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection. Bioinformatics 2024; 40:btae138. [PMID: 38449288 PMCID: PMC10960928 DOI: 10.1093/bioinformatics/btae138] [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: 07/03/2023] [Revised: 01/10/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
MOTIVATION Topologically associating domains (TADs) are fundamental building blocks of 3D genome. TAD-like domains in single cells are regarded as the underlying genesis of TADs discovered in bulk cells. Understanding the organization of TAD-like domains helps to get deeper insights into their regulatory functions. Unfortunately, it remains a challenge to identify TAD-like domains on single-cell Hi-C data due to its ultra-sparsity. RESULTS We propose scKTLD, an in silico tool for the identification of TAD-like domains on single-cell Hi-C data. It takes Hi-C contact matrix as the adjacency matrix for a graph, embeds the graph structures into a low-dimensional space with the help of sparse matrix factorization followed by spectral propagation, and the TAD-like domains can be identified using a kernel-based changepoint detection in the embedding space. The results tell that our scKTLD is superior to the other methods on the sparse contact matrices, including downsampled bulk Hi-C data as well as simulated and experimental single-cell Hi-C data. Besides, we demonstrated the conservation of TAD-like domain boundaries at single-cell level apart from heterogeneity within and across cell types, and found that the boundaries with higher frequency across single cells are more enriched for architectural proteins and chromatin marks, and they preferentially occur at TAD boundaries in bulk cells, especially at those with higher hierarchical levels. AVAILABILITY AND IMPLEMENTATION scKTLD is freely available at https://github.com/lhqxinghun/scKTLD.
Collapse
Affiliation(s)
- Erhu Liu
- School of Information and Control Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Hongqiang Lyu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi'an 710049, China
| | - Yuan Liu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi'an 710049, China
| | - Laiyi Fu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi'an 710049, China
| | - Xiaoliang Cheng
- Department of Pharmacy, The First Affiliated Hospital of Xi’an Jiaotong University, Xi'an 710061, China
| | - Xiaoran Yin
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an 710004, China
| |
Collapse
|
9
|
Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, Ma J. Computational methods for analysing multiscale 3D genome organization. Nat Rev Genet 2024; 25:123-141. [PMID: 37673975 PMCID: PMC11127719 DOI: 10.1038/s41576-023-00638-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 09/08/2023]
Abstract
Recent progress in whole-genome mapping and imaging technologies has enabled the characterization of the spatial organization and folding of the genome in the nucleus. In parallel, advanced computational methods have been developed to leverage these mapping data to reveal multiscale three-dimensional (3D) genome features and to provide a more complete view of genome structure and its connections to genome functions such as transcription. Here, we discuss how recently developed computational tools, including machine-learning-based methods and integrative structure-modelling frameworks, have led to a systematic, multiscale delineation of the connections among different scales of 3D genome organization, genomic and epigenomic features, functional nuclear components and genome function. However, approaches that more comprehensively integrate a wide variety of genomic and imaging datasets are still needed to uncover the functional role of 3D genome structure in defining cellular phenotypes in health and disease.
Collapse
Affiliation(s)
- Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Lorenzo Boninsegna
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Muyu Yang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tom Misteli
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Frank Alber
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
| |
Collapse
|
10
|
Ciriello G, Magnani L, Aitken SJ, Akkari L, Behjati S, Hanahan D, Landau DA, Lopez-Bigas N, Lupiáñez DG, Marine JC, Martin-Villalba A, Natoli G, Obenauf AC, Oricchio E, Scaffidi P, Sottoriva A, Swarbrick A, Tonon G, Vanharanta S, Zuber J. Cancer Evolution: A Multifaceted Affair. Cancer Discov 2024; 14:36-48. [PMID: 38047596 PMCID: PMC10784746 DOI: 10.1158/2159-8290.cd-23-0530] [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: 05/04/2023] [Revised: 08/29/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023]
Abstract
Cancer cells adapt and survive through the acquisition and selection of molecular modifications. This process defines cancer evolution. Building on a theoretical framework based on heritable genetic changes has provided insights into the mechanisms supporting cancer evolution. However, cancer hallmarks also emerge via heritable nongenetic mechanisms, including epigenetic and chromatin topological changes, and interactions between tumor cells and the tumor microenvironment. Recent findings on tumor evolutionary mechanisms draw a multifaceted picture where heterogeneous forces interact and influence each other while shaping tumor progression. A comprehensive characterization of the cancer evolutionary toolkit is required to improve personalized medicine and biomarker discovery. SIGNIFICANCE Tumor evolution is fueled by multiple enabling mechanisms. Importantly, genetic instability, epigenetic reprogramming, and interactions with the tumor microenvironment are neither alternative nor independent evolutionary mechanisms. As demonstrated by findings highlighted in this perspective, experimental and theoretical approaches must account for multiple evolutionary mechanisms and their interactions to ultimately understand, predict, and steer tumor evolution.
Collapse
Affiliation(s)
- Giovanni Ciriello
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Luca Magnani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Epigenetic Plasticity and Evolution Laboratory, Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Sarah J. Aitken
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Leila Akkari
- Division of Tumor Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Douglas Hanahan
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Dan A. Landau
- New York Genome Center, New York, New York
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Darío G. Lupiáñez
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, Leuven, Belgium
| | - Ana Martin-Villalba
- Department of Molecular Neurobiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Anna C. Obenauf
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Elisa Oricchio
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Paola Scaffidi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Cancer Epigenetic Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Sottoriva
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
| | - Giovanni Tonon
- Vita-Salute San Raffaele University, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sakari Vanharanta
- Translational Cancer Medicine Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| |
Collapse
|
11
|
Fok ET, Moorlag SJCFM, Negishi Y, Groh LA, Dos Santos JC, Gräwe C, Monge VV, Craenmehr DDD, van Roosmalen M, da Cunha Jolvino DP, Migliorini LB, Neto AS, Severino P, Vermeulen M, Joosten LAB, Netea MG, Fanucchi S, Mhlanga MM. A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation. Nat Genet 2024; 56:85-99. [PMID: 38092881 DOI: 10.1038/s41588-023-01598-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/26/2023] [Indexed: 12/23/2023]
Abstract
Inflammation is characterized by a biphasic cycle consisting initially of a proinflammatory phase that is subsequently resolved by anti-inflammatory processes. Interleukin-1β (IL-1β) is a master regulator of proinflammation and is encoded within the same topologically associating domain (TAD) as IL-37, which is an anti-inflammatory cytokine that opposes the function of IL-1β. Within this TAD, we identified a long noncoding RNA called AMANZI, which negatively regulates IL-1β expression and trained immunity through the induction of IL37 transcription. We found that the activation of IL37 occurs through the formation of a dynamic long-range chromatin contact that leads to the temporal delay of anti-inflammatory responses. The common variant rs16944 present in AMANZI augments this regulatory circuit, predisposing individuals to enhanced proinflammation or immunosuppression. Our work illuminates a chromatin-mediated biphasic circuit coordinating expression of IL-1β and IL-37, thereby regulating two functionally opposed states of inflammation from within a single TAD.
Collapse
Affiliation(s)
- Ezio T Fok
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Lemba Therapeutics, Nijmegen, the Netherlands
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yutaka Negishi
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Laszlo A Groh
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jéssica Cristina Dos Santos
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
| | | | | | | | - David Pablo da Cunha Jolvino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
- Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Victoria, Australia
| | - Letícia Busato Migliorini
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Ary Serpa Neto
- Department of Critical Care Medicine, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Musa M Mhlanga
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
| |
Collapse
|
12
|
Okhovat M, VanCampen J, Nevonen KA, Harshman L, Li W, Layman CE, Ward S, Herrera J, Wells J, Sheng RR, Mao Y, Ndjamen B, Lima AC, Vigh-Conrad KA, Stendahl AM, Yang R, Fedorov L, Matthews IR, Easow SA, Chan DK, Jan TA, Eichler EE, Rugonyi S, Conrad DF, Ahituv N, Carbone L. TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function. Nat Commun 2023; 14:8111. [PMID: 38062027 PMCID: PMC10703881 DOI: 10.1038/s41467-023-43841-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find 14% of all human TAD boundaries to be shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons compared to species-specific boundaries. CRISPR-Cas9 knockouts of an ultraconserved boundary in a mouse model lead to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in the upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations and showcases the functional importance of TAD evolution.
