1
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Fan D, Feng H, Song M, Tan P. Gene expression profiles, potential targets and treatments of cardiac remodeling. Mol Cell Biochem 2024:10.1007/s11010-024-05126-6. [PMID: 39367915 DOI: 10.1007/s11010-024-05126-6] [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: 07/08/2024] [Accepted: 09/24/2024] [Indexed: 10/07/2024]
Abstract
Hypertensive and ischemic heart diseases have high morbidity all over the world, and they primarily contribute to heart failure associated with high mortality. Cardiac remodeling, as a basic pathological process in heart diseases, is mainly comprised of cardiac hypertrophy and fibrosis, as well as cell death which occurs especially in the ischemic cardiomyopathy. Myocardial remodeling has been widely investigated by a variety of animal models, including pressure overload, angiotensin II stimulation, and myocardial infarction. Pressure overload can cause compensatory cardiac hypertrophy at the early stage, followed by decompensatory hypertrophy and heart failure at the end. Recently, RNA sequencing and differentially expressed gene (DEG) analyses have been extensively employed to elucidate the molecular mechanisms of cardiac remodeling and related heart failure, which also provide potential targets for high-throughput drug screenings. In this review, we summarize recent advancements in gene expression profiling, related gene functions, and signaling pathways pertinent to myocardial remodeling induced by pressure overload at distinct stages, ischemia-reperfusion, myocardial infarction, and diabetes. We also discuss the effects of sex differences and inflammation on DEGs and their transcriptional regulatory mechanisms in cardiac remodeling. Additionally, we summarize emerging therapeutic agents and strategies aimed at modulating gene expression profiles during myocardial remodeling.
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Affiliation(s)
- Dong Fan
- Department of Pathophysiology, Zhuhai Campus of Zunyi Medical University, Zhuhai, 519041, China.
| | - Han Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Mengyu Song
- Department of Pathophysiology, Zhuhai Campus of Zunyi Medical University, Zhuhai, 519041, China
| | - Penglin Tan
- Department of Pathophysiology, Zhuhai Campus of Zunyi Medical University, Zhuhai, 519041, China
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2
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Liufu C, Luo L, Pang T, Zheng H, Yang L, Lu L, Chang S. Integration of multi-omics summary data reveals the role of N6-methyladenosine in neuropsychiatric disorders. Mol Psychiatry 2024; 29:3141-3150. [PMID: 38684796 DOI: 10.1038/s41380-024-02574-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
N6-methyladenosine (m6A) methylation regulates gene expression/protein by influencing numerous aspects of mRNA metabolism and contributes to neuropsychiatric diseases. Here, we integrated multi-omics data and genome-wide association study summary data of schizophrenia (SCZ), bipolar disorder (BP), attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), major depressive disorder (MDD), Alzheimer's disease (AD), and Parkinson's disease (PD) to reveal the role of m6A in neuropsychiatric disorders by using transcriptome-wide association study (TWAS) tool and Summary-data-based Mendelian randomization (SMR). Our investigation identified 86 m6A sites associated with seven neuropsychiatric diseases and then revealed 7881 associations between m6A sites and gene expressions. Based on these results, we discovered 916 significant m6A-gene associations involving 82 disease-related m6A sites and 606 genes. Further integrating the 58 disease-related genes from TWAS and SMR analysis, we obtained 61, 8, 7, 3, and 2 associations linking m6A-disease, m6A-gene, and gene-disease for SCZ, BP, AD, MDD, and PD separately. Functional analysis showed the m6A mapped genes were enriched in "response to stimulus" pathway. In addition, we also analyzed the effect of gene expression on m6A and the post-transcription effect of m6A on protein. Our study provided new insights into the genetic component of m6A in neuropsychiatric disorders and unveiled potential pathogenic mechanisms where m6A exerts influences on disease through gene expression/protein regulation.
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Affiliation(s)
- Chao Liufu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Lingxue Luo
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Tao Pang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Haohao Zheng
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Li Yang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Lin Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
- Research Units of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China
| | - Suhua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China.
- Research Units of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China.
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3
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Adolph MB, Warren GM, Couch FB, Greer BH, Eichman BF, Cortez D. Strand dependent bypass of DNA lesions during fork reversal by ATP-dependent translocases SMARCAL1, ZRANB3, and HLTF. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613558. [PMID: 39345618 PMCID: PMC11429910 DOI: 10.1101/2024.09.17.613558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
During DNA replication, the replisome encounters obstacles including DNA lesions, transcription-replication conflicts, and other sources of replication stress. These obstacles must be efficiently overcome to complete DNA synthesis and minimize genome instability. One pathway to tolerate replication stress is replication fork reversal, in which parental template DNA strands are reannealed and a nascent-nascent DNA duplex is formed. Several enzymes promote replication fork reversal, including the ATP-dependent translocases SMARCAL1, ZRANB3, and HLTF. How these enzymes translocate on DNA that contains fork-stalling lesions is unknown. Here, we examined the abilities of SMARCAL1, ZRANB3, and HLTF to tolerate various lesions on leading or lagging template strands. We demonstrate that SMARCAL1 and ZRANB3 are selectively inhibited by lesions on the leading template strand, whereas HLTF is insensitive to bulky lesions on either strand. These results suggest that SMARCAL1 and ZRANB3 contact the leading strand during fork reversal and therefore are more sensitive to inhibition by bulky lesions on this strand. In contrast, HLTF DNA translocation is inherently insensitive to DNA lesions. These biochemical differences between the fork reversal enzymes provide insights into their mechanism of DNA remodeling and suggest they may act in lesion-specific contexts.
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Affiliation(s)
- Madison B. Adolph
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
- Present Address: Department of Biochemistry and Molecular Biology, Saint Louis School of Medicine, St. Louis MO 63104
| | - Garrett M. Warren
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Present Address: Molecular Biology Program, Sloan Kettering Institute, New York NY 10065
| | - Frank B. Couch
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
- Present Address: Twin Sun LLC, Nashville TN 37203
| | - Briana H. Greer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
| | - Brandt F. Eichman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
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4
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Reid XJ, Zhong Y, Mackay JP. How does CHD4 slide nucleosomes? Biochem Soc Trans 2024:BST20230070. [PMID: 39221830 DOI: 10.1042/bst20230070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Chromatin remodelling enzymes reposition nucleosomes throughout the genome to regulate the rate of transcription and other processes. These enzymes have been studied intensively since the 1990s, and yet the mechanism by which they operate has only very recently come into focus, following advances in cryoelectron microscopy and single-molecule biophysics. CHD4 is an essential and ubiquitous chromatin remodelling enzyme that until recently has received less attention than remodellers such as Snf2 and CHD1. Here we review what recent work in the field has taught us about how CHD4 reshapes the genome. Cryoelectron microscopy and single-molecule studies demonstrate that CHD4 shares a central remodelling mechanism with most other chromatin remodellers. At the same time, differences between CHD4 and other chromatin remodellers result from the actions of auxiliary domains that regulate remodeller activity by for example: (1) making differential interactions with nucleosomal epitopes such as the acidic patch and the N-terminal tail of histone H4, and (2) inducing the formation of distinct multi-protein remodelling complexes (e.g. NuRD vs ChAHP). Thus, although we have learned much about remodeller activity, there is still clearly much more waiting to be revealed.
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Affiliation(s)
- Xavier J Reid
- School of Life and Environmental Sciences, University of Sydney, Darlington, NSW 2006, Australia
| | - Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, Darlington, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Darlington, NSW 2006, Australia
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5
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Malone HA, Roberts CWM. Chromatin remodellers as therapeutic targets. Nat Rev Drug Discov 2024; 23:661-681. [PMID: 39014081 DOI: 10.1038/s41573-024-00978-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2024] [Indexed: 07/18/2024]
Abstract
Large-scale cancer genome sequencing studies have revealed that chromatin regulators are frequently mutated in cancer. In particular, more than 20% of cancers harbour mutations in genes that encode subunits of SWI/SNF (BAF) chromatin remodelling complexes. Additional links of SWI/SNF complexes to disease have emerged with the findings that some oncogenes drive transformation by co-opting SWI/SNF function and that germline mutations in select SWI/SNF subunits are the basis of several neurodevelopmental disorders. Other chromatin remodellers, including members of the ISWI, CHD and INO80/SWR complexes, have also been linked to cancer and developmental disorders. Consequently, therapeutic manipulation of SWI/SNF and other remodelling complexes has become of great interest, and drugs that target SWI/SNF subunits have entered clinical trials. Genome-wide perturbation screens in cancer cell lines with SWI/SNF mutations have identified additional synthetic lethal targets and led to further compounds in clinical trials, including one that has progressed to FDA approval. Here, we review the progress in understanding the structure and function of SWI/SNF and other chromatin remodelling complexes, mechanisms by which SWI/SNF mutations cause cancer and neurological diseases, vulnerabilities that arise because of these mutations and efforts to target SWI/SNF complexes and synthetic lethal targets for therapeutic benefit.
