1
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Li H, Gigi L, Zhao D. CHD1, a multifaceted epigenetic remodeler in prostate cancer. Front Oncol 2023; 13:1123362. [PMID: 36776288 PMCID: PMC9909554 DOI: 10.3389/fonc.2023.1123362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Chromatin remodeling proteins contribute to DNA replication, transcription, repair, and recombination. The chromodomain helicase DNA-binding (CHD) family of remodelers plays crucial roles in embryonic development, hematopoiesis, and neurogenesis. As the founding member, CHD1 is capable of assembling nucleosomes, remodeling chromatin structure, and regulating gene transcription. Dysregulation of CHD1 at genetic, epigenetic, and post-translational levels is common in malignancies and other human diseases. Through interacting with different genetic alterations, CHD1 possesses the capabilities to exert oncogenic or tumor-suppressive functions in context-dependent manners. In this Review, we summarize the biochemical properties and dysregulation of CHD1 in cancer cells, and then discuss CHD1's roles in different contexts of prostate cancer, with an emphasis on its crosstalk with diverse signaling pathways. Furthermore, we highlight the potential therapeutic strategies for cancers with dysregulated CHD1. At last, we discuss current research gaps in understanding CHD1's biological functions and molecular basis during disease progression, as well as the modeling systems for biology study and therapeutic development.
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Affiliation(s)
- Haoyan Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Loraine Gigi
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Texas A&M School of Public Health, Texas A&M University, College Station, TX, United States
| | - Di Zhao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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2
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Schoberleitner I, Mertens B, Bauer I, Lusser A. Regulation of sensory perception and motor abilities by brain-specific action of chromatin remodeling factor CHD1. Front Mol Neurosci 2022; 15:840966. [PMID: 35983070 PMCID: PMC9378821 DOI: 10.3389/fnmol.2022.840966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
The ATP-dependent chromatin remodeling factor CHD1 (chromodomain-helicase-DNA binding protein 1) is involved in both the de novo assembly and the remodeling of chromatin. Recently, we discovered a crucial role of CHD1 in the incorporation of the histone variant H3.3 in the fly brain illustrated by widespread transcriptional upregulation and shortened lifespan in Chd1-mutant animals. Because many genes linked to sensory perception were dysregulated in Chd1-mutant heads, we studied the role of CHD1 in these processes. Here we show that Chd1-mutant flies have severe defects in their response behavior to olfactory and gustatory but not visual stimuli. Further analyses suggested that poor performance in gustatory response assays was caused by reduced motivation for foraging and feeding rather than defects in taste perception. Moreover, we show that shortened lifespan of Chd1-mutant flies is accompanied by indications of premature functional aging as suggested by defects in negative geotaxis and exploratory walking assays. The latter phenotype was rescued by neuronal re-expression of Chd1, while the olfactory defects were not. Interestingly, we found evidence for indirect regulation of the non-neuronal expression of odorant binding proteins (Obp) by neuronal expression of Chd1. Together, these results emphasize the crucial role of CHD1 activity controlling diverse neuronal processes thereby affecting healthy lifespan.
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Affiliation(s)
| | | | | | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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3
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Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP. Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state. Nat Struct Mol Biol 2022; 29:121-129. [PMID: 35173352 DOI: 10.1038/s41594-021-00719-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022]
Abstract
Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. Here we report a complex of the Chd1 remodeler bound to a nucleosome in a nucleotide-free state, determined by cryo-EM to 2.3 Å resolution. The remodeler stimulates the nucleosome to absorb an additional nucleotide on each strand at two different locations: on the tracking strand within the ATPase binding site and on the guide strand one helical turn from the ATPase motor. Remarkably, the additional nucleotide on the tracking strand is associated with a local transformation toward an A-form geometry, explaining how sequential ratcheting of each DNA strand occurs. The structure also reveals a histone-binding motif, ChEx, which can block opposing remodelers on the nucleosome and may allow Chd1 to participate in histone reorganization during transcription.