Collapse
Affiliation(s)
- Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA.
| | - Jake VanCampen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Lana Harshman
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Weiyu Li
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Cora E Layman
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Samantha Ward
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Jarod Herrera
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Jackson Wells
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Rory R Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Blaise Ndjamen
- Histology and Light Microscopy Core Facility, Gladstone Institutes, San Francisco, CA, USA
| | - Ana C Lima
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
| | | | - Alexandra M Stendahl
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Ran Yang
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Lev Fedorov
- OHSU Transgenic Mouse Models Core Lab, Oregon Health and Science University, Portland, OR, USA
| | - Ian R Matthews
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA
| | - Sarah A Easow
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA
| | - Dylan K Chan
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA
| | - Taha A Jan
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Sandra Rugonyi
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA.
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA.
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA.
| |
Collapse
|
13
|
Rahman S, Dong P, Apontes P, Fernando M, Kosoy R, Townsley KG, Girdhar K, Bendl J, Shao Z, Misir R, Tsankova N, Kleopoulos S, Brennand K, Fullard J, Roussos P. Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome. Nucleic Acids Res 2023; 51:11142-11161. [PMID: 37811875 PMCID: PMC10639075 DOI: 10.1093/nar/gkad798] [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: 03/03/2023] [Revised: 08/18/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
The human brain is a complex organ comprised of distinct cell types, and the contribution of the 3D genome to lineage specific gene expression remains poorly understood. To decipher cell type specific genome architecture, and characterize fine scale changes in the chromatin interactome across neural development, we compared the 3D genome of the human fetal cortical plate to that of neurons and glia isolated from the adult prefrontal cortex. We found that neurons have weaker genome compartmentalization compared to glia, but stronger TADs, which emerge during fetal development. Furthermore, relative to glia, the neuronal genome shifts more strongly towards repressive compartments. Neurons have differential TAD boundaries that are proximal to active promoters involved in neurodevelopmental processes. CRISPRi on CNTNAP2 in hIPSC-derived neurons reveals that transcriptional inactivation correlates with loss of insulation at the differential boundary. Finally, re-wiring of chromatin loops during neural development is associated with transcriptional and functional changes. Importantly, differential loops in the fetal cortex are associated with autism GWAS loci, suggesting a neuropsychiatric disease mechanism affecting the chromatin interactome. Furthermore, neural development involves gaining enhancer-promoter loops that upregulate genes that control synaptic activity. Altogether, our study provides multi-scale insights on the 3D genome in the human brain.
Collapse
Affiliation(s)
- Samir Rahman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pengfei Dong
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pasha Apontes
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Michael B Fernando
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Roman Kosoy
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla G Townsley
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kiran Girdhar
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhiping Shao
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth Misir
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nadia Tsankova
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular, and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven P Kleopoulos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| |
Collapse
|
14
|
Rautajoki KJ, Jaatinen S, Hartewig A, Tiihonen AM, Annala M, Salonen I, Valkonen M, Simola V, Vuorinen EM, Kivinen A, Rauhala MJ, Nurminen R, Maass KK, Lahtela SL, Jukkola A, Yli-Harja O, Helén P, Pajtler KW, Ruusuvuori P, Haapasalo J, Zhang W, Haapasalo H, Nykter M. Genomic characterization of IDH-mutant astrocytoma progression to grade 4 in the treatment setting. Acta Neuropathol Commun 2023; 11:176. [PMID: 37932833 PMCID: PMC10629206 DOI: 10.1186/s40478-023-01669-9] [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: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
As the progression of low-grade diffuse astrocytomas into grade 4 tumors significantly impacts patient prognosis, a better understanding of this process is of paramount importance for improved patient care. In this project, we analyzed matched IDH-mutant astrocytomas before and after progression to grade 4 from six patients (discovery cohort) with genome-wide sequencing, 21 additional patients with targeted sequencing, and 33 patients from Glioma Longitudinal AnalySiS cohort for validation. The Cancer Genome Atlas data from 595 diffuse gliomas provided supportive information. All patients in our discovery cohort received radiation, all but one underwent chemotherapy, and no patient received temozolomide (TMZ) before progression to grade 4 disease. One case in the discovery cohort exhibited a hypermutation signature associated with the inactivation of the MSH2 and DNMT3A genes. In other patients, the number of chromosomal rearrangements and deletions increased in grade 4 tumors. The cell cycle checkpoint gene CDKN2A, or less frequently RB1, was most commonly inactivated after receiving both chemo- and radiotherapy when compared to other treatment groups. Concomitant activating PDGFRA/MET alterations were detected in tumors that acquired a homozygous CDKN2A deletion. NRG3 gene was significantly downregulated and recurrently altered in progressed tumors. Its decreased expression was associated with poorer overall survival in both univariate and multivariate analysis. We also detected progression-related alterations in RAD51B and other DNA repair pathway genes associated with the promotion of error-prone DNA repair, potentially facilitating tumor progression. In our retrospective analysis of patient treatment and survival timelines (n = 75), the combination of postoperative radiation and chemotherapy (mainly TMZ) outperformed radiation, especially in the grade 3 tumor cohort, in which it was typically given after primary surgery. Our results provide further insight into the contribution of treatment and genetic alterations in cell cycle, growth factor signaling, and DNA repair-related genes to tumor evolution and progression.
Collapse
Affiliation(s)
- Kirsi J Rautajoki
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland.
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland.
| | - Serafiina Jaatinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Aliisa M Tiihonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Iida Salonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Masi Valkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Vili Simola
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Elisa M Vuorinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Anni Kivinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Minna J Rauhala
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Riikka Nurminen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Kendra K Maass
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro Oncology, German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sirpa-Liisa Lahtela
- Department of Oncology, Tampere University Hospital and Tays Cancer Centre, Tampere, Finland
| | - Arja Jukkola
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Department of Oncology, Tampere University Hospital and Tays Cancer Centre, Tampere, Finland
| | - Olli Yli-Harja
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Pauli Helén
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro Oncology, German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Pekka Ruusuvuori
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Joonas Haapasalo
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Hannu Haapasalo
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| |
Collapse
|
15
|
Zhang M, Ehmann ME, Matukumalli S, Boob AG, Gilbert DM, Zhao H. SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells. Nat Commun 2023; 14:5616. [PMID: 37699958 PMCID: PMC10497619 DOI: 10.1038/s41467-023-41468-3] [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: 10/06/2022] [Accepted: 09/04/2023] [Indexed: 09/14/2023] Open
Abstract
Chromatin boundary elements contribute to the partitioning of mammalian genomes into topological domains to regulate gene expression. Certain boundary elements are adopted as DNA insulators for safe and stable transgene expression in mammalian cells. These elements, however, are ill-defined and less characterized in the non-coding genome, partially due to the lack of a platform to readily evaluate boundary-associated activities of putative DNA sequences. Here we report SHIELD (Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains), a platform tailored for the high-throughput screening of barrier-type DNA elements in human cells. SHIELD takes advantage of the high specificity of serine integrase at heterochromatin, and exploits the natural heterochromatin spreading inside lamina-associated domains (LADs) for the discovery of potent barrier elements. We adopt SHIELD to evaluate the barrier activity of 1000 DNA elements in a high-throughput manner and identify 8 candidates with barrier activities comparable to the core region of cHS4 element in human HCT116 cells. We anticipate SHIELD could facilitate the discovery of novel barrier DNA elements from the non-coding genome in human cells.
Collapse
Affiliation(s)
- Meng Zhang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mary Elisabeth Ehmann
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Srija Matukumalli
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Chemistry, Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| |
Collapse
|
16
|
Senapati S, Irshad IU, Sharma AK, Kumar H. Fundamental insights into the correlation between chromosome configuration and transcription. Phys Biol 2023; 20:051002. [PMID: 37467757 DOI: 10.1088/1478-3975/ace8e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain, and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research.