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Affiliation(s)
- Hayden A Malone
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Lee JH, Sánchez-Rivera FJ, He L, Basnet H, Chen FX, Spina E, Li L, Torner C, Chan JE, Yarlagadda DVK, Park JS, Sussman C, Rudin CM, Lowe SW, Tammela T, Macias MJ, Koche RP, Massagué J. TGF-β and RAS jointly unmask primed enhancers to drive metastasis. Cell 2024:S0092-8674(24)00905-X. [PMID: 39243762 DOI: 10.1016/j.cell.2024.08.014] [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: 02/19/2024] [Revised: 05/08/2024] [Accepted: 08/07/2024] [Indexed: 09/09/2024]
Abstract
Epithelial-to-mesenchymal transitions (EMTs) and extracellular matrix (ECM) remodeling are distinct yet important processes during carcinoma invasion and metastasis. Transforming growth factor β (TGF-β) and RAS, signaling through SMAD and RAS-responsive element-binding protein 1 (RREB1), jointly trigger expression of EMT and fibrogenic factors as two discrete arms of a common transcriptional response in carcinoma cells. Here, we demonstrate that both arms come together to form a program for lung adenocarcinoma metastasis and identify chromatin determinants tying the expression of the constituent genes to TGF-β and RAS inputs. RREB1 localizes to H4K16acK20ac marks in histone H2A.Z-loaded nucleosomes at enhancers in the fibrogenic genes interleukin-11 (IL11), platelet-derived growth factor-B (PDGFB), and hyaluronan synthase 2 (HAS2), as well as the EMT transcription factor SNAI1, priming these enhancers for activation by a SMAD4-INO80 nucleosome remodeling complex in response to TGF-β. These regulatory properties segregate the fibrogenic EMT program from RAS-independent TGF-β gene responses and illuminate the operation and vulnerabilities of a bifunctional program that promotes metastatic outgrowth.
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Affiliation(s)
- Jun Ho Lee
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Francisco J Sánchez-Rivera
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Lan He
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Harihar Basnet
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fei Xavier Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elena Spina
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Liangji Li
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carles Torner
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Jason E Chan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dig Vijay Kumar Yarlagadda
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional Graduate Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jin Suk Park
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carleigh Sussman
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tuomas Tammela
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maria J Macias
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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7
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Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB. Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex. Mol Cell 2024:S1097-2765(24)00669-5. [PMID: 39226902 DOI: 10.1016/j.molcel.2024.08.015] [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: 11/03/2023] [Revised: 05/17/2024] [Accepted: 08/09/2024] [Indexed: 09/05/2024]
Abstract
The yeast SWR1 complex catalyzes the exchange of histone H2A/H2B dimers in nucleosomes with Htz1/H2B dimers. We use cryoelectron microscopy to determine the structure of an enzyme-bound hexasome intermediate in the reaction pathway of histone exchange, in which an H2A/H2B dimer has been extracted from a nucleosome prior to the insertion of a dimer comprising Htz1/H2B. The structure reveals a key role for the Swc5 subunit in stabilizing the unwrapping of DNA from the histone core of the hexasome. By engineering a crosslink between an Htz1/H2B dimer and its chaperone protein Chz1, we show that this blocks histone exchange by SWR1 but allows the incoming chaperone-dimer complex to insert into the hexasome. We use this reagent to trap an SWR1/hexasome complex with an incoming Htz1/H2B dimer that shows how the reaction progresses to the next step. Taken together the structures reveal insights into the mechanism of histone exchange by SWR1 complex.
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Affiliation(s)
- Adam S B Jalal
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Paul Girvan
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; Single Molecule Imaging Group, MRC Laboratory of Medical Sciences, Du Cane Road, London W12 0HS, UK
| | - Eugene Y D Chua
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Lexin Liu
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Shijie Wang
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Elizabeth A McCormack
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Michael T Skehan
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Carol L Knight
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - David S Rueda
- Single Molecule Imaging Group, MRC Laboratory of Medical Sciences, Du Cane Road, London W12 0HS, UK; Section of Virology, Department Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK
| | - Dale B Wigley
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
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Park G, Patel AB, Wu C, Louder RK. Structures of H2A.Z-associated human chromatin remodelers SRCAP and TIP60 reveal divergent mechanisms of chromatin engagement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605802. [PMID: 39131301 PMCID: PMC11312561 DOI: 10.1101/2024.07.30.605802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
H2A.Z is a conserved histone variant that is localized to specific genomic regions where it plays important roles in transcription, DNA repair, and replication. Central to the biochemistry of human H2A.Z are the SRCAP and TIP60 chromatin remodelers, homologs of yeast SWR1 which catalyzes ATP-dependent H2A.Z exchange. Here, we use cryo-electron microscopy to resolve six structural states of the native SRCAP complex, uncovering conformational intermediates interpreted as a stepwise path to full nucleosome engagement. We also resolve the structure of the native TIP60 complex which consists of a structured core from which flexibly tethered chromatin binding domains emerge. Despite the shared subunit composition, the core of TIP60 displays divergent architectures from SRCAP that structurally disfavor nucleosome engagement, suggesting a distinct biochemical function.
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Affiliation(s)
- Giho Park
- Biochemistry, Cellular and Molecular Graduate Program, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
| | - Avinash B. Patel
- Department of Biophysics, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Carl Wu
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Robert K. Louder
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD 21218, USA
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9
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Willige BC, Yoo CY, Saldierna Guzmán JP. What is going on inside of phytochrome B photobodies? THE PLANT CELL 2024; 36:2065-2085. [PMID: 38511271 PMCID: PMC11132900 DOI: 10.1093/plcell/koae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 03/22/2024]
Abstract
Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.
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Affiliation(s)
- Björn Christopher Willige
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Chan Yul Yoo
- School of Biological Sciences, University of Utah, UT 84112, USA
| | - Jessica Paola Saldierna Guzmán
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
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10
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Warnock JL, Ball JA, Najmi SM, Henes M, Vazquez A, Koshnevis S, Wieden HJ, Conn GL, Ghalei H. Differential roles of putative arginine fingers of AAA + ATPases Rvb1 and Rvb2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593962. [PMID: 38798342 PMCID: PMC11118528 DOI: 10.1101/2024.05.13.593962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The evolutionarily conserved AAA+ ATPases Rvb1 and Rvb2 proteins form a heteromeric complex (Rvb1/2) required for assembly or remodeling of macromolecular complexes in essential cellular processes ranging from chromatin remodeling to ribosome biogenesis. Rvb1 and Rvb2 have a high degree of sequence and structural similarity, and both contain the classical features of ATPases of their clade, including an N-terminal AAA+ subdomain with the Walker A motif, an insertion domain that typically interacts with various binding partners, and a C-terminal AAA+ subdomain containing a Walker B motif, the Sensor I and II motifs, and an arginine finger. In this study, we find that despite the high degree of structural similarity, Rvb1 and Rvb2 have distinct active sites that impact their activities and regulation within the Rvb1/2 complex. Using a combination of biochemical and genetic approaches, we show that replacing the homologous arginine fingers of Rvb1 and Rvb2 with different amino acids not only has distinct effects on the catalytic activity of the complex, but also impacts cell growth, and the Rvb1/2 interactions with binding partners. Using molecular dynamics simulations, we find that changes near the active site of Rvb1 and Rvb2 cause long-range effects on the protein dynamics in the insertion domain, suggesting a molecular basis for how enzymatic activity within the catalytic site of ATP hydrolysis can be relayed to other domains of the Rvb1/2 complex to modulate its function. Further, we show the impact that the arginine finger variants have on snoRNP biogenesis and validate the findings from molecular dynamics simulations using a targeted genetic screen. Together, our results reveal new aspects of the regulation of the Rvb1/2 complex by identifying a relay of long-range molecular communication from the ATPase active site of the complex to the binding site of cofactors. Most importantly, our findings suggest that despite high similarity and cooperation within the same protein complex, the two proteins have evolved with unique properties critical for the regulation and function of the Rvb1/2 complex.
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Affiliation(s)
- Jennifer L. Warnock
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Jacob A. Ball
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Saman M. Najmi
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Mina Henes
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
- Graduate Program in Biochemistry, Cell & Developmental Biology (BCDB), Emory University, Atlanta, Georgia, USA
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Amanda Vazquez
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Sohail Koshnevis
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Hans-Joachim Wieden
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Graeme L. Conn
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Homa Ghalei
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
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11
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Garcia J, Paul S, Shukla S, Zhong Y, Beauchemin K, Bartholomew B. Conformational switching of Arp5 subunit differentially regulates INO80 chromatin remodeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593625. [PMID: 38766108 PMCID: PMC11100795 DOI: 10.1101/2024.05.10.593625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The INO80 chromatin remodeler is a versatile enzyme capable of several functions, including spacing nucleosomes equal distances apart, precise positioning of nucleosomes based on DNA shape/sequence and exchanging histone dimers. Within INO80, the Arp5 subunit plays a central role in INO80 remodeling, evidenced by its interactions with the histone octamer, nucleosomal and extranucleosomal DNA, and its necessity in linking INO80's ATPase activity to nucleosome movement. Our investigation reveals that the grappler domain of Arp5 interacts with the acidic pocket of nucleosomes through two distinct mechanisms: an arginine anchor or a hydrophobic/acidic patch. These two modes of binding serve distinct functions within INO80 as shown in vivo by mutations in these regions resulting in varying phenotypes and in vitro by diverse effects on nucleosome mobilization. Our findings suggest that the hydrophobic/acidic patch of Arp5 is likely important for dimer exchange by INO80, while the arginine anchor is crucial for mobilizing nucleosomes.
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Affiliation(s)
- Jeison Garcia
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
- Department of Internal Medicine, Division of Medical Genetics. McGovern Medical School, UT Health Science Center at Houston, TX 77030
- These authors contributed equally
| | - Somnath Paul
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
- These authors contributed equally
| | - Shagun Shukla
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
- These authors contributed equally
| | - Yuan Zhong
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
| | - Karissa Beauchemin
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
- Department of Biology, Texas A&M University, College Station, TX 77843-3474
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
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12
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Rhodes D. To slide or not to slide: key role of the hexasome in chromatin remodeling revealed. Nat Struct Mol Biol 2024; 31:742-746. [PMID: 38769465 DOI: 10.1038/s41594-024-01278-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/14/2024] [Indexed: 05/22/2024]
Abstract
Hexasomes are non-canonical nucleosomes that package DNA with six instead of eight histones. First discovered 40 years ago as a consequence of transcription, two near-atomic-resolution cryo-EM structures of the hexasome in complex with the chromatin remodeler INO80 have now started to unravel its mechanistic impact on the regulatory landscape of chromatin. Loss of one histone H2A-H2B dimer converts inactive nucleosomes into distinct and favorable substrates for ATP-dependent chromatin remodeling.