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Affiliation(s)
- Ilana M Nodelman
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Sayan Das
- Department of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | | | - Stephen D Fried
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.,Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory D Bowman
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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4
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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5
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CHD8 safeguards early neuroectoderm differentiation in human ESCs and protects from apoptosis during neurogenesis. Cell Death Dis 2021; 12:981. [PMID: 34686651 PMCID: PMC8536677 DOI: 10.1038/s41419-021-04292-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022]
Abstract
The chromatin remodeler CHD8, which belongs to the ATP-dependent chromatin remodelers CHD family, is one of the most high-risk mutated genes in autism spectrum disorders. However, the role of CHD8 in neural differentiation and the mechanism of CHD8 in autism remains unclear, despite there are a few studies based on the CHD8 haploinsufficient models. Here, we generate the CHD8 knockout human ESCs by CRISPR/Cas9 technology and characterize the effect of loss-of-function of CHD8 on pluripotency maintenance and lineage determination by utilizing efficient directed differentiation protocols. The results show loss-of-function of CHD8 does not affect human ESC maintenance although having slight effect on proliferation and cell cycle. Interestingly, CHD8 depletion results in defective neuroectoderm differentiation, along with severe cell death in neural progenitor stage. Transcriptome analysis also indicates CHD8 does not alter the expression of pluripotent genes in ESC stage, but in neural progenitor cells depletion of CHD8 induces the abnormal expression of the apoptosis genes and suppresses neuroectoderm-related genes. These results provide the evidence that CHD8 plays an essential role in the pluripotency exit and neuroectoderm differentiation as well as the regulation of apoptosis during neurogenesis.
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6
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Lee HR, Yang SJ, Choi HK, Kim JA, Oh IH. The Chromatin Remodeling Complex CHD1 Regulates the Primitive State of Mesenchymal Stromal Cells to Control Their Stem Cell Supporting Activity. Stem Cells Dev 2021; 30:363-373. [PMID: 33593142 DOI: 10.1089/scd.2020.0166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The primitive state (stemness) of mesenchymal stromal cells (MSCs) is responsible for supporting the function of tissue-specific stem cells to regenerate damaged tissues. However, molecular mechanisms regulating the stemness of MSCs remain unknown. In this study, we found that the primitive state of MSCs is hierarchically regulated by the expression levels of the chromatin remodeling complex, CHD1, with CHD1 expression levels higher in the undifferentiated state, and decreasing upon MSC differentiation. Consistently, CHD1 expression levels decrease during progressive loss of clonogenic progenitors (CFU-F) induced by passage cultures. Moreover, knockdown (KD) of CHD1 decreased CFU-F frequency, whereas CHD1 overexpression increased it. In addition, the expression of stem cell-specific genes was down- or upregulated upon KD or overexpression of CHD1, respectively, accompanied by associated changes in chromatin condensation. Importantly, altering CHD1 expression levels affected the ability of MSCs to support the self-renewing expansion of hematopoietic stem cells (HSCs). Furthermore, CHD1 levels were significantly decreased in MSCs from acute myeloid leukemia or aplastic anemia patients, where CFU-F and HSC-supporting activities are lost. Altogether, these findings show that chromatin remodeling by CHD1 is a molecular parameter that influences the primitive state of MSCs and their stem cell-supporting activity, which controls tissue regeneration.
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Affiliation(s)
- Hae-Ri Lee
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung-Jip Yang
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyun-Kyung Choi
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin-A Kim
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Il-Hoan Oh
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
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7
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Xiong X, Lai X, Li A, Liu Z, Ma N. Diversity roles of CHD1L in normal cell function and tumorigenesis. Biomark Res 2021; 9:16. [PMID: 33663617 PMCID: PMC7934534 DOI: 10.1186/s40364-021-00269-w] [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: 10/13/2020] [Accepted: 02/16/2021] [Indexed: 12/14/2022] Open
Abstract
Chromodomain helicase/ATPase DNA binding protein 1-like gene (CHD1L) is a multifunctional protein participated in diverse cellular processes, including chromosome remodeling, cell differentiation and development. CHD1L is a regulator of chromosomal integrity maintenance, DNA repair and transcriptional regulation through its bindings to DNA. By regulating kinds of complex networks, CHD1L has been identified as a potent anti-apoptotic and pro-proliferative factor. CHD1L is also an oncoprotein since its overexpression leads to dysregulation of related downstream targets in various cancers. The latest advances in the functional molecular basis of CHD1L in normal cells will be described in this review. As the same time, we will describe the current understanding of CHD1L in terms of structure, characteristics, function and the molecular mechanisms underlying CHD1L in tumorigenesis. We inference that the role of CHD1L which involve in multiple cellular processes and oncogenesis is well worth further studying in basic biology and clinical relevance.
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Affiliation(s)
- Xifeng Xiong
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, 510220, China
| | - Xudong Lai
- Departement of infectious disease, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, 510220, China
| | - Aiguo Li
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, 510220, China.
| | - Zhihe Liu
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, 510220, China.
| | - Ningfang Ma
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China. .,Department of Histology and Embryology, Guangzhou Medical University, Xinzao Town, Panyu District, Guangzhou, 511436, China.