Collapse
Affiliation(s)
- Swayamshree Senapati
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
| | - Inayat Ullah Irshad
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
| | - Ajeet K Sharma
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, Jammu 181221, India
| | - Hemant Kumar
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
| |
Collapse
|
17
|
Wurfbain LF, Cox IL, van Dooren MF, Lachmeijer AMA, Verhoeven VJM, van Hagen JM, Heijligers M, Klein Wassink-Ruiter JS, Koene S, Maas SM, Veenstra-Knol HE, Ploos van Amstel JK, Massink MPG, Mink van der Molen AB, van den Boogaard MJH. Diagnostic Gene Panel Testing in (Non)-Syndromic Patients with Cleft Lip, Alveolus and/or Palate in the Netherlands. Mol Syndromol 2023; 14:270-282. [PMID: 37589029 PMCID: PMC10425715 DOI: 10.1159/000530256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/14/2023] [Indexed: 08/18/2023] Open
Abstract
Objectives Clefts of the lip, alveolus and/or palate (CLA/P) are the most common craniofacial congenital malformations in humans. These oral clefts can be divided into non-syndromic (isolated) and syndromic forms. Many cleft-related syndromes are clinically variable and genetically heterogeneous, making it challenging to distinguish syndromic from non-syndromic cases. Recognition of syndromic/genetic causes is important for personalized tailored care, identification of (unrecognized) comorbidities, and accurate genetic counseling. Therefore, next generation sequencing (NGS)-based targeted gene panel testing is increasingly implemented in diagnostics of CLA/P patients. In this retrospective study, we assess the yield of NGS gene panel testing in a cohort of CLA/P cases. Methods Whole exome sequencing (WES) followed by variant detection and interpretation in an a priori selected set of genes associated with CLA/P phenotypes was performed in 212 unrelated CLA/P patients after genetic counseling between 2015 and 2020. Medical records including family history and results of additional genetic tests were evaluated. Results In 24 CLA/P cases (11.3%), a pathogenic genetic variant was identified. Twenty out of these 24 had a genetic syndrome requiring specific monitoring and follow-up. Six of these 24 cases (25%) were presumed to be isolated CLA/P cases prior to testing, corresponding to 2.8% of the total cohort. In eight CLA/P cases (3.8%) without a diagnosis after NGS-based gene panel testing, a molecular diagnosis was established by additional genetic analyses (e.g., SNP array, single gene testing, trio WES). Conclusion This study illustrates NGS-based gene panel testing is a powerful diagnostic tool in the diagnostic workup of CLA/P patients. Also, in apparently isolated cases and non-familial cases, a genetic diagnosis can be identified. Early diagnosis facilitates personalized care for patients and accurate genetic counseling of their families.
Collapse
Affiliation(s)
- Lisca Florence Wurfbain
- Department of Pediatric Plastic Surgery, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Inge Lucia Cox
- Department of Pediatric Plastic Surgery, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | - Johanna Maria van Hagen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Malou Heijligers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Saskia Mariska Maas
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Aebele Barber Mink van der Molen
- Department of Pediatric Plastic Surgery, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | |
Collapse
|
18
|
Liu H, Tsai H, Yang M, Li G, Bian Q, Ding G, Wu D, Dai J. Three-dimensional genome structure and function. MedComm (Beijing) 2023; 4:e326. [PMID: 37426677 PMCID: PMC10329473 DOI: 10.1002/mco2.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.
Collapse
Affiliation(s)
- Hao Liu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Hsiangyu Tsai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Maoquan Yang
- School of Clinical MedicineWeifang Medical UniversityWeifangChina
| | - Guozhi Li
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Qian Bian
- Shanghai Institute of Precision MedicineShanghaiChina
| | - Gang Ding
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Dandan Wu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Jiewen Dai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Razin SV, Ulianov SV, Iarovaia OV. Enhancer Function in the 3D Genome. Genes (Basel) 2023; 14:1277. [PMID: 37372457 DOI: 10.3390/genes14061277] [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: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
In this review, we consider various aspects of enhancer functioning in the context of the 3D genome. Particular attention is paid to the mechanisms of enhancer-promoter communication and the significance of the spatial juxtaposition of enhancers and promoters in 3D nuclear space. A model of an activator chromatin compartment is substantiated, which provides the possibility of transferring activating factors from an enhancer to a promoter without establishing direct contact between these elements. The mechanisms of selective activation of individual promoters or promoter classes by enhancers are also discussed.
Collapse
Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Olga V Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| |
Collapse
|
21
|
Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Nowakowski T, Ahituv N, Pollen A, Pollard KS. Three-dimensional genome rewiring in loci with human accelerated regions. Science 2023; 380:eabm1696. [PMID: 37104607 PMCID: PMC10999243 DOI: 10.1126/science.abm1696] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/01/2023] [Indexed: 04/29/2023]
Abstract
Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.
Collapse
Affiliation(s)
- Kathleen C Keough
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Tyler Fair
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marilyn Steyert
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Hane Ryu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Alex Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics and Bakar Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
22
|
Rajderkar S, Barozzi I, Zhu Y, Hu R, Zhang Y, Li B, Alcaina Caro A, Fukuda-Yuzawa Y, Kelman G, Akeza A, Blow MJ, Pham Q, Harrington AN, Godoy J, Meky EM, von Maydell K, Hunter RD, Akiyama JA, Novak CS, Plajzer-Frick I, Afzal V, Tran S, Lopez-Rios J, Talkowski ME, Lloyd KCK, Ren B, Dickel DE, Visel A, Pennacchio LA. Topologically associating domain boundaries are required for normal genome function. Commun Biol 2023; 6:435. [PMID: 37081156 PMCID: PMC10119121 DOI: 10.1038/s42003-023-04819-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1-3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.
Collapse
Affiliation(s)
- Sudha Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ana Alcaina Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide Junta de Andalucía, 41013, Seville, Spain
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adyam Akeza
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Quan Pham
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Anne N Harrington
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Janeth Godoy
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Eman M Meky
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide Junta de Andalucía, 41013, Seville, Spain
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, Davis, CA, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
23
|
Tiukacheva EA, Ulianov SV, Karpukhina A, Razin SV, Vassetzky Y. 3D genome alterations and editing in pathology. Mol Ther 2023; 31:924-933. [PMID: 36755493 PMCID: PMC10124079 DOI: 10.1016/j.ymthe.2023.02.005] [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: 07/25/2022] [Revised: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The human genome is folded into a multi-level 3D structure that controls many nuclear functions including gene expression. Recently, alterations in 3D genome organization were associated with several genetic diseases and cancer. As a consequence, experimental approaches are now being developed to modify the global 3D genome organization and that of specific loci. Here, we discuss emerging experimental approaches of 3D genome editing that may prove useful in biomedicine.
Collapse
Affiliation(s)
- Eugenia A Tiukacheva
- CNRS UMR9018, Institut Gustave Roussy, 94805 Villejuif, France; Institute of Gene Biology, Moscow 119334, Russia; Moscow Institute of Physics and Technology, Moscow 141700, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; Koltzov Institute of Developmental Biology, Moscow 119334, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Moscow 119334, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anna Karpukhina
- CNRS UMR9018, Institut Gustave Roussy, 94805 Villejuif, France; Koltzov Institute of Developmental Biology, Moscow 119334, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Moscow 119334, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Yegor Vassetzky
- CNRS UMR9018, Institut Gustave Roussy, 94805 Villejuif, France; Koltzov Institute of Developmental Biology, Moscow 119334, Russia.
| |
Collapse
|
24
|
Dominguez-Alonso S, Carracedo A, Rodriguez-Fontenla C. The non-coding genome in Autism Spectrum Disorders. Eur J Med Genet 2023; 66:104752. [PMID: 37023975 DOI: 10.1016/j.ejmg.2023.104752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/10/2023] [Accepted: 03/19/2023] [Indexed: 04/08/2023]
Abstract
Autism Spectrum Disorders (ASD) are a group of neurodevelopmental disorders (NDDs) characterized by difficulties in social interaction and communication, repetitive behavior, and restricted interests. While ASD have been proven to have a strong genetic component, current research largely focuses on coding regions of the genome. However, non-coding DNA, which makes up for ∼99% of the human genome, has recently been recognized as an important contributor to the high heritability of ASD, and novel sequencing technologies have been a milestone in opening up new directions for the study of the gene regulatory networks embedded within the non-coding regions. Here, we summarize current progress on the contribution of non-coding alterations to the pathogenesis of ASD and provide an overview of existing methods allowing for the study of their functional relevance, discussing potential ways of unraveling ASD's "missing heritability".