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Affiliation(s)
- Daniela Rhodes
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK.
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13
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [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: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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14
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Ren Z, Zhao W, Li D, Yu P, Mao L, Zhao Q, Yao L, Zhang X, Liu Y, Zhou B, Wang L. INO80-Dependent Remodeling of Transcriptional Regulatory Network Underlies the Progression of Heart Failure. Circulation 2024; 149:1121-1138. [PMID: 38152931 DOI: 10.1161/circulationaha.123.065440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/05/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Progressive remodeling of cardiac gene expression underlies decline in cardiac function, eventually leading to heart failure. However, the major determinants of transcriptional network switching from normal to failed hearts remain to be determined. METHODS In this study, we integrated human samples, genetic mouse models, and genomic approaches, including bulk RNA sequencing, single-cell RNA sequencing, chromatin immunoprecipitation followed by high-throughput sequencing, and assay for transposase-accessible chromatin with high-throughput sequencing, to identify the role of chromatin remodeling complex INO80 in heart homeostasis and dysfunction. RESULTS The INO80 chromatin remodeling complex was abundantly expressed in mature cardiomyocytes, and its expression further increased in mouse and human heart failure. Cardiomyocyte-specific overexpression of Ino80, its core catalytic subunit, induced heart failure within 4 days. Combining RNA sequencing, chromatin immunoprecipitation followed by high-throughput sequencing, and assay for transposase-accessible chromatin with high-throughput sequencing, we revealed INO80 overexpression-dependent reshaping of the nucleosomal landscape that remodeled a core set of transcription factors, most notably the MEF2 (Myocyte Enhancer Factor 2) family, whose target genes were closely associated with cardiac function. Conditional cardiomyocyte-specific deletion of Ino80 in an established mouse model of heart failure demonstrated remarkable preservation of cardiac function. CONCLUSIONS In summary, our findings shed light on the INO80-dependent remodeling of the chromatin landscape and transcriptional networks as a major mechanism underlying cardiac dysfunction in heart failure, and suggest INO80 as a potential preventative or interventional target.
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Affiliation(s)
- Zongna Ren
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, China (Z.R., W.Z., B.Z., L.W.)
| | - Wanqing Zhao
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, China (Z.R., W.Z., B.Z., L.W.)
| | - Dandan Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (D.L., P.Y., L.M., Q.Z., L.Y., X.Z., Y.L., B.Z., L.W.)
| | - Peng Yu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (D.L., P.Y., L.M., Q.Z., L.Y., X.Z., Y.L., B.Z., L.W.)
| | - Lin Mao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (D.L., P.Y., L.M., Q.Z., L.Y., X.Z., Y.L., B.Z., L.W.)
| | - Quanyi Zhao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (D.L., P.Y., L.M., Q.Z., L.Y., X.Z., Y.L., B.Z., L.W.)
| | - Luyan Yao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (D.L., P.Y., L.M., Q.Z., L.Y., X.Z., Y.L., B.Z., L.W.)
| | - Xuelin Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (D.L., P.Y., L.M., Q.Z., L.Y., X.Z., Y.L., B.Z., L.W.)
| | - Yandan Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (D.L., P.Y., L.M., Q.Z., L.Y., X.Z., Y.L., B.Z., L.W.)
| | - Bingying Zhou
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, China (Z.R., W.Z., B.Z., L.W.)
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (D.L., P.Y., L.M., Q.Z., L.Y., X.Z., Y.L., B.Z., L.W.)
| | - Li Wang
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, China (Z.R., W.Z., B.Z., L.W.)
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (D.L., P.Y., L.M., Q.Z., L.Y., X.Z., Y.L., B.Z., L.W.)
- Key Laboratory of Application of Pluripotent Stem Cells in Heart Regeneration, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (L.W.)
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15
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Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Nat Rev Mol Cell Biol 2024; 25:309-332. [PMID: 38081975 DOI: 10.1038/s41580-023-00683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 03/28/2024]
Abstract
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re)arrange nucleosomes at the first level of chromatin organization. Their Snf2-type motor ATPases alter histone-DNA interactions through a common DNA translocation mechanism. Whether remodeller activities mainly catalyse nucleosome dynamics or accurately co-determine nucleosome organization remained unclear. In this Review, we discuss the emerging mechanisms of chromatin remodelling: dynamic remodeller architectures and their interactions, the inner workings of the ATPase cycle, allosteric regulation and pathological dysregulation. Recent mechanistic insights argue for a decisive role of remodellers in the energy-driven self-organization of chromatin, which enables both stability and plasticity of genome regulation - for example, during development and stress. Different remodellers, such as members of the SWI/SNF, ISWI, CHD and INO80 families, process (epi)genetic information through specific mechanisms into distinct functional outputs. Combinatorial assembly of remodellers and their interplay with histone modifications, histone variants, DNA sequence or DNA-bound transcription factors regulate nucleosome mobilization or eviction or histone exchange. Such input-output relationships determine specific nucleosome positions and compositions with distinct DNA accessibilities and mediate differential genome regulation. Finally, remodeller genes are often mutated in diseases characterized by genome dysregulation, notably in cancer, and we discuss their physiological relevance.
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Affiliation(s)
- Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Avinash B Patel
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Faculty of Chemistry and Pharmacy, LMU Munich, Munich, Germany
| | - Yuan He
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, LMU Munich, Martinsried, Germany.
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16
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Zhang M, Wu K, Zhang W, Lin X, Cao Q, Zhang L, Chen K. The therapeutic potential of targeting the CHD protein family in cancer. Pharmacol Ther 2024; 256:108610. [PMID: 38367868 PMCID: PMC10942663 DOI: 10.1016/j.pharmthera.2024.108610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/06/2024] [Accepted: 02/02/2024] [Indexed: 02/19/2024]
Abstract
Accumulating evidence indicates that epigenetic events undergo deregulation in various cancer types, playing crucial roles in tumor development. Among the epigenetic factors involved in the epigenetic remodeling of chromatin, the chromodomain helicase DNA-binding protein (CHD) family frequently exhibits gain- or loss-of-function mutations in distinct cancer types. Therefore, targeting CHD remodelers holds the potential for antitumor treatment. In this review, we discuss epigenetic regulations of cancer development. We emphasize proteins in the CHD family, delving deeply into the intricate mechanisms governing their functions. Additionally, we provide an overview of current therapeutic strategies targeting CHD family members in preclinical trials. We further discuss the promising approaches that have demonstrated early signs of success in cancer treatment.
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Affiliation(s)
- Min Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Kaiyuan Wu
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Weijie Zhang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Orthopaedic Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xia Lin
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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17
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Ferrer P, Upadhyay S, Cai JJ, Clement TM. Novel Nuclear Roles for Testis-Specific ACTL7A and ACTL7B Supported by In Vivo Characterizations and AI Facilitated In Silico Mechanistic Modeling with Implications for Epigenetic Regulation in Spermiogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582797. [PMID: 38464253 PMCID: PMC10925299 DOI: 10.1101/2024.02.29.582797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
A mechanistic role for nuclear function of testis-specific actin related proteins (ARPs) is proposed here through contributions of ARP subunit swapping in canonical chromatin regulatory complexes. This is significant to our understanding of both mechanisms controlling regulation of spermiogenesis, and the expanding functional roles of the ARPs in cell biology. Among these roles, actins and ARPs are pivotal not only in cytoskeletal regulation, but also in intranuclear chromatin organization, influencing gene regulation and nucleosome remodeling. This study focuses on two testis-specific ARPs, ACTL7A and ACTL7B, exploring their intranuclear activities and broader implications utilizing combined in vivo, in vitro, and in silico approaches. ACTL7A and ACTL7B, previously associated with structural roles, are hypothesized here to serve in chromatin regulation during germline development. This study confirms the intranuclear presence of ACTL7B in spermatocytes and round spermatids, revealing a potential role in intranuclear processes, and identifies a putative nuclear localization sequence conserved across mammalian ACTL7B, indicating a potentially unique mode of nuclear transport which differs from conventional actin. Ablation of ACTL7B leads to varied transcriptional changes reported here. Additionally, in the absence of ACTL7A or ACTL7B there is a loss of intranuclear localization of HDAC1 and HDAC3, which are known regulators of epigenetic associated acetylation changes that in turn regulate gene expression. Thus, these HDACs are implicated as contributors to the aberrant gene expression observed in the KO mouse testis transcriptomic analysis. Furthermore, this study employed and confirmed the accuracy of in silico models to predict ARP interactions with Helicase-SANT-associated (HSA) domains, uncovering putative roles for testis-specific ARPs in nucleosome remodeling complexes. In these models, ACTL7A and ACTL7B were found capable of binding to INO80 and SWI/SNF nucleosome remodeler family members in a manner akin to nuclear actin and ACTL6A. These models thus implicate germline-specific ARP subunit swapping within chromatin regulatory complexes as a potential regulatory mechanism for chromatin and associated molecular machinery adaptations in nuclear reorganizations required during spermiogenesis. These results hold implications for male fertility and epigenetic programing in the male-germline that warrant significant future investigation. In summary, this study reveals that ACTL7A and ACTL7B play intranuclear gene regulation roles in male gametogenesis, adding to the multifaceted roles identified also spanning structural, acrosomal, and flagellar stability. ACTL7A and ACTL7B unique nuclear transport, impact on HDAC nuclear associations, impact on transcriptional processes, and proposed mechanism for involvement in nucleosome remodeling complexes supported by AI facilitated in silico modeling contribute to a more comprehensive understanding of the indispensable functions of ARPs broadly in cell biology, and specifically in male fertility.