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8
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ATP-Dependent Chromatin Remodeling Complex in the Lineage Specification of Mesenchymal Stem Cells. Stem Cells Int 2020; 2020:8839703. [PMID: 32963551 PMCID: PMC7499328 DOI: 10.1155/2020/8839703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Mesenchymal stem cells (MSCs) present in multiple tissues can self-renew and differentiate into multiple lineages including the bone, cartilage, muscle, cardiac tissue, and connective tissue. Key events, including cell proliferation, lineage commitment, and MSC differentiation, are ensured by precise gene expression regulation. ATP-dependent chromatin alteration is one form of epigenetic modifications that can regulate the transcriptional level of specific genes by utilizing the energy from ATP hydrolysis to reorganize chromatin structure. ATP-dependent chromatin remodeling complexes consist of a variety of subunits that together perform multiple functions in self-renewal and lineage specification. This review highlights the important role of ATP-dependent chromatin remodeling complexes and their different subunits in modulating MSC fate determination and discusses the proposed mechanisms by which ATP-dependent chromatin remodelers function.
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9
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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10
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Zhou J, Li J, Serafim RB, Ketchum S, Ferreira CG, Liu JC, Coe KA, Price BD, Yusufzai T. Human CHD1 is required for early DNA-damage signaling and is uniquely regulated by its N terminus. Nucleic Acids Res 2019. [PMID: 29529298 PMCID: PMC5934646 DOI: 10.1093/nar/gky128] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
CHD1 is a conserved chromatin remodeling enzyme required for development and linked to prostate cancer in adults, yet its role in human cells is poorly understood. Here, we show that targeted disruption of the CHD1 gene in human cells leads to a defect in early double-strand break (DSB) repair via homologous recombination (HR), resulting in hypersensitivity to ionizing radiation as well as PARP and PTEN inhibition. CHD1 knockout cells show reduced H2AX phosphorylation (γH2AX) and foci formation as well as impairments in CtIP recruitment to the damaged sites. Chromatin immunoprecipitation following a single DSB shows that the reduced levels of γH2AX accumulation at DSBs in CHD1-KO cells are due to both a global reduction in H2AX incorporation and poor retention of H2AX at the DSBs. We also identified a unique N-terminal region of CHD1 that inhibits the DNA binding, ATPase, and chromatin assembly and remodeling activities of CHD1. CHD1 lacking the N terminus was more active in rescuing the defects in γH2AX formation and CtIP recruitment in CHD1-KO cells than full-length CHD1, suggesting the N terminus is a negative regulator in cells. Our data point to a role for CHD1 in the DSB repair process and identify a novel regulatory region of the protein.
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Affiliation(s)
- Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Jiaqi Li
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Rodolfo B Serafim
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Steven Ketchum
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Catarina G Ferreira
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jessica C Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Graduate Program: Molecules, Cells, and Organisms, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kathryn A Coe
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
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11
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Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer Cell 2019; 35:603-617.e8. [PMID: 30930119 PMCID: PMC6467783 DOI: 10.1016/j.ccell.2019.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/06/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
Deletion of the gene encoding the chromatin remodeler CHD1 is among the most common alterations in prostate cancer (PCa); however, the tumor-suppressive functions of CHD1 and reasons for its tissue-specific loss remain undefined. We demonstrated that CHD1 occupied prostate-specific enhancers enriched for the androgen receptor (AR) and lineage-specific cofactors. Upon CHD1 loss, the AR cistrome was redistributed in patterns consistent with the oncogenic AR cistrome in PCa samples and drove tumor formation in the murine prostate. Notably, this cistrome shift was associated with a unique AR transcriptional signature enriched for pro-oncogenic pathways unique to this tumor subclass. Collectively, these data credential CHD1 as a tumor suppressor in the prostate that constrains AR binding/function to limit tumor progression.