Collapse
Affiliation(s)
- S Dominguez-Alonso
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - C Rodriguez-Fontenla
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
| |
Collapse
|
25
|
Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, Harrell JC. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep 2023; 13:5420. [PMID: 37012431 PMCID: PMC10070455 DOI: 10.1038/s41598-023-32568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2 Mb) interactions, chromatin looping, formation of TAD, chromatin state switching into a more active state, and amplification of ATP-binding cassette transporters. Transcriptome changes suggested the role of long-noncoding RNAs in carboplatin resistance. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of aggressiveness-, metastasis- and other cancer-related pathways. Integrative analysis highlighted increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial energy metabolism. Our results suggest that 3D genome remodeling may be a key mechanism underlying carboplatin resistance.
Collapse
Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| | - Maggie A Marshall
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Narmeen S Rashid
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biology, University of Richmond, Richmond, VA, 23173, USA
| | - Jacqueline M Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Aaron Valentine
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biochemistry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Kavita Murthy
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Abhijit Chakraborty
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Joaquin Reyna
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Daniela Salgado Figueroa
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Laura Hinojosa-Gonzalez
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Erika Da-Inn Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Brittany A Baur
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Ferhat Ay
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Department of Pediatrics, UC San Diego-School of Medicine, La Jolla, CA, 92093, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| |
Collapse
|
26
|
Sumimoto H, Takano A, Igarashi T, Hanaoka J, Teramoto K, Daigo Y. Oncogenic epidermal growth factor receptor signal-induced histone deacetylation suppresses chemokine gene expression in human lung adenocarcinoma. Sci Rep 2023; 13:5087. [PMID: 36991099 PMCID: PMC10060241 DOI: 10.1038/s41598-023-32177-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Epidermal growth factor receptor (EGFR)-mutated (mt) lung adenocarcinoma (LA) is refractory to immune checkpoint inhibitors (ICIs). However, the mechanisms have not been fully elucidated. CD8+ T cell infiltration was significantly lower in EGFR-mt than in EGFR-wild-type LA, which was associated with suppression of chemokine expression. Since this T cell-deserted tumor microenvironment may lead to the refractoriness of ICIs against EGFR-mt LA, we investigated the mechanism by focusing on the regulation of chemokine expression. The expression of C-X-C motif ligand (CXCL) 9, 10 and 11, which constitute a gene cluster on chromosome 4, was suppressed under EGFR signaling. The assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) revealed open chromatin peaks near this gene cluster following EGFR-tyrosine kinase inhibitor (TKI) treatment. The histone deacetylase (HDAC) inhibitor recovered the expression of CXCL9, 10 and 11 in EGFR-mt LA. Nuclear HDAC activity, as well as histone H3 deacetylation, were dependent on oncogenic EGFR signaling. Furthermore, the Cleavage Under Targets and Tagmentation (CUT & Tag) assay revealed a histone H3K27 acetylation peak at 15 kb upstream of CXCL11 after treatment with EGFR-TKI, which corresponded to one of the open chromatin peaks detected by ATAC-seq. The data suggest that EGFR-HDAC axis mediates silencing of the chemokine gene cluster through chromatin conformational change, which might be relevant to the ICI resistance by creating T cell-deserted tumor microenvironment. Targeting this axis may develop a new therapeutic strategy to overcome the ICI resistance of EGFR-mt LA.
Collapse
Affiliation(s)
- Hidetoshi Sumimoto
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga, Japan
- Center for Advanced Medicine Against Cancer, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Atsushi Takano
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga, Japan
- Center for Advanced Medicine Against Cancer, Shiga University of Medical Science, Otsu, Shiga, Japan
- Center for Antibody and Vaccine Therapy, Institute of Medical Science, Research Hospital, The University of Tokyo, Tokyo, Japan
| | - Tomoyuki Igarashi
- Department of Surgery, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Jun Hanaoka
- Department of Surgery, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Koji Teramoto
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga, Japan
- Center for Advanced Medicine Against Cancer, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Yataro Daigo
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga, Japan.
- Center for Advanced Medicine Against Cancer, Shiga University of Medical Science, Otsu, Shiga, Japan.
- Center for Antibody and Vaccine Therapy, Institute of Medical Science, Research Hospital, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
27
|
Tamura T, Shimojima Yamamoto K, Imaizumi T, Yamamoto H, Miyamoto Y, Yagasaki H, Morioka I, Kanno H, Yamamoto T. Breakpoint analysis for cytogenetically balanced translocation revealed unexpected complex structural abnormalities and suggested the position effect for MEF2C. Am J Med Genet A 2023; 191:1632-1638. [PMID: 36916329 DOI: 10.1002/ajmg.a.63182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/27/2023] [Accepted: 03/02/2023] [Indexed: 03/15/2023]
Abstract
Many disease-causing genes have been identified by determining the breakpoints of balanced chromosomal translocations. Recent progress in genomic analysis has accelerated the analysis of chromosomal translocation-breakpoints at the nucleotide level. Using a long-read whole-genome sequence, we analyzed the breakpoints of the cytogenetically balanced chromosomal translocation t(5;15)(q21;26.3), which was confirmed to be of de novo origin, in a patient with a neurodevelopmental disorder. The results showed complex rearrangements with seven fragments consisting of five breakpoint-junctions (BJs). Four of the five BJs showed microhomologies of 1-3-bp, and only one BJ displayed a signature of blunt-end ligation, indicating chromothripsis as the underlying mechanism. Although the BJs did not disrupt any disease-causing gene, the clinical features of the patient were compatible with MEF2C haploinsufficiency syndrome. Complex rearrangements were located approximately 2.5-Mb downstream of MEF2C. Therefore, position effects were considered the mechanism of the occurrence of MEF2C haploinsufficiency syndrome.
Collapse
Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.,Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Taichi Imaizumi
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hisako Yamamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yusaku Miyamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hiroshi Yagasaki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| |
Collapse
|
28
|
Okhovat M, VanCampen J, Lima AC, Nevonen KA, Layman CE, Ward S, Herrera J, Stendahl AM, Yang R, Harshman L, Li W, Sheng RR, Mao Y, Fedorov L, Ndjamen B, Vigh-Conrad KA, Matthews IR, Easow SA, Chan DK, Jan TA, Eichler EE, Rugonyi S, Conrad DF, Ahituv N, Carbone L. TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531534. [PMID: 36945527 PMCID: PMC10028908 DOI: 10.1101/2023.03.07.531534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species, and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find that only 14% of all human TAD boundaries are shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons, compared to species-specific boundaries. CRISPR-Cas9 knockouts of two ultraconserved boundaries in mouse models leads to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations, and showcase the functional importance of TAD evolution.
Collapse
|
29
|
A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination. Mol Cell 2023; 83:681-697.e7. [PMID: 36736317 DOI: 10.1016/j.molcel.2023.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 11/04/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023]
Abstract
Interactions between transcription and cohesin-mediated loop extrusion can influence 3D chromatin architecture. However, their relevance in biology is unclear. Here, we report a direct role for such interactions in the mechanism of antibody class switch recombination (CSR) at the murine immunoglobulin heavy chain locus (Igh). Using Tri-C to measure higher-order multiway interactions on single alleles, we find that the juxtaposition (synapsis) of transcriptionally active donor and acceptor Igh switch (S) sequences, an essential step in CSR, occurs via the interaction of loop extrusion complexes with a de novo topologically associating domain (TAD) boundary formed via transcriptional activity across S regions. Surprisingly, synapsis occurs predominantly in proximity to the 3' CTCF-binding element (3'CBE) rather than the Igh super-enhancer, suggesting a two-step mechanism whereby transcription of S regions is not topologically coupled to synapsis, as has been previously proposed. Altogether, these insights advance our understanding of how 3D chromatin architecture regulates CSR.
Collapse
|
30
|
Davidson C, Wordsworth BP, Cohen CJ, Knight JC, Vecellio M. Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis. Front Genet 2023; 14:1129207. [PMID: 36760998 PMCID: PMC9905691 DOI: 10.3389/fgene.2023.1129207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Ankylosing Spondylitis (AS) is a chronic inflammatory arthritis of the spine exhibiting a strong genetic background. The mechanistic and functional understanding of the AS-associated genomic loci, identified with Genome Wide Association Studies (GWAS), remains challenging. Chromosome conformation capture (3C) and derivatives are recent techniques which are of great help in elucidating the spatial genome organization and of enormous support in uncover a mechanistic explanation for disease-associated genetic variants. The perturbation of three-dimensional (3D) genome hierarchy may lead to a plethora of human diseases, including rheumatological disorders. Here we illustrate the latest approaches and related findings on the field of genome organization, highlighting how the instability of 3D genome conformation may be among the causes of rheumatological disease phenotypes. We suggest a new perspective on the inclusive potential of a 3C approach to inform GWAS results in rheumatic diseases. 3D genome organization may ultimately lead to a more precise and comprehensive functional interpretation of AS association, which is the starting point for emerging and more specific therapies.