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Affiliation(s)
- Pierre Ferrer
- Interdisciplinary Faculty of Toxicology Program, Texas A&M University, College Station, TX 77843
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843
| | - Srijana Upadhyay
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843
| | - James J Cai
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Tracy M Clement
- Interdisciplinary Faculty of Toxicology Program, Texas A&M University, College Station, TX 77843
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843
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18
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Mao YQ, Seraphim TV, Wan Y, Wu R, Coyaud E, Bin Munim M, Mollica A, Laurent E, Babu M, Mennella V, Raught B, Houry WA. DPCD is a regulator of R2TP in ciliogenesis initiation through Akt signaling. Cell Rep 2024; 43:113713. [PMID: 38306274 DOI: 10.1016/j.celrep.2024.113713] [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: 02/23/2023] [Revised: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024] Open
Abstract
R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass spectrometry, we identified deleted in primary ciliary dyskinesia (DPCD) as an adaptor of R2TP. Here, we demonstrate that R2TP-DPCD influences ciliogenesis initiation through a unique mechanism by interaction with Akt kinase to regulate its phosphorylation levels rather than its stability. We further show that DPCD is a heart-shaped monomeric protein with two domains. A highly conserved region in the cysteine- and histidine-rich domains-containing proteins and SGT1 (CS) domain of DPCD interacts with the RUVBL2 DII domain with high affinity to form a stable R2TP-DPCD complex both in cellulo and in vitro. Considering that DPCD is one among several CS-domain-containing proteins found to associate with RUVBL1/2, we propose that RUVBL1/2 are CS-domain-binding proteins that regulate complex assembly and downstream signaling.
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Affiliation(s)
- Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yimei Wan
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ruikai Wu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Muhammad Bin Munim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Antonio Mollica
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Vito Mennella
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UK; Department of Pathology, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QP, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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19
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Lei ZC, Wang X, Yang L, Qu H, Sun Y, Yang Y, Li W, Zhang WB, Cao XY, Fan C, Li G, Wu J, Tian ZQ. What can molecular assembly learn from catalysed assembly in living organisms? Chem Soc Rev 2024; 53:1892-1914. [PMID: 38230701 DOI: 10.1039/d3cs00634d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Molecular assembly is the process of organizing individual molecules into larger structures and complex systems. The self-assembly approach is predominantly utilized in creating artificial molecular assemblies, and was believed to be the primary mode of molecular assembly in living organisms as well. However, it has been shown that the assembly of many biological complexes is "catalysed" by other molecules, rather than relying solely on self-assembly. In this review, we summarize these catalysed-assembly (catassembly) phenomena in living organisms and systematically analyse their mechanisms. We then expand on these phenomena and discuss related concepts, including catalysed-disassembly and catalysed-reassembly. Catassembly proves to be an efficient and highly selective strategy for synergistically controlling and manipulating various noncovalent interactions, especially in hierarchical molecular assemblies. Overreliance on self-assembly may, to some extent, hinder the advancement of artificial molecular assembly with powerful features. Furthermore, inspired by the biological catassembly phenomena, we propose guidelines for designing artificial catassembly systems and developing characterization and theoretical methods, and review pioneering works along this new direction. Overall, this approach may broaden and deepen our understanding of molecular assembly, enabling the construction and control of intelligent assembly systems with advanced functionality.
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Affiliation(s)
- Zhi-Chao Lei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinchang Wang
- School of Electronic Science and Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P. R. China
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Hang Qu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Yibin Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xiao-Yu Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science, Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jiarui Wu
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, P. R. China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, P. R. China
| | - Zhong-Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
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20
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López-Perrote A, Serna M, Llorca O. Maturation and Assembly of mTOR Complexes by the HSP90-R2TP-TTT Chaperone System: Molecular Insights and Mechanisms. Subcell Biochem 2024; 104:459-483. [PMID: 38963496 DOI: 10.1007/978-3-031-58843-3_17] [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] [Indexed: 07/05/2024]
Abstract
The mechanistic target of rapamycin (mTOR) is a master regulator of cell growth and metabolism, integrating environmental signals to regulate anabolic and catabolic processes, regulating lipid synthesis, growth factor-induced cell proliferation, cell survival, and migration. These activities are performed as part of two distinct complexes, mTORC1 and mTORC2, each with specific roles. mTORC1 and mTORC2 are elaborated dimeric structures formed by the interaction of mTOR with specific partners. mTOR functions only as part of these large complexes, but their assembly and activation require a dedicated and sophisticated chaperone system. mTOR folding and assembly are temporarily separated with the TELO2-TTI1-TTI2 (TTT) complex assisting the cotranslational folding of mTOR into a native conformation. Matured mTOR is then transferred to the R2TP complex for assembly of active mTORC1 and mTORC2 complexes. R2TP works in concert with the HSP90 chaperone to promote the incorporation of additional subunits to mTOR and dimerization. This review summarizes our current knowledge on how the HSP90-R2TP-TTT chaperone system facilitates the maturation and assembly of active mTORC1 and mTORC2 complexes, discussing interactions, structures, and mechanisms.
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Affiliation(s)
- Andrés López-Perrote
- Spanish National Cancer Research Centre (CNIO), Structural Biology Programme, Melchor Fernández Almagro 3, Madrid, Spain.
| | - Marina Serna
- Spanish National Cancer Research Centre (CNIO), Structural Biology Programme, Melchor Fernández Almagro 3, Madrid, Spain
| | - Oscar Llorca
- Spanish National Cancer Research Centre (CNIO), Structural Biology Programme, Melchor Fernández Almagro 3, Madrid, Spain.
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21
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Bartholomew B, Shukla S, Ngubo M, Paul S, Persinger J, Brahma S. New insights into the mechanism and DNA-sequence specificity of INO80 chromatin remodeling. RESEARCH SQUARE 2023:rs.3.rs-3443329. [PMID: 37961512 PMCID: PMC10635376 DOI: 10.21203/rs.3.rs-3443329/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The INO80 complex stood out in a large family of ATP-dependent chromatin remodelers because of its ATPase domain binding and translocating on DNA at the edge of nucleosomes, rather than at two helical turns from the center of DNA that is wrapped around nucleosomes. This unique property of INO80 was thought to account for its singular role in nucleosome placement at gene promoters in a DNA-sequence dependent manner that is crucial for transcription regulation. Now, we uncover INO80 functions differently than previously thought with its ATPase domain translocating on DNA close to the center of nucleosomes, like other remodelers. Our discovery also reveals the physical properties of the first ~36 bp of DNA on the entry side of nucleosomes is the main determinant for the DNA specificity of INO80 rather than the properties of the extranucleosomal DNA. The DNA sequence sensitive step of INO80 is after DNA is displaced from the histone octamer on the entry side of nucleosomes and 20 bp of DNA are moved out the exit side. We find the ATPase domain and Arp5 subunit of INO80 are likely involved in INO80's DNA specificity and the mechanism of INO80 remodeling is substantially different than originally proposed.
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22
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Park S, Brandani GB, Ha T, Bowman G. Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning. Nucleic Acids Res 2023; 51:10326-10343. [PMID: 37738162 PMCID: PMC10602870 DOI: 10.1093/nar/gkad738] [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: 03/11/2022] [Revised: 08/02/2023] [Accepted: 08/26/2023] [Indexed: 09/24/2023] Open
Abstract
Chromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone core. Although not directly reading out the DNA sequence, some chromatin remodelers exhibit a sequence-dependent bias in nucleosome positioning, which presumably reflects properties of the DNA duplex. Here, we show how nucleosome positioning by the Chd1 remodeler is influenced by local DNA perturbations throughout the nucleosome footprint. Using site-specific DNA cleavage coupled with next-generation sequencing, we show that nucleosomes shifted by Chd1 can preferentially localize DNA perturbations - poly(dA:dT) tracts, DNA mismatches, and single-nucleotide insertions - about a helical turn outside the Chd1 motor domain binding site, super helix location 2 (SHL2). This phenomenon occurs with both the Widom 601 positioning sequence and the natural +1 nucleosome sequence from the Saccharomyces cerevisiae SWH1 gene. Our modeling indicates that localization of DNA perturbations about a helical turn outward from SHL2 results from back-and-forth sliding due to remodeler action on both sides of the nucleosome. Our results also show that barrier effects from DNA perturbations can be extended by the strong phasing of nucleosome positioning sequences.
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Affiliation(s)
- Sangwoo Park
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregory D Bowman
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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23
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Jorstad NL, Song JH, Exposito-Alonso D, Suresh H, Castro-Pacheco N, Krienen FM, Yanny AM, Close J, Gelfand E, Long B, Seeman SC, Travaglini KJ, Basu S, Beaudin M, Bertagnolli D, Crow M, Ding SL, Eggermont J, Glandon A, Goldy J, Kiick K, Kroes T, McMillen D, Pham T, Rimorin C, Siletti K, Somasundaram S, Tieu M, Torkelson A, Feng G, Hopkins WD, Höllt T, Keene CD, Linnarsson S, McCarroll SA, Lelieveldt BP, Sherwood CC, Smith K, Walsh CA, Dobin A, Gillis J, Lein ES, Hodge RD, Bakken TE. Comparative transcriptomics reveals human-specific cortical features. Science 2023; 382:eade9516. [PMID: 37824638 PMCID: PMC10659116 DOI: 10.1126/science.ade9516] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/13/2023] [Indexed: 10/14/2023]
Abstract
The cognitive abilities of humans are distinctive among primates, but their molecular and cellular substrates are poorly understood. We used comparative single-nucleus transcriptomics to analyze samples of the middle temporal gyrus (MTG) from adult humans, chimpanzees, gorillas, rhesus macaques, and common marmosets to understand human-specific features of the neocortex. Human, chimpanzee, and gorilla MTG showed highly similar cell-type composition and laminar organization as well as a large shift in proportions of deep-layer intratelencephalic-projecting neurons compared with macaque and marmoset MTG. Microglia, astrocytes, and oligodendrocytes had more-divergent expression across species compared with neurons or oligodendrocyte precursor cells, and neuronal expression diverged more rapidly on the human lineage. Only a few hundred genes showed human-specific patterning, suggesting that relatively few cellular and molecular changes distinctively define adult human cortical structure.
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Affiliation(s)
| | - Janet H.T. Song
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - David Exposito-Alonso
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hamsini Suresh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Fenna M. Krienen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jennie Close
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Emily Gelfand
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Brian Long
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | | | | | - Soumyadeep Basu
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - Marc Beaudin
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | | | - Megan Crow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Jeroen Eggermont
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
| | | | - Jeff Goldy
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Katelyn Kiick
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Thomas Kroes
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
| | | | | | | | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Michael Tieu
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William D. Hopkins
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, Houston, TX 78602, USA
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 981915, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Boudewijn P. Lelieveldt
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
- Pattern Recognition and Bioinformatics group, Delft University of Technology, Delft, Netherlands
| | - Chet C. Sherwood
- Department of Anthropology, The George Washington University, Washington, DC 20037, USA
| | - Kimberly Smith
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Christopher A. Walsh
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Ed S. Lein
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
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24
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Sokolova V, Lee G, Mullins A, Mody P, Watanabe S, Tan D. DNA-translocation-independent role of INO80 remodeler in DNA damage repairs. J Biol Chem 2023; 299:105245. [PMID: 37696438 PMCID: PMC10570696 DOI: 10.1016/j.jbc.2023.105245] [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: 06/12/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
Chromatin remodelers utilize ATP hydrolysis to reposition histone octamers on DNA, facilitating transcription by promoting histone displacements. Although their actions on chromatin with damaged DNA are assumed to be similar, the precise mechanisms by which they modulate damaged nucleosomes and their specific roles in DNA damage response (DDR) remain unclear. INO80-C, a versatile chromatin remodeler, plays a crucial role in the efficient repair of various types of damage. In this study, we have demonstrated that both abasic sites and UV-irradiation damage abolish the DNA translocation activity of INO80-C. Additionally, we have identified compromised ATP hydrolysis within the Ino80 catalytic subunit as the primary cause of the inhibition of DNA translocation, while its binding to damaged nucleosomes remains unaffected. Moreover, we have uncovered a novel function of INO80-C that operates independently of its DNA translocation activity, namely, its facilitation of apurinic/apyrimidinic (AP) site cleavage by the AP-endonuclease 1 (APE1). Our findings provide valuable insights into the role of the INO80-C chromatin remodeler in DDR, thereby advancing our understanding of chromatin remodeling during DNA damage repairs.
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Affiliation(s)
- Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Gahyun Lee
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Amber Mullins
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Preesha Mody
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Shinya Watanabe
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA.
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25
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Karl LA, Galanti L, Bantele SC, Metzner F, Šafarić B, Rajappa L, Foster B, Pires VB, Bansal P, Chacin E, Basquin J, Duderstadt KE, Kurat CF, Bartke T, Hopfner KP, Pfander B. A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler. Life Sci Alliance 2023; 6:e202201790. [PMID: 37468166 PMCID: PMC10355287 DOI: 10.26508/lsa.202201790] [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: 10/31/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Fun30 is the prototype of the Fun30-SMARCAD1-ETL subfamily of nucleosome remodelers involved in DNA repair and gene silencing. These proteins appear to act as single-subunit nucleosome remodelers, but their molecular mechanisms are, at this point, poorly understood. Using multiple sequence alignment and structure prediction, we identify an evolutionarily conserved domain that is modeled to contain a SAM-like fold with one long, protruding helix, which we term SAM-key. Deletion of the SAM-key within budding yeast Fun30 leads to a defect in DNA repair and gene silencing similar to that of the fun30Δ mutant. In vitro, Fun30 protein lacking the SAM-key is able to bind nucleosomes but is deficient in DNA-stimulated ATPase activity and nucleosome sliding and eviction. A structural model based on AlphaFold2 prediction and verified by crosslinking-MS indicates an interaction of the long SAM-key helix with protrusion I, a subdomain located between the two ATPase lobes that is critical for control of enzymatic activity. Mutation of the interaction interface phenocopies the domain deletion with a lack of DNA-stimulated ATPase activation and a nucleosome-remodeling defect, thereby confirming a role of the SAM-key helix in regulating ATPase activity. Our data thereby demonstrate a central role of the SAM-key domain in mediating the activation of Fun30 catalytic activity, thus highlighting the importance of allosteric activation for this class of enzymes.
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Affiliation(s)
- Leonhard A Karl
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Susanne Cs Bantele
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Felix Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Barbara Šafarić
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Benjamin Foster
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Vanessa Borges Pires
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Priyanka Bansal
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Erika Chacin
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Jerôme Basquin
- Crystallization Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
- Physik Department, Technische Universität München, Munich, Germany
| | - Christoph F Kurat
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
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26
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Moleri P, Wilkins BJ. Unnatural Amino Acid Crosslinking for Increased Spatiotemporal Resolution of Chromatin Dynamics. Int J Mol Sci 2023; 24:12879. [PMID: 37629060 PMCID: PMC10454095 DOI: 10.3390/ijms241612879] [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: 07/27/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The utilization of an expanded genetic code and in vivo unnatural amino acid crosslinking has grown significantly in the past decade, proving to be a reliable system for the examination of protein-protein interactions. Perhaps the most utilized amino acid crosslinker, p-benzoyl-(l)-phenylalanine (pBPA), has delivered a vast compendium of structural and mechanistic data, placing it firmly in the upper echelons of protein analytical techniques. pBPA contains a benzophenone group that is activated with low energy radiation (~365 nm), initiating a diradical state that can lead to hydrogen abstraction and radical recombination in the form of a covalent bond to a neighboring protein. Importantly, the expanded genetic code system provides for site-specific encoding of the crosslinker, yielding spatial control for protein surface mapping capabilities. Paired with UV-activation, this process offers a practical means for spatiotemporal understanding of protein-protein dynamics in the living cell. The chromatin field has benefitted particularly well from this technique, providing detailed mapping and mechanistic insight for numerous chromatin-related pathways. We provide here a brief history of unnatural amino acid crosslinking in chromatin studies and outlooks into future applications of the system for increased spatiotemporal resolution in chromatin related research.
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Affiliation(s)
| | - Bryan J. Wilkins
- Department of Chemistry and Biochemistry, Manhattan College, 4513 Manhattan College Parkway, Riverdale, NY 10471, USA
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27
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Wu H, Muñoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y. Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility. Science 2023; 381:319-324. [PMID: 37384669 PMCID: PMC10480058 DOI: 10.1126/science.adf4197] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 06/17/2023] [Indexed: 07/01/2023]
Abstract
Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report structures of Saccharomyces cerevisiae INO80 bound to a hexasome or a nucleosome. INO80 binds the two substrates in substantially different orientations. On a hexasome, INO80 places its ATPase subunit, Ino80, at superhelical location -2 (SHL -2), in contrast to SHL -6 and SHL -7, as previously seen on nucleosomes. Our results suggest that INO80 action on hexasomes resembles action by other remodelers on nucleosomes such that Ino80 is maximally active near SHL -2. The SHL -2 position also plays a critical role for nucleosome remodeling by INO80. Overall, the mechanistic adaptations used by INO80 for preferential hexasome sliding imply that subnucleosomal particles play considerable regulatory roles.
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Affiliation(s)
- Hao Wu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elise N. Muñoz
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Laura J. Hsieh
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Un Seng Chio
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Muryam A. Gourdet
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA
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28
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Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S. Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling. Science 2023; 381:313-319. [PMID: 37384673 DOI: 10.1126/science.adf6287] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Loss of H2A-H2B histone dimers is a hallmark of actively transcribed genes, but how the cellular machinery functions in the context of noncanonical nucleosomal particles remains largely elusive. In this work, we report the structural mechanism for adenosine 5'-triphosphate-dependent chromatin remodeling of hexasomes by the INO80 complex. We show how INO80 recognizes noncanonical DNA and histone features of hexasomes that emerge from the loss of H2A-H2B. A large structural rearrangement switches the catalytic core of INO80 into a distinct, spin-rotated mode of remodeling while its nuclear actin module remains tethered to long stretches of unwrapped linker DNA. Direct sensing of an exposed H3-H4 histone interface activates INO80, independently of the H2A-H2B acidic patch. Our findings reveal how the loss of H2A-H2B grants remodelers access to a different, yet unexplored layer of energy-driven chromatin regulation.