Collapse
Affiliation(s)
- Connor Davidson
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - B. Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Carla J. Cohen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Julian C. Knight
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
- Centro Ricerche Fondazione Italiana Ricerca Sull’Artrite (FIRA), Fondazione Pisana x la Scienza ONLUS, San Giuliano Terme, Italy
| |
Collapse
|
31
|
Contessoto VG, Dudchenko O, Aiden EL, Wolynes PG, Onuchic JN, Di Pierro M. Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nat Commun 2023; 14:326. [PMID: 36658127 PMCID: PMC9852290 DOI: 10.1038/s41467-023-35909-2] [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: 02/16/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023] Open
Abstract
We use data-driven physical simulations to study the three-dimensional architecture of the Aedes aegypti genome. Hi-C maps exhibit both a broad diagonal and compartmentalization with telomeres and centromeres clustering together. Physical modeling reveals that these observations correspond to an ensemble of 3D chromosomal structures that are folded over and partially condensed. Clustering of the centromeres and telomeres near the nuclear lamina appears to be a necessary condition for the formation of the observed structures. Further analysis of the mechanical properties of the genome reveals that the chromosomes of Aedes aegypti, by virtue of their atypical structural organization, are highly sensitive to the deformation of the nuclei. This last finding provides a possible physical mechanism linking mechanical cues to gene regulation.
Collapse
Affiliation(s)
- Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Instituto de Biociências, Letras e Ciências Exatas, UNESP - Univ. Estadual Paulista, Departamento de Física, São José do Rio Preto, SP, Brazil.
| | - Olga Dudchenko
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Erez Lieberman Aiden
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Physics & Astronomy, Rice University, Houston, TX, USA.,Department of Chemistry, Rice University, Houston, TX, USA.,Department of Biosciences, Rice University, Houston, TX, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Department of Physics & Astronomy, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA. .,Department of Biosciences, Rice University, Houston, TX, USA.
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA, USA. .,Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA.
| |
Collapse
|
32
|
Galupa R, Alvarez-Canales G, Borst NO, Fuqua T, Gandara L, Misunou N, Richter K, Alves MRP, Karumbi E, Perkins ML, Kocijan T, Rushlow CA, Crocker J. Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development. Dev Cell 2023; 58:51-62.e4. [PMID: 36626871 PMCID: PMC9860173 DOI: 10.1016/j.devcel.2022.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/18/2022] [Accepted: 12/07/2022] [Indexed: 01/11/2023]
Abstract
Developmental enhancers bind transcription factors and dictate patterns of gene expression during development. Their molecular evolution can underlie phenotypical evolution, but the contributions of the evolutionary pathways involved remain little understood. Here, using mutation libraries in Drosophila melanogaster embryos, we observed that most point mutations in developmental enhancers led to changes in gene expression levels but rarely resulted in novel expression outside of the native pattern. In contrast, random sequences, often acting as developmental enhancers, drove expression across a range of cell types; random sequences including motifs for transcription factors with pioneer activity acted as enhancers even more frequently. Our findings suggest that the phenotypic landscapes of developmental enhancers are constrained by enhancer architecture and chromatin accessibility. We propose that the evolution of existing enhancers is limited in its capacity to generate novel phenotypes, whereas the activity of de novo elements is a primary source of phenotypic novelty.
Collapse
Affiliation(s)
- Rafael Galupa
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | | | | | - Timothy Fuqua
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lautaro Gandara
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Natalia Misunou
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kerstin Richter
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Esther Karumbi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Tin Kocijan
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Justin Crocker
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| |
Collapse
|
33
|
Liu K, Li HD, Li Y, Wang J, Wang J. A Comparison of Topologically Associating Domain Callers Based on Hi-C Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:15-29. [PMID: 35104223 DOI: 10.1109/tcbb.2022.3147805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Topologically associating domains (TADs) are local chromatin interaction domains, which have been shown to play an important role in gene expression regulation. TADs were originally discovered in the investigation of 3D genome organization based on High-throughput Chromosome Conformation Capture (Hi-C) data. Continuous considerable efforts have been dedicated to developing methods for detecting TADs from Hi-C data. Different computational methods for TADs identification vary in their assumptions and criteria in calling TADs. As a consequence, the TADs called by these methods differ in their similarities and biological features they are enriched in. In this work, we performed a systematic comparison of twenty-six TAD callers. We first compared the TADs and gaps between adjacent TADs across different methods, resolutions, and sequencing depths. We then assessed the quality of TADs and TAD boundaries according to three criteria: the decay of contact frequencies over the genomic distance, enrichment and depletion of regulatory elements around TAD boundaries, and reproducibility of TADs and TAD boundaries in replicate samples. Last, due to the lack of a gold standard of TADs, we also evaluated the performance of the methods on synthetic datasets. We discussed the key principles of TAD callers, and pinpointed current situation in the detection of TADs. We provide a concise, comprehensive, and systematic framework for evaluating the performance of TAD callers, and expect our work will provide useful guidance in choosing suitable approaches for the detection and evaluation of TADs.
Collapse
|
34
|
Zhu X, Huang Q, Luo J, Kong D, Zhang Y. Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology. Comput Struct Biotechnol J 2023; 21:1728-1737. [PMID: 36890880 PMCID: PMC9986247 DOI: 10.1016/j.csbj.2023.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Gene regulatory networks are now at the forefront of precision biology, which can help researchers better understand how genes and regulatory elements interact to control cellular gene expression, offering a more promising molecular mechanism in biological research. Interactions between the genes and regulatory elements involve different promoters, enhancers, transcription factors, silencers, insulators, and long-range regulatory elements, which occur at a ∼10 µm nucleus in a spatiotemporal manner. In this way, three-dimensional chromatin conformation and structural biology are critical for interpreting the biological effects and the gene regulatory networks. In the review, we have briefly summarized the latest processes in three-dimensional chromatin conformation, microscopic imaging, and bioinformatics, and we have presented the outlook and future directions for these three aspects.
Collapse
Affiliation(s)
- Xiusheng Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qitong Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
| | - Jing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Dashuai Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,College of Life Science and Engineering, Foshan University, Foshan, China
| |
Collapse
|
35
|
Jouret G, Egloff M, Landais E, Tassy O, Giuliano F, Karmous-Benailly H, Coutton C, Satre V, Devillard F, Dieterich K, Vieville G, Kuentz P, le Caignec C, Beneteau C, Isidor B, Nizon M, Callier P, Marquet V, Bieth E, Lévy J, Tabet AC, Lyonnet S, Baujat G, Rio M, Cartault F, Scheidecker S, Gouronc A, Schalk A, Jacquin C, Spodenkiewicz M, Angélini C, Pennamen P, Rooryck C, Doco-Fenzy M, Poirsier C. Clinical and genomic delineation of the new proximal 19p13.3 microduplication syndrome. Am J Med Genet A 2023; 191:52-63. [PMID: 36196855 DOI: 10.1002/ajmg.a.62983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
Abstract
A small but growing body of scientific literature is emerging about clinical findings in patients with 19p13.3 microdeletion or duplication. Recently, a proximal 19p13.3 microduplication syndrome was described, associated with growth delay, microcephaly, psychomotor delay and dysmorphic features. The aim of our study was to better characterize the syndrome associated with duplications in the proximal 19p13.3 region (prox 19p13.3 dup), and to propose a comprehensive analysis of the underlying genomic mechanism. We report the largest cohort of patients with prox 19p13.3 dup through a collaborative study. We collected 24 new patients with terminal or interstitial 19p13.3 duplication characterized by array-based Comparative Genomic Hybridization (aCGH). We performed mapping, phenotype-genotype correlations analysis, critical region delineation and explored three-dimensional chromatin interactions by analyzing Topologically Associating Domains (TADs). We define a new 377 kb critical region (CR 1) in chr19: 3,116,922-3,494,377, GRCh37, different from the previously described critical region (CR 2). The new 377 kb CR 1 includes a TAD boundary and two enhancers whose common target is PIAS4. We hypothesize that duplications of CR 1 are responsible for tridimensional structural abnormalities by TAD disruption and misregulation of genes essentials for the control of head circumference during development, by breaking down the interactions between enhancers and the corresponding targeted gene.