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Affiliation(s)
- Min Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anna Jungblut
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Franziska Kunert
- Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Luis Hauptmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thomas Hoffmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Olga Kolesnikova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Felix Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Manuela Moldt
- Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Felix Weis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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29
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Otto JE, Ursu O, Wu AP, Winter EB, Cuoco MS, Ma S, Qian K, Michel BC, Buenrostro JD, Berger B, Regev A, Kadoch C. Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens. Mol Cell 2023; 83:1350-1367.e7. [PMID: 37028419 DOI: 10.1016/j.molcel.2023.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/07/2023] [Accepted: 03/10/2023] [Indexed: 04/09/2023]
Abstract
The mammalian SWI/SNF (mSWI/SNF or BAF) family of chromatin remodeling complexes play critical roles in regulating DNA accessibility and gene expression. The three final-form subcomplexes-cBAF, PBAF, and ncBAF-are distinct in biochemical componentry, chromatin targeting, and roles in disease; however, the contributions of their constituent subunits to gene expression remain incompletely defined. Here, we performed Perturb-seq-based CRISPR-Cas9 knockout screens targeting mSWI/SNF subunits individually and in select combinations, followed by single-cell RNA-seq and SHARE-seq. We uncovered complex-, module-, and subunit-specific contributions to distinct regulatory networks and defined paralog subunit relationships and shifted subcomplex functions upon perturbations. Synergistic, intra-complex genetic interactions between subunits reveal functional redundancy and modularity. Importantly, single-cell subunit perturbation signatures mapped across bulk primary human tumor expression profiles both mirror and predict cBAF loss-of-function status in cancer. Our findings highlight the utility of Perturb-seq to dissect disease-relevant gene regulatory impacts of heterogeneous, multi-component master regulatory complexes.
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Affiliation(s)
- Jordan E Otto
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Chemical Biology Program, Harvard University, Cambridge, MA, USA
| | - Oana Ursu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander P Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Evan B Winter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Sai Ma
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kristin Qian
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Brittany C Michel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Bonnie Berger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, UA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Chemical Biology Program, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, UA.
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30
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Ciafrè SA, Russo M, Michienzi A, Galardi S. Long Noncoding RNAs and Cancer Stem Cells: Dangerous Liaisons Managing Cancer. Int J Mol Sci 2023; 24:ijms24031828. [PMID: 36768150 PMCID: PMC9915130 DOI: 10.3390/ijms24031828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Decades of research have investigated the mechanisms that lead to the origin of cancer, striving to identify tumor-initiating cells. These cells, also known as cancer stem cells, are characterized by the ability to self-renew, to give rise to differentiated tumor populations, and on a larger scale, are deemed responsible not only for tumor initiation but also for recurrent tumors, often resistant to chemotherapy and radiotherapy. Long noncoding RNAs are RNA molecules longer than 200 nt, lacking the ability to code for proteins, with recognized roles as fine regulators of gene expression. They can exert these functions through a variety of mechanisms, acting at almost all steps of gene expression, from modulation of the epigenetic state of chromatin to modulation of protein stability. In all cases, lncRNAs do not work alone, but they always interact with other RNA molecules, either coding or non-coding, or with protein factors. In this review, we summarize the latest results obtained about the involvement of lncRNAs in the initiating cells of several types of tumors, and highlight the different mechanisms through which they work, while discussing how the modulation of a lncRNA can affect several aspects of tumor onset and progression.
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Affiliation(s)
- Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (S.A.C.); (S.G.)
| | - Monia Russo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Silvia Galardi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (S.A.C.); (S.G.)
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Xu X, Chan AKN, Li M, Liu Q, Mattson N, Pangeni Pokharel S, Chang WH, Yuan YC, Wang J, Moore RE, Pirrotte P, Wu J, Su R, Müschen M, Rosen ST, Chen J, Yang L, Chen CW. ACTR5 controls CDKN2A and tumor progression in an INO80-independent manner. SCIENCE ADVANCES 2022; 8:eadc8911. [PMID: 36563143 PMCID: PMC9788768 DOI: 10.1126/sciadv.adc8911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/10/2022] [Indexed: 05/19/2023]
Abstract
Epigenetic dysregulation of cell cycle is a hallmark of tumorigenesis in multiple cancers, including hepatocellular carcinoma (HCC). Nonetheless, the epigenetic mechanisms underlying the aberrant cell cycle signaling and therapeutic response remain unclear. Here, we used an epigenetics-focused CRISPR interference screen and identified ACTR5 (actin-related protein 5), a component of the INO80 chromatin remodeling complex, to be essential for HCC tumor progression. Suppression of ACTR5 activated CDKN2A expression, ablated CDK/E2F-driven cell cycle signaling, and attenuated HCC tumor growth. Furthermore, high-density CRISPR gene tiling scans revealed a distinct HCC-specific usage of ACTR5 and its interacting partner IES6 compared to the other INO80 complex members, suggesting an INO80-independent mechanism of ACTR5/IES6 in supporting the HCC proliferation. Last, our study revealed the synergism between ACTR5/IES6-targeting and pharmacological inhibition of CDK in treating HCC. These results indicate that the dynamic interplay between epigenetic regulators, tumor suppressors, and cell cycle machinery could provide novel opportunities for combinational HCC therapy.
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Affiliation(s)
- Xiaobao Xu
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
| | - Anthony K. N. Chan
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
| | - Mingli Li
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
| | - Qiao Liu
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
| | - Nicole Mattson
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
| | | | - Wen-Han Chang
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
| | | | - Jinhui Wang
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Roger E. Moore
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Patrick Pirrotte
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Jun Wu
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | | | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute - City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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Kunert F, Metzner FJ, Jung J, Höpfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP. Structural mechanism of extranucleosomal DNA readout by the INO80 complex. SCIENCE ADVANCES 2022; 8:eadd3189. [PMID: 36490333 PMCID: PMC9733932 DOI: 10.1126/sciadv.add3189] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.
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Affiliation(s)
- Franziska Kunert
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Felix J. Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - James Jung
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Höpfler
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stephan Woike
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kevin Schall
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Kostrewa
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Manuela Moldt
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Susanne Bantele
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Eustermann
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Corresponding author.
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Zukin SA, Marunde MR, Popova IK, Soczek KM, Nogales E, Patel AB. Structure and flexibility of the yeast NuA4 histone acetyltransferase complex. eLife 2022; 11:e81400. [PMID: 36263929 PMCID: PMC9643008 DOI: 10.7554/elife.81400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
The NuA4 protein complex acetylates histones H4 and H2A to activate both transcription and DNA repair. We report the 3.1-Å resolution cryo-electron microscopy structure of the central hub of NuA4, which flexibly tethers the histone acetyltransferase (HAT) and Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) modules. The hub contains the large Tra1 subunit and a core that includes Swc4, Arp4, Act1, Eaf1, and the C-terminal region of Epl1. Eaf1 stands out as the primary scaffolding factor that interacts with the Tra1, Swc4, and Epl1 subunits and contributes the conserved HSA helix to the Arp module. Using nucleosome-binding assays, we find that the HAT module, which is anchored to the core through Epl1, recognizes H3K4me3 nucleosomes with hyperacetylated H3 tails, while the TINTIN module, anchored to the core via Eaf1, recognizes nucleosomes that have hyperacetylated H2A and H4 tails. Together with the known interaction of Tra1 with site-specific transcription factors, our data suggest a model in which Tra1 recruits NuA4 to specific genomic sites then allowing the flexible HAT and TINTIN modules to select nearby nucleosomes for acetylation.
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Affiliation(s)
- Stefan A Zukin
- College of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | | | - Irina K Popova
- EpiCypher, Inc, Research Triangle ParkDurhamUnited States
| | - Katarzyna M Soczek
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
| | - Eva Nogales
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Avinash B Patel
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
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Takizawa Y, Kurumizaka H. Chromatin structure meets cryo-EM: Dynamic building blocks of the functional architecture. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194851. [PMID: 35952957 DOI: 10.1016/j.bbagrm.2022.194851] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Chromatin is a dynamic molecular complex composed of DNA and proteins that package the DNA in the nucleus of eukaryotic cells. The basic structural unit of chromatin is the nucleosome core particle, composed of ~150 base pairs of genomic DNA wrapped around a histone octamer containing two copies each of four histones, H2A, H2B, H3, and H4. Individual nucleosome core particles are connected by short linker DNAs, forming a nucleosome array known as a beads-on-a-string fiber. Higher-order structures of chromatin are closely linked to nuclear events such as replication, transcription, recombination, and repair. Recently, a variety of chromatin structures have been determined by single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), and their structural details have provided clues about the chromatin architecture functions in the cell. In this review, we highlight recent cryo-EM structural studies of a fundamental chromatin unit to clarify the functions of chromatin.
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Affiliation(s)
- Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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Li Z, Zhao B, Qin C, Wang Y, Li T, Wang W. Chromatin Dynamics in Digestive System Cancer: Commander and Regulator. Front Oncol 2022; 12:935877. [PMID: 35965507 PMCID: PMC9372441 DOI: 10.3389/fonc.2022.935877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Digestive system tumors have a poor prognosis due to complex anatomy, insidious onset, challenges in early diagnosis, and chemoresistance. Epidemiological statistics has verified that digestive system tumors rank first in tumor-related death. Although a great number of studies are devoted to the molecular biological mechanism, early diagnostic markers, and application of new targeted drugs in digestive system tumors, the therapeutic effect is still not satisfactory. Epigenomic alterations including histone modification and chromatin remodeling are present in human cancers and are now known to cooperate with genetic changes to drive the cancer phenotype. Chromatin is the carrier of genetic information and consists of DNA, histones, non-histone proteins, and a small amount of RNA. Chromatin and nucleosomes control the stability of the eukaryotic genome and regulate DNA processes such as transcription, replication, and repair. The dynamic structure of chromatin plays a key role in this regulatory function. Structural fluctuations expose internal DNA and thus provide access to the nuclear machinery. The dynamic changes are affected by various complexes and epigenetic modifications. Variation of chromatin dynamics produces early and superior regulation of the expression of related genes and downstream pathways, thereby controlling tumor development. Intervention at the chromatin level can change the process of cancer earlier and is a feasible option for future tumor diagnosis and treatment. In this review, we introduced chromatin dynamics including chromatin remodeling, histone modifications, and chromatin accessibility, and current research on chromatin regulation in digestive system tumors was also summarized.
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36
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Dos Santos Morais R, Santo PE, Ley M, Schelcher C, Abel Y, Plassart L, Deslignière E, Chagot ME, Quinternet M, Paiva ACF, Hessmann S, Morellet N, M F Sousa P, Vandermoere F, Bertrand E, Charpentier B, Bandeiras TM, Plisson-Chastang C, Verheggen C, Cianférani S, Manival X. Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases. J Mol Biol 2022; 434:167760. [PMID: 35901867 DOI: 10.1016/j.jmb.2022.167760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
Abstract
DPCD is a protein that may play a role in cilia formation and whose absence leads to primary ciliary dyskinesia (PCD), a rare disease caused by impairment of ciliated cells. Except for high-throughput studies that identified DPCD as a possible RUVBL1 (R1) and RUVBL2 (R2) partner, no in-depth cellular, biochemical, and structural investigation involving DPCD have been reported so far. R1 and R2 proteins are ubiquitous highly conserved AAA+ family ATPases that assemble and mature a plethora of macromolecular complexes and are pivotal in numerous cellular processes, especially by guaranteeing a co-chaperoning function within R2TP or R2TP-like machineries. In the present study, we identified DPCD as a new R1R2 partner in vivo. We show that DPCD interacts directly with R1 and R2 in vitro and in cells. We characterized the physico-chemical properties of DPCD in solution and built a 3D model of DPCD. In addition, we used a variety of orthogonal biophysical techniques including small-angle X-ray scattering, structural mass spectrometry and electron microscopy to assess the molecular determinants of DPCD interaction with R1R2. Interestingly, DPCD disrupts the dodecameric state of R1R2 complex upon binding and this interaction occurs mainly via the DII domains of R1R2.
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Affiliation(s)
| | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marie Ley
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | | | - Yoann Abel
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | - Laura Plassart
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | | | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, IBSLor, Biophysics and Structural Biology Core Facility, F-54000, France
| | - Ana C F Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Nelly Morellet
- Très Grandes Infrastructures de Recherche, Institut de Chimie des Substances Naturelles - CNRS, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Pedro M F Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | | | - Edouard Bertrand
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | | | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Célia Plisson-Chastang
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Céline Verheggen
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Xavier Manival
- IMoPA, CNRS, Université de Lorraine, Nancy F-54000, France
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37
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Cui S, Walker JR, Batenburg NL, Zhu XD. Cockayne syndrome group B protein uses its DNA translocase activity to promote mitotic DNA synthesis. DNA Repair (Amst) 2022; 116:103354. [PMID: 35738143 DOI: 10.1016/j.dnarep.2022.103354] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/30/2022] [Accepted: 06/07/2022] [Indexed: 11/24/2022]
Abstract
Mitotic DNA synthesis, also known as MiDAS, has been suggested to be a form of RAD52-dependent break-induced replication (BIR) that repairs under-replicated DNA regions of the genome in mitosis prior to chromosome segregation. Cockayne syndrome group B (CSB) protein, a chromatin remodeler of the SNF2 family, has been implicated in RAD52-dependent BIR repair of stalled replication forks. However, whether CSB plays a role in MiDAS has not been characterized. Here, we report that CSB functions epistatically with RAD52 to promote MiDAS at common fragile sites in response to replication stress, and prevents genomic instability associated with defects in MiDAS. We show that CSB is dependent upon the conserved phenylalanine at position 796 (F796), which lies in the recently-reported pulling pin that is required for CSB's translocase activity, to mediate MiDAS, suggesting that CSB uses its DNA translocase activity to promote MiDAS. Structural analysis reveals that CSB shares with a subset of SNF2 family proteins a translocase regulatory region (TRR), which is important for CSB's function in MiDAS. We further demonstrate that phosphorylation of S1013 in the TRR regulates the function of CSB in MiDAS and restart of stalled forks but not in fork degradation in BRCA2-deficient cells and UV repair. Taken together, these results suggest that the DNA translocase activity of CSB in vivo is likely to be highly regulated by post-translational modification in a context-specific manner.
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Affiliation(s)
- Shixin Cui
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - John R Walker
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Nicole L Batenburg
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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38
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Hsieh LJ, Gourdet MA, Moore CM, Muñoz EN, Gamarra N, Ramani V, Narlikar GJ. A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Mol Cell 2022; 82:2098-2112.e4. [PMID: 35597239 PMCID: PMC9351570 DOI: 10.1016/j.molcel.2022.04.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 12/10/2021] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
Abstract
The critical role of the INO80 chromatin remodeling complex in transcription is commonly attributed to its nucleosome sliding activity. Here, we have found that INO80 prefers to mobilize hexasomes over nucleosomes. INO80's preference for hexasomes reaches up to ∼60 fold when flanking DNA overhangs approach ∼18-bp linkers in yeast gene bodies. Correspondingly, deletion of INO80 significantly affects the positions of hexasome-sized particles within yeast genes in vivo. Our results raise the possibility that INO80 promotes nucleosome sliding by dislodging an H2A-H2B dimer, thereby making a nucleosome transiently resemble a hexasome. We propose that this mechanism allows INO80 to rapidly mobilize nucleosomes at promoters and hexasomes within gene bodies. Rapid repositioning of hexasomes that are generated in the wake of transcription may mitigate spurious transcription. More generally, such versatility may explain how INO80 regulates chromatin architecture during the diverse processes of transcription, replication, and repair.
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Affiliation(s)
- Laura J Hsieh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Muryam A Gourdet
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Camille M Moore
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elise N Muñoz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Vijay Ramani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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Steenwyk JL, Phillips MA, Yang F, Date SS, Graham TR, Berman J, Hittinger CT, Rokas A. An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. SCIENCE ADVANCES 2022; 8:eabn0105. [PMID: 35507651 PMCID: PMC9067921 DOI: 10.1126/sciadv.abn0105] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
The evolutionary rates of functionally related genes often covary. We present a gene coevolution network inferred from examining nearly 3 million orthologous gene pairs from 332 budding yeast species spanning ~400 million years of evolution. Network modules provide insight into cellular and genomic structure and function. Examination of the phenotypic impact of network perturbation using deletion mutant data from the baker's yeast Saccharomyces cerevisiae, which were obtained from previously published studies, suggests that fitness in diverse environments is affected by orthologous gene neighborhood and connectivity. Mapping the network onto the chromosomes of S. cerevisiae and Candida albicans revealed that coevolving orthologous genes are not physically clustered in either species; rather, they are often located on different chromosomes or far apart on the same chromosome. The coevolution network captures the hierarchy of cellular structure and function, provides a roadmap for genotype-to-phenotype discovery, and portrays the genome as a linked ensemble of genes.
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Affiliation(s)
- Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Megan A. Phillips
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Feng Yang
- Shmunis School of Biomedical and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Swapneeta S. Date
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R. Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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40
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Mechanistic insights into the multiple activities of the Rad5 family of enzymes. J Mol Biol 2022; 434:167581. [DOI: 10.1016/j.jmb.2022.167581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 11/18/2022]
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41
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Acidic patch histone mutations and their effects on nucleosome remodeling. Biochem Soc Trans 2022; 50:907-919. [PMID: 35356970 DOI: 10.1042/bst20210773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 12/15/2022]
Abstract
Structural and biochemical studies have identified a histone surface on each side of the nucleosome disk termed 'the nucleosome acidic patch' that acts as a regulatory hub for the function of numerous nuclear proteins, including ATP-dependent chromatin complexes (remodelers). Four major remodeler subfamilies, SWI/SNF, ISWI, CHD, and INO80, have distinct modes of interaction with one or both nucleosome acidic patches, contributing to their specific remodeling outcomes. Genome-wide sequencing analyses of various human cancers have uncovered high-frequency mutations in histone coding genes, including some that map to the acidic patch. How cancer-related acidic patch histone mutations affect nucleosome remodeling is mainly unknown. Recent advances in in vitro chromatin reconstitution have enabled access to physiologically relevant nucleosomes, including asymmetric nucleosomes that possess both wild-type and acidic patch mutant histone copies. Biochemical investigation of these substrates revealed unexpected remodeling outcomes with far-reaching implications for alteration of chromatin structure. This review summarizes recent findings of how different remodeler families interpret wild-type and mutant acidic patches for their remodeling functions and discusses models for remodeler-mediated changes in chromatin landscapes as a consequence of acidic patch mutations.
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Poyton MF, Feng XA, Ranjan A, Lei Q, Wang F, Zarb JS, Louder RK, Park G, Jo MH, Ye J, Liu S, Ha T, Wu C. Coordinated DNA and histone dynamics drive accurate histone H2A.Z exchange. SCIENCE ADVANCES 2022; 8:eabj5509. [PMID: 35263135 PMCID: PMC8906749 DOI: 10.1126/sciadv.abj5509] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Nucleosomal histone H2A is exchanged for its variant H2A.Z by the SWR1 chromatin remodeler, but the mechanism and timing of histone exchange remain unclear. Here, we quantify DNA and histone dynamics during histone exchange in real time using a three-color single-molecule FRET assay. We show that SWR1 operates with timed precision to unwrap DNA with large displacement from one face of the nucleosome, remove H2A-H2B from the same face, and rewrap DNA, all within 2.3 s. This productive DNA unwrapping requires full SWR1 activation and differs from unproductive, smaller-scale DNA unwrapping caused by SWR1 binding alone. On an asymmetrically positioned nucleosome, SWR1 intrinsically senses long-linker DNA to preferentially exchange H2A.Z on the distal face as observed in vivo. The displaced H2A-H2B dimer remains briefly associated with the SWR1-nucleosome complex and is dissociated by histone chaperones. These findings reveal how SWR1 coordinates DNA unwrapping with histone dynamics to rapidly and accurately place H2A.Z at physiological sites on chromatin.