Collapse
Affiliation(s)
- Guillaume Jouret
- Department of Genetics, Reims University Hospital, Reims, France.,National Center of Genetics (NCG), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Matthieu Egloff
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France
| | - Emilie Landais
- Department of Genetics, Reims University Hospital, Reims, France
| | | | | | | | - Charles Coutton
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France.,ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France
| | - Véronique Satre
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Françoise Devillard
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Klaus Dieterich
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Gaëlle Vieville
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Paul Kuentz
- Génétique Biologique, PCBio, Besançon University Hospital, Besançon, France
| | - Cédric le Caignec
- ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,Department of Genetics, Nantes University Hospital, Nantes, France
| | - Claire Beneteau
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Bertrand Isidor
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Mathilde Nizon
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Patrick Callier
- ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,Department of Genetics, Dijon University Hospital, Dijon, France
| | - Valentine Marquet
- ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,Department of Genetics, Limoges University Hospital, Limoges, France
| | - Eric Bieth
- Department of Genetics, Toulouse University Hospital, Toulouse, France
| | - Jonathan Lévy
- Department of Genetics, Robert-Debré University Hospital, Paris, France
| | - Anne-Claude Tabet
- Department of Genetics, Robert-Debré University Hospital, Paris, France
| | - Stanislas Lyonnet
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France.,INSERM U-1163, Université de Paris, Paris, France
| | - Geneviève Baujat
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France
| | - Marlène Rio
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France
| | - François Cartault
- Department of Genetics, La Réunion University Hospital, Saint Denis, France
| | | | | | | | - Clémence Jacquin
- Department of Genetics, Reims University Hospital, Reims, France
| | | | - Chloé Angélini
- CHU Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | | | | | - Martine Doco-Fenzy
- Department of Genetics, Reims University Hospital, Reims, France.,ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,EA3801, SFR CAPSANTE, Reims, France
| | - Céline Poirsier
- Department of Genetics, Reims University Hospital, Reims, France
| |
Collapse
|
36
|
The Role of Long Noncoding RNA (lncRNAs) Biomarkers in Renal Cell Carcinoma. Int J Mol Sci 2022; 24:ijms24010643. [PMID: 36614082 PMCID: PMC9820502 DOI: 10.3390/ijms24010643] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
Renal cell carcinoma is one of the common cancers whose incidence and mortality are continuously growing worldwide. Initially, this type of tumour is usually asymptomatic. Due to the lack of reliable diagnostic markers, one-third of ccRCC patients already have distant metastases at the time of diagnosis. This underlines the importance of establishing biomarkers that would enable the prediction of the disease's course and the risk of metastasis. LncRNA, which modulates genes at the epigenetic, transcriptional, and post-transcriptional levels, appears promising. The actions of lncRNA involve sponging and sequestering target miRNAs, thus affecting numerous biological processes. Studies have confirmed the involvement of RNAs in various diseases, including RCC. In this review, we focused on MALAT1 (a marker of serious pathological changes and a factor in the promotion of tumorigenesis), RCAT1 (tumour promoter in RCC), DUXAP9 (a plausible marker of localized ccRCC), TCL6 (exerting tumour-suppressive effects in renal cancer), LINC00342 (acting as an oncogene), AGAP2 Antisense1 (plausible predictor of RCC progression), DLEU2 (factor promoting tumours growth via the regulation of epithelial-mesenchymal transition), NNT-AS1 (sponge of miR-22 contributing to tumour progression), LINC00460 (favouring ccRCC development and progression) and Lnc-LSG1 (a factor that may stimulate ccRCC metastasis).
Collapse
|
37
|
Valton AL, Venev SV, Mair B, Khokhar ES, Tong AHY, Usaj M, Chan K, Pai AA, Moffat J, Dekker J. A cohesin traffic pattern genetically linked to gene regulation. Nat Struct Mol Biol 2022; 29:1239-1251. [PMID: 36482254 PMCID: PMC10228515 DOI: 10.1038/s41594-022-00890-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 11/01/2022] [Indexed: 12/13/2022]
Abstract
Cohesin-mediated loop extrusion has been shown to be blocked at specific cis-elements, including CTCF sites, producing patterns of loops and domain boundaries along chromosomes. Here we explore such cis-elements, and their role in gene regulation. We find that transcription termination sites of active genes form cohesin- and RNA polymerase II-dependent domain boundaries that do not accumulate cohesin. At these sites, cohesin is first stalled and then rapidly unloaded. Start sites of transcriptionally active genes form cohesin-bound boundaries, as shown before, but are cohesin-independent. Together with cohesin loading, possibly at enhancers, these sites create a pattern of cohesin traffic that guides enhancer-promoter interactions. Disrupting this traffic pattern, by removing CTCF, renders cells sensitive to knockout of genes involved in transcription initiation, such as the SAGA complexes, and RNA processing such DEAD/H-Box RNA helicases. Without CTCF, these factors are less efficiently recruited to active promoters.
Collapse
Affiliation(s)
- Anne-Laure Valton
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Barbara Mair
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Eraj Shafiq Khokhar
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amy H Y Tong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Chan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
38
|
Rossini R, Kumar V, Mathelier A, Rognes T, Paulsen J. MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions. Genome Biol 2022; 23:247. [PMID: 36451166 PMCID: PMC9710047 DOI: 10.1186/s13059-022-02815-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.
Collapse
Affiliation(s)
- Roberto Rossini
- grid.5510.10000 0004 1936 8921Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Vipin Kumar
- grid.5510.10000 0004 1936 8921Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Anthony Mathelier
- grid.5510.10000 0004 1936 8921Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Torbjørn Rognes
- grid.5510.10000 0004 1936 8921Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0424 Oslo, Norway
| | - Jonas Paulsen
- grid.5510.10000 0004 1936 8921Department of Biosciences, University of Oslo, 0316 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
| |
Collapse
|
39
|
Wibowo AT, Antunez-Sanchez J, Dawson A, Price J, Meehan C, Wrightsman T, Collenberg M, Bezrukov I, Becker C, Benhamed M, Weigel D, Gutierrez-Marcos J. Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor. PLoS Genet 2022; 18:e1010479. [PMID: 36383565 PMCID: PMC9731469 DOI: 10.1371/journal.pgen.1010479] [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: 04/27/2022] [Revised: 12/08/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022] Open
Abstract
Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations.
Collapse
Affiliation(s)
- Anjar Tri Wibowo
- School of Life Science, University of Warwick, Coventry, United Kingdom
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
- Department of Biology, Faculty of Science and Technology, Airlangga University, Surabaya City, East Java, Indonesia
| | | | - Alexander Dawson
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | - Jonathan Price
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | - Cathal Meehan
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | - Travis Wrightsman
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
| | - Maximillian Collenberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
| | - Ilja Bezrukov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
- Ludwig-Maximilians-University of Munich, Faculty of Biology, Biocenter, Martinsried, Germany
| | - Moussa Benhamed
- Université Paris-Saclay, Centre National de la Recherche Scientifique, Institut National De La Recherche Agronomique, University of Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
- * E-mail: (DW); (JGM)
| | - Jose Gutierrez-Marcos
- School of Life Science, University of Warwick, Coventry, United Kingdom
- * E-mail: (DW); (JGM)
| |
Collapse
|
40
|
Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function. Nat Commun 2022; 13:6663. [PMID: 36333314 PMCID: PMC9636150 DOI: 10.1038/s41467-022-34366-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Tight control of cell fate choices is crucial for normal development. Here we show that lamin A/C plays a key role in chromatin organization in embryonic stem cells (ESCs), which safeguards naïve pluripotency and ensures proper cell fate choices during cardiogenesis. We report changes in chromatin compaction and localization of cardiac genes in Lmna-/- ESCs resulting in precocious activation of a transcriptional program promoting cardiomyocyte versus endothelial cell fate. This is accompanied by premature cardiomyocyte differentiation, cell cycle withdrawal and abnormal contractility. Gata4 is activated by lamin A/C loss and Gata4 silencing or haploinsufficiency rescues the aberrant cardiovascular cell fate choices induced by lamin A/C deficiency. We uncover divergent functions of lamin A/C in naïve pluripotent stem cells and cardiomyocytes, which have distinct contributions to the transcriptional alterations of patients with LMNA-associated cardiomyopathy. We conclude that disruption of lamin A/C-dependent chromatin architecture in ESCs is a primary event in LMNA loss-of-function cardiomyopathy.