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Affiliation(s)
- Matthew F. Poyton
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Xinyu A. Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Anand Ranjan
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Qin Lei
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Feng Wang
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jasmin S. Zarb
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Robert K. Louder
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Giho Park
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Myung Hyun Jo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joseph Ye
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sheng Liu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Karl LA, Peritore M, Galanti L, Pfander B. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Front Genet 2022; 12:821543. [PMID: 35096025 PMCID: PMC8790285 DOI: 10.3389/fgene.2021.821543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.
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Affiliation(s)
- Leonhard Andreas Karl
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Peritore
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
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Peng Q, Wan D, Zhou R, Luo H, Wang J, Ren L, Zeng Y, Yu C, Zhang S, Huang X, Peng Y. The biological function of metazoan-specific subunit nuclear factor related to kappaB binding protein of INO80 complex. Int J Biol Macromol 2022; 203:176-183. [PMID: 35093437 DOI: 10.1016/j.ijbiomac.2022.01.155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 12/24/2022]
Abstract
The INO80 chromatin remodeling complex plays an essential role in the regulation of gene transcription, which participate in a variety of important biological processes in cells including DNA repair and DNA replication. Difference from the yeast INO80 complex, metazoan INO80 complex have the specific subunit G, which is known as nuclear factor related to kappaB binding protein (NFRKB). Recently, NFRKB has been received much attention in many aspects, such as DNA repair, cell pluripotency, telomere protection, and protein activity regulation. To dig the new function of metazoan INO80 complex, a better understanding of the role of NFRKB is required. In this review, we provide an overview of the structure and function of NFRKB and discuss its potential role in cancer treatment and telomere regulation. Overall, this review provides an important reference for further research of the INO80 complex and NFRKB.
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Affiliation(s)
- Qiyao Peng
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Dan Wan
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Rongrong Zhou
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Hongyu Luo
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 410016, China
| | - Junyi Wang
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Lingyan Ren
- School of Safety Engineering, Chongqing University of Science & Technology, Chongqing 401331, China
| | - Yajun Zeng
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Department of Pharmacy, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Chao Yu
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Shuihan Zhang
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Xuekuan Huang
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 410016, China.
| | - Yongbo Peng
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China.
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45
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Yang Y, Zhang L, Xiong C, Chen J, Wang L, Wen Z, Yu J, Chen P, Xu Y, Jin J, Cai Y, Li G. HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs. Nucleic Acids Res 2022; 50:191-206. [PMID: 34893908 PMCID: PMC8754660 DOI: 10.1093/nar/gkab1221] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 12/21/2022] Open
Abstract
Histone variants have been implicated in regulating chromatin dynamics and genome functions. Previously, we have shown that histone variant H3.3 actively marks enhancers and cooperates with H2A.Z at promoters to prime the genes into a poised state in mouse embryonic stem cells (mESCs). However, how these two important histone variants collaboratively function in this process still remains elusive. In this study, we found that depletion of different components of HIRA complex, a specific chaperone of H3.3, results in significant decreases of H2A.Z enrichment at genome scale. In addition, CUT&Tag data revealed a genomic colocalization between HIRA complex and SRCAP complex. In vivo and in vitro biochemical assays verified that HIRA complex could interact with SRCAP complex through the Hira subunit. Furthermore, our chromatin accessibility and transcription analyses demonstrated that HIRA complex contributed to preset a defined chromatin feature around TSS region for poising gene transcription. In summary, our results unveiled that while regulating the H3.3 incorporation in the regulatory regions, HIRA complex also collaborates with SRCAP to deposit H2A.Z onto the promoters, which cooperatively determines the transcriptional potential of the poised genes in mESCs.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liwei Zhang
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chaoyang Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jingji Jin
- School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- National Engineering Laboratory for AIDS Vaccine, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yong Cai
- School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- National Engineering Laboratory for AIDS Vaccine, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing, China
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Abstract
Actin is a highly conserved protein in mammals. The actin dynamics is regulated by actin-binding proteins and actin-related proteins. Nuclear actin and these regulatory proteins participate in multiple nuclear processes, including chromosome architecture organization, chromatin remodeling, transcription machinery regulation, and DNA repair. It is well known that the dysfunctions of these processes contribute to the development of cancer. Moreover, emerging evidence has shown that the deregulated actin dynamics is also related to cancer. This chapter discusses how the deregulation of nuclear actin dynamics contributes to tumorigenesis via such various nuclear events.
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Affiliation(s)
- Yuanjian Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shengzhe Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jae-Il Park
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center and Health Science Center, Houston, TX, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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47
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Determining translocation orientations of nucleic acid helicases. Methods 2021; 204:160-171. [PMID: 34758393 PMCID: PMC9076756 DOI: 10.1016/j.ymeth.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Helicase enzymes translocate along an RNA or DNA template with a defined polarity to unwind, separate, or remodel duplex strands for a variety of genome maintenance processes. Helicase mutations are commonly associated with a variety of diseases including aging, cancer, and neurodegeneration. Biochemical characterization of these enzymes has provided a wealth of information on the kinetics of unwinding and substrate preferences, and several high-resolution structures of helicases alone and bound to oligonucleotides have been solved. Together, they provide mechanistic insights into the structural translocation and unwinding orientations of helicases. However, these insights rely on structural inferences derived from static snapshots. Instead, continued efforts should be made to combine structure and kinetics to better define active translocation orientations of helicases. This review explores many of the biochemical and biophysical methods utilized to map helicase binding orientation to DNA or RNA substrates and includes several time-dependent methods to unequivocally map the active translocation orientation of these enzymes to better define the active leading and trailing faces.
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48
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Arimura Y, Shih RM, Froom R, Funabiki H. Structural features of nucleosomes in interphase and metaphase chromosomes. Mol Cell 2021; 81:4377-4397.e12. [PMID: 34478647 PMCID: PMC8571072 DOI: 10.1016/j.molcel.2021.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/17/2022]
Abstract
Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.
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Affiliation(s)
- Yasuhiro Arimura
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Rochelle M Shih
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
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49
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Vysotskiy M, Zhong X, Miller-Fleming TW, Zhou D, Cox NJ, Weiss LA. Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes. Genome Med 2021; 13:172. [PMID: 34715901 PMCID: PMC8557010 DOI: 10.1186/s13073-021-00972-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 09/16/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Deletions and duplications of the multigenic 16p11.2 and 22q11.2 copy number variant (CNV) regions are associated with brain-related disorders including schizophrenia, intellectual disability, obesity, bipolar disorder, and autism spectrum disorder (ASD). The contribution of individual CNV genes to each of these identified phenotypes is unknown, as well as the contribution of these CNV genes to other potentially subtler health implications for carriers. Hypothesizing that DNA copy number exerts most effects via impacts on RNA expression, we attempted a novel in silico fine-mapping approach in non-CNV carriers using both GWAS and biobank data. METHODS We first asked whether gene expression level in any individual gene in the CNV region alters risk for a known CNV-associated behavioral phenotype(s). Using transcriptomic imputation, we performed association testing for CNV genes within large genotyped cohorts for schizophrenia, IQ, BMI, bipolar disorder, and ASD. Second, we used a biobank containing electronic health data to compare the medical phenome of CNV carriers to controls within 700,000 individuals in order to investigate the full spectrum of health effects of the CNVs. Third, we used genotypes for over 48,000 individuals within the biobank to perform phenome-wide association studies between imputed expressions of individual 16p11.2 and 22q11.2 genes and over 1500 health traits. RESULTS Using large genotyped cohorts, we found individual genes within 16p11.2 associated with schizophrenia (TMEM219, INO80E, YPEL3), BMI (TMEM219, SPN, TAOK2, INO80E), and IQ (SPN), using conditional analysis to identify upregulation of INO80E as the driver of schizophrenia, and downregulation of SPN and INO80E as increasing BMI. We identified both novel and previously observed over-represented traits within the electronic health records of 16p11.2 and 22q11.2 CNV carriers. In the phenome-wide association study, we found seventeen significant gene-trait pairs, including psychosis (NPIPB11, SLX1B) and mood disorders (SCARF2), and overall enrichment of mental traits. CONCLUSIONS Our results demonstrate how integration of genetic and clinical data aids in understanding CNV gene function and implicates pleiotropy and multigenicity in CNV biology.
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Affiliation(s)
- Mikhail Vysotskiy
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, 513 Parnassus Ave., Health Sciences East 9th floor HSE901E, San Francisco, CA, 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, USA
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Xue Zhong
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Dan Zhou
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Lauren A Weiss
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, 513 Parnassus Ave., Health Sciences East 9th floor HSE901E, San Francisco, CA, 94143, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA.
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, USA.
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50
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Sanchez A, Lee D, Kim DI, Miller KM. Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin. Front Genet 2021; 12:747734. [PMID: 34659365 PMCID: PMC8514019 DOI: 10.3389/fgene.2021.747734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/31/2021] [Indexed: 01/25/2023] Open
Abstract
DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.
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Affiliation(s)
- Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Doohyung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Dae In Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
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