Collapse
|
41
|
Gong H, Yang Y, Zhang X, Li M, Zhang S, Chen Y. CASPIAN: A method to identify chromatin topological associated domains based on spatial density cluster. Comput Struct Biotechnol J 2022; 20:4816-4824. [PMID: 36147659 PMCID: PMC9464881 DOI: 10.1016/j.csbj.2022.08.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/10/2022] [Accepted: 08/27/2022] [Indexed: 11/25/2022] Open
Abstract
With the development of Hi-C technology, the detection of topologically associated domains (TADs) boundaries plays an important role in exploring the relationship between gene structure and expression. However, a method that can identify accurate TAD boundaries from the Hi-C contact matrix with different resolutions is currently lacking. We proposed a method named CASPIAN that can identify chromatin TAD boundaries based on the spatial density clustering algorithm. CASPIAN requires few parameters to call TADs. This method is realized using the hierarchical density-based clustering method HDBSCAN, where the distance of pairwise bins is calculated based on three distance metrics (Euclidean, Manhattan, and Chebyshev distance metric) to adapt to the characteristics of the Hi-C contact matrix generated from simulation experiments or normalized methods. Our results show that, same as standard methods (e.g., Insulation Score, TopDom), CASPIAN can enrich factors related to promoting the gene expression, such as CTCF, H3K4me1, H3K4me3, RAD21, POLR2A, and SMC3. We also calculated the approximate proportion of various factors anchored at the TAD boundaries to observe the distribution of these factors surrounding the TAD boundaries. In conclusion, CASPIAN is an easy method to explore the relationship between transcription factors and TAD boundaries. CASPIAN is available online (https://gitee.com/ghaiyan/caspian).
Collapse
Affiliation(s)
- Haiyan Gong
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yi Yang
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xiaotong Zhang
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China.,Shunde Graduate School, University of Science and Technology Beijing, Foshan 528399, Guangdong, China
| | - Minghong Li
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Sichen Zhang
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yang Chen
- The State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| |
Collapse
|
42
|
Cohesin is required for long-range enhancer action at the Shh locus. Nat Struct Mol Biol 2022; 29:891-897. [PMID: 36097291 DOI: 10.1038/s41594-022-00821-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 07/20/2022] [Indexed: 11/08/2022]
Abstract
The regulatory landscapes of developmental genes in mammals can be complex, with enhancers spread over many hundreds of kilobases. It has been suggested that three-dimensional genome organization, particularly topologically associating domains formed by cohesin-mediated loop extrusion, is important for enhancers to act over such large genomic distances. By coupling acute protein degradation with synthetic activation by targeted transcription factor recruitment, here we show that cohesin, but not CTCF, is required for activation of the target gene Shh by distant enhancers in mouse embryonic stem cells. Cohesin is not required for activation directly at the promoter or by an enhancer located closer to the Shh gene. Our findings support the hypothesis that chromatin compaction via cohesin-mediated loop extrusion allows for genes to be activated by enhancers that are located many hundreds of kilobases away in the linear genome and suggests that cohesin is dispensable for enhancers located more proximally.
Collapse
|
43
|
Qin G, Yang J, Zhao C, Ren J, Qu X. Manipulating complex chromatin folding via CRISPR-guided bioorthogonal chemistry. Proc Natl Acad Sci U S A 2022; 119:e2204725119. [PMID: 36037371 PMCID: PMC9457169 DOI: 10.1073/pnas.2204725119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Precise manipulation of chromatin folding is important for understanding the relationship between the three-dimensional genome and nuclear function. Existing tools can reversibly establish individual chromatin loops but fail to manipulate two or more chromatin loops. Here, we engineer a powerful CRISPR system which can manipulate multiple chromatin contacts using bioorthogonal reactions, termed the bioorthogonal reaction-mediated programmable chromatin loop (BPCL) system. The multiinput BPCL system employs engineered single-guide RNAs recognized by discrete bioorthogonal adaptors to independently and dynamically control different chromatin loops formation without cross-talk in the same cell or to establish hubs of multiway chromatin contacts. We use the BPCL system to successfully juxtapose the pluripotency gene promoters to enhancers and activate their endogenous expression. BPCL enables us to independently engineer multiway chromatin contacts without cross-talk, which provides a way to precisely dissect the high complexity and dynamic nature of chromatin folding.
Collapse
Affiliation(s)
- Geng Qin
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Jie Yang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Chuanqi Zhao
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Jinsong Ren
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Xiaogang Qu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| |
Collapse
|
44
|
Zhong W, Liu W, Chen J, Sun Q, Hu M, Li Y. Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variants. Front Cell Dev Biol 2022; 10:957292. [PMID: 36060805 PMCID: PMC9437546 DOI: 10.3389/fcell.2022.957292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/21/2022] [Indexed: 01/11/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified a vast number of variants associated with various complex human diseases and traits. However, most of these GWAS variants reside in non-coding regions producing no proteins, making the interpretation of these variants a daunting challenge. Prior evidence indicates that a subset of non-coding variants detected within or near cis-regulatory elements (e.g., promoters, enhancers, silencers, and insulators) might play a key role in disease etiology by regulating gene expression. Advanced sequencing- and imaging-based technologies, together with powerful computational methods, enabling comprehensive characterization of regulatory DNA interactions, have substantially improved our understanding of the three-dimensional (3D) genome architecture. Recent literature witnesses plenty of examples where using chromosome conformation capture (3C)-based technologies successfully links non-coding variants to their target genes and prioritizes relevant tissues or cell types. These examples illustrate the critical capability of 3D genome organization in annotating non-coding GWAS variants. This review discusses how 3D genome organization information contributes to elucidating the potential roles of non-coding GWAS variants in disease etiology.
Collapse
Affiliation(s)
- Wujuan Zhong
- Biostatistics and Research Decision Sciences, Merck & Co, Inc, Rahway, NJ, United States
| | - Weifang Liu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
45
|
Li D, Strong A, Hou C, Downes H, Pritchard AB, Mazzeo P, Zackai EH, Conlin LK, Hakonarson H. Interstitial deletion 4p15.32p16.1 and complex chromoplexy in a female proband with severe neurodevelopmental delay, growth failure and dysmorphism. Mol Cytogenet 2022; 15:33. [PMID: 35932041 PMCID: PMC9354344 DOI: 10.1186/s13039-022-00610-4] [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: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Complex chromosomal rearrangements involve the restructuring of genetic material within a single chromosome or across multiple chromosomes. These events can cause serious human disease by disrupting coding DNA and gene regulatory elements via deletions, duplications, and structural rearrangements. Here we describe a 5-year-old female with severe developmental delay, dysmorphic features, multi-suture craniosynostosis, and growth failure found to have a complex series of balanced intra- and inter-chromosomal rearrangements involving chromosomes 4, 11, 13, and X. Initial clinical studies were performed by karyotype, chromosomal microarray, and FISH with research-based short-read genome sequencing coupled with sanger sequencing to precisely map her breakpoints to the base pair resolution to understand the molecular basis of her phenotype. Genome analysis revealed two pathogenic deletions at 4p16.1-p15.32 and 4q31.1, accounting for her developmental delay and dysmorphism. We identified over 60 breakpoints, many with blunt ends and limited homology, supporting a role for non-homologous end joining in restructuring and resolution of the seminal chromoplexy event. We propose that the complexity of our patient’s genomic rearrangements with a high number of breakpoints causes dysregulation of gene expression by three-dimensional chromatin interactions or topologically associating domains leading to growth failure and craniosynostosis. Our work supports an important role for genome sequencing in understanding the molecular basis of complex chromosomal rearrangements in human disease.
Collapse
Affiliation(s)
- Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA. .,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Alanna Strong
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cuiping Hou
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA
| | - Helen Downes
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA
| | - Amanda Barone Pritchard
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, University of Michigan Health, Ann Arbor, MI, USA
| | - Pamela Mazzeo
- Division of General Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elaine H Zackai
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Abramson Research Building, Suite 1016I, 3615 Civic Center Boulevard, Philadelphia, PA, 19104-4318, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| |
Collapse
|
46
|
Wright D, Schaeffer SW. The relevance of chromatin architecture to genome rearrangements in Drosophila. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210206. [PMID: 35694744 PMCID: PMC9189500 DOI: 10.1098/rstb.2021.0206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA within chromosomes in the nucleus is non-randomly organized into chromosome territories, compartments and topologically associated domains (TADs). Chromosomal rearrangements have the potential to alter chromatin organization and modify gene expression leading to selection against these structural variants. Drosophila pseudoobscura has a wealth of naturally occurring gene arrangements that were generated by overlapping inversion mutations caused by two chromosomal breaks that rejoin the central region in reverse order. Unlike humans, Drosophila inversion heterozygotes do not have negative effects associated with crossing over during meiosis because males use achiasmate mechanisms for proper segregation, and aberrant recombinant meiotic products generated in females are lost in polar bodies. As a result, Drosophila populations are found to harbour extensive inversion polymorphisms. It is not clear, however, whether chromatin architecture constrains which inversions breakpoints persist in populations. We mapped the breakpoints of seven inversions in D. pseudoobscura to the TAD map to determine if persisting inversion breakpoints are more likely to occur at boundaries between TADs. Our results show that breakpoints occur at TAD boundaries more than expected by chance. Some breakpoints may alter gene expression within TADs supporting the hypothesis that position effects contribute to inversion establishment. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
Collapse
Affiliation(s)
- Dynisty Wright
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
47
|
Li Y, Agrawal V, Virk RKA, Roth E, Li WS, Eshein A, Frederick J, Huang K, Almassalha L, Bleher R, Carignano MA, Szleifer I, Dravid VP, Backman V. Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM). Sci Rep 2022; 12:12198. [PMID: 35842472 PMCID: PMC9288481 DOI: 10.1038/s41598-022-16028-2] [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: 01/10/2022] [Accepted: 07/04/2022] [Indexed: 11/09/2022] Open
Abstract
Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein, we introduce ChromSTEM, a method that utilizes high-angle annular dark-field imaging and tomography in scanning transmission electron microscopy combined with DNA-specific staining for electron microscopy. We utilized ChromSTEM for an in-depth quantification of 3D chromatin conformation with high spatial resolution and contrast, allowing for characterization of higher-order chromatin structure almost down to the level of the DNA base pair. Employing mass scaling analysis on ChromSTEM mass density tomograms, we observed that chromatin forms spatially well-defined higher-order domains, around 80 nm in radius. Within domains, chromatin exhibits a polymeric fractal-like behavior and a radially decreasing mass-density from the center to the periphery. Unlike other nanoimaging and analysis techniques, we demonstrate that our unique combination of this high-resolution imaging technique with polymer physics-based analysis enables us to (i) investigate the chromatin conformation within packing domains and (ii) quantify statistical descriptors of chromatin structure that are relevant to transcription. We observe that packing domains have heterogeneous morphological properties even within the same cell line, underlying the potential role of statistical chromatin packing in regulating gene expression within eukaryotic nuclei.
Collapse
Affiliation(s)
- Yue Li
- Applied Physics Program, Northwestern University, Evanston, IL, 60208, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Ranya K A Virk
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Eric Roth
- Department of Materials Sciences and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Wing Shun Li
- Applied Physics Program, Northwestern University, Evanston, IL, 60208, USA
| | - Adam Eshein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Kai Huang
- Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen, 518132, China
| | - Luay Almassalha
- Medical Scientist Training Program, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60611, USA
| | - Reiner Bleher
- Department of Materials Sciences and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Marcelo A Carignano
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.,Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Vinayak P Dravid
- Department of Materials Sciences and Engineering, Northwestern University, Evanston, IL, 60208, USA.
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
| |
Collapse
|
48
|
Razin SV, Zhegalova IV, Kantidze OL. Domain Model of Eukaryotic Genome Organization: From DNA Loops Fixed on the Nuclear Matrix to TADs. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:667-680. [PMID: 36154886 DOI: 10.1134/s0006297922070082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 06/16/2023]
Abstract
The article reviews the development of ideas on the domain organization of eukaryotic genome, with special attention on the studies of DNA loops anchored to the nuclear matrix and their role in the emergence of the modern model of eukaryotic genome spatial organization. Critical analysis of results demonstrating that topologically associated chromatin domains are structural-functional blocks of the genome supports the notion that these blocks are fundamentally different from domains whose existence was proposed by the domain hypothesis of eukaryotic genome organization formulated in the 1980s. Based on the discussed evidence, it is concluded that the model postulating that eukaryotic genome is built from uniformly organized structural-functional blocks has proven to be untenable.
Collapse
Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Zhegalova
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Kharkevich Institute for Information Transmission Problems, Moscow, 127051, Russia
| | - Omar L Kantidze
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| |
Collapse
|
49
|
Peng A, Peng W, Wang R, Zhao H, Yu X, Sun Y. Regulation of 3D Organization and Its Role in Cancer Biology. Front Cell Dev Biol 2022; 10:879465. [PMID: 35757006 PMCID: PMC9213882 DOI: 10.3389/fcell.2022.879465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Three-dimensional (3D) genomics is the frontier field in the post-genomics era, its foremost content is the relationship between chromatin spatial conformation and regulation of gene transcription. Cancer biology is a complex system resulting from genetic alterations in key tumor oncogenes and suppressor genes for cell proliferation, DNA replication, cell differentiation, and homeostatic functions. Although scientific research in recent decades has revealed how the genome sequence is mutated in many cancers, high-order chromosomal structures involved in the development and fate of cancer cells represent a crucial but rarely explored aspect of cancer genomics. Hence, dissection of the 3D genome conformation of cancer helps understand the unique epigenetic patterns and gene regulation processes that distinguish cancer biology from normal physiological states. In recent years, research in tumor 3D genomics has grown quickly. With the rapid progress of 3D genomics technology, we can now better determine the relationship between cancer pathogenesis and the chromatin structure of cancer cells. It is becoming increasingly explicit that changes in 3D chromatin structure play a vital role in controlling oncogene transcription. This review focuses on the relationships between tumor gene expression regulation, tumor 3D chromatin structure, and cancer phenotypic plasticity. Furthermore, based on the functional consequences of spatial disorganization in the cancer genome, we look forward to the clinical application prospects of 3D genomic biomarkers.
Collapse
Affiliation(s)
- Anghui Peng
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Wang Peng
- Department of Oncology, Liuzhou People's Hospital, Liuzhou, China
| | - Ruiqi Wang
- Department of Pharmacy, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Hao Zhao
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Xinyang Yu
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yihao Sun
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| |
Collapse
|
50
|
Liu E, Lyu H, Peng Q, Liu Y, Wang T, Han J. TADfit is a multivariate linear regression model for profiling hierarchical chromatin domains on replicate Hi-C data. Commun Biol 2022; 5:608. [PMID: 35725901 PMCID: PMC9209495 DOI: 10.1038/s42003-022-03546-y] [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: 11/10/2021] [Accepted: 05/31/2022] [Indexed: 11/26/2022] Open
Abstract
Topologically associating domains (TADs) are fundamental building blocks of three dimensional genome, and organized into complex hierarchies. Identifying hierarchical TADs on Hi-C data helps to understand the relationship between genome architectures and gene regulation. Herein we propose TADfit, a multivariate linear regression model for profiling hierarchical chromatin domains, which tries to fit the interaction frequencies in Hi-C contact matrix with and without replicates using all-possible hierarchical TADs, and the significant ones can be determined by the regression coefficients obtained with the help of an online learning solver called Follow-The-Regularized-Leader (FTRL). Beyond the existing methods, TADfit has an ability to handle multiple contact matrix replicates and find partially overlapping TADs on them, which helps to find the comprehensive underlying TADs across replicates from different experiments. The comparative results tell that TADfit has better accuracy and reproducibility, and the hierarchical TADs called by it exhibit a reasonable biological relevance. TADfit is a computational method that can identify hierarchical or partially overlapping TADs from Hi-C data, in part by using information from multiple replicates to improve detection power.
Collapse
Affiliation(s)
- Erhu Liu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi, 710049, China
| | - Hongqiang Lyu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi, 710049, China. .,Guangdong Artificial Intelligence and Digital Economy Laboratory, Guangdong, 510335, China.
| | - Qinke Peng
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi, 710049, China
| | - Yuan Liu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi, 710049, China
| | - Tian Wang
- Institute of Artificial Intelligence, Beihang University, Beijing, 100191, China
| | - Jiuqiang Han
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi, 710049, China.,Guangdong Artificial Intelligence and Digital Economy Laboratory, Guangdong, 510335, China
| |
Collapse
|