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Affiliation(s)
- Michael A Augello
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Deli Liu
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lesa D Deonarine
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brian D Robinson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dennis Huang
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirjam Blattner
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ashley S Doane
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Elissa W P Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark A Rubin
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Himisha Beltran
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Andrea Sboner
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Noah Dephoure
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Christopher E Barbieri
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
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12
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Il’ina IA, Konev AY. The role of aTp-dependent chromatin remodeling factors in chromatin assembly in vivo. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromatin assembly is a fundamental process essential for chromosome duplication subsequent to DNA replication. In addition, histone removal and incorporation take place constantly throughout the cell cycle in the course of DNA-utilizing processes, such as transcription, damage repair or recombination. In vitro studies have revealed that nucleosome assembly relies on the combined action of core histone chaperones and ATP-utilizing molecular motor proteins such as ACF or CHD1. Despite extensive biochemical characterization of ATP-dependent chromatin assembly and remodeling factors, it has remained unclear to what extent nucleosome assembly is an ATP-dependent process in vivo. Our original and published data about the functions of ATP-dependent chromatin assembly and remodeling factors clearly demonstrated that these proteins are important for nucleosome assembly and histone exchange in vivo. During male pronucleus reorganization after fertilization CHD1 has a critical role in the genomescale, replication-independent nucleosome assembly involving the histone variant H3.3. Thus, the molecular motor proteins, such as CHD1, function not only in the remodeling of existing nucleosomes but also in de novo nucleosome assembly from DNA and histones in vivo. ATP-dependent chromatin assembly and remodeling factors have been implicated in the process of histone exchange during transcription and DNA repair, in the maintenance of centromeric chromatin and in the loading and remodeling of nucleosomes behind a replication fork. Thus, chromatin remodeling factors are involved in the processes of both replication-dependent and replication-independent chromatin assembly. The role of these proteins is especially prominent in the processes of large-scale chromatin reorganization; for example, during male pronucleus formation or in DNA repair. Together, ATP-dependent chromatin assembly factors, histone chaperones and chromatin modifying enzymes form a “chromatin integrity network” to ensure proper maintenance and propagation of chromatin landscape.
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Affiliation(s)
- Iu. A. Il’ina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”
| | - A. Yu. Konev
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”
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13
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Schoberleitner I, Mutti A, Sah A, Wille A, Gimeno-Valiente F, Piatti P, Kharitonova M, Torres L, López-Rodas G, Liu JJ, Singewald N, Schwarzer C, Lusser A. Role for Chromatin Remodeling Factor Chd1 in Learning and Memory. Front Mol Neurosci 2019; 12:3. [PMID: 30728766 PMCID: PMC6351481 DOI: 10.3389/fnmol.2019.00003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/08/2019] [Indexed: 12/21/2022] Open
Abstract
Precise temporal and spatial regulation of gene expression in the brain is a prerequisite for cognitive processes such as learning and memory. Epigenetic mechanisms that modulate the chromatin structure have emerged as important regulators in this context. While posttranslational modification of histones or the modification of DNA bases have been examined in detail in many studies, the role of ATP-dependent chromatin remodeling factors (ChRFs) in learning- and memory-associated gene regulation has largely remained obscure. Here we present data that implicate the highly conserved chromatin assembly and remodeling factor Chd1 in memory formation and the control of immediate early gene (IEG) response in the hippocampus. We used various paradigms to assess short-and long-term memory in mice bearing a mutated Chd1 gene that gives rise to an N-terminally truncated protein. Our data demonstrate that the Chd1 mutation negatively affects long-term object recognition and short- and long-term spatial memory. We found that Chd1 regulates hippocampal expression of the IEG early growth response 1 (Egr1) and activity-regulated cytoskeleton-associated (Arc) but not cFos and brain derived neurotrophic factor (Bdnf), because the Chd1-mutation led to dysregulation of Egr1 and Arc expression in naive mice and in mice analyzed at different stages of object location memory (OLM) testing. Of note, Chd1 likely regulates Egr1 in a direct manner, because chromatin immunoprecipitation (ChIP) assays revealed enrichment of Chd1 upon stimulation at the Egr1 genomic locus in the hippocampus and in cultured cells. Together these data support a role for Chd1 as a critical regulator of molecular mechanisms governing memory-related processes, and they show that this function involves the N-terminal serine-rich region of the protein.
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Affiliation(s)
- Ines Schoberleitner
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna Mutti
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Anupam Sah
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Centre for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Alexandra Wille
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Francisco Gimeno-Valiente
- Institute of Health Research, INCLIVA, and Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Paolo Piatti
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Maria Kharitonova
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Centre for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Luis Torres
- Institute of Health Research, INCLIVA, and Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Gerardo López-Rodas
- Institute of Health Research, INCLIVA, and Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Jeffrey J. Liu
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Centre for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Christoph Schwarzer
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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14
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Sisakhtnezhad S. In silico analysis of single‐cell RNA sequencing data from 3 and 7 days old mouse spermatogonial stem cells to identify their differentially expressed genes and transcriptional regulators. J Cell Biochem 2018; 119:7556-7569. [DOI: 10.1002/jcb.27066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
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15
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Trixl L, Amort T, Wille A, Zinni M, Ebner S, Hechenberger C, Eichin F, Gabriel H, Schoberleitner I, Huang A, Piatti P, Nat R, Troppmair J, Lusser A. RNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity. Cell Mol Life Sci 2018; 75:1483-1497. [PMID: 29103146 PMCID: PMC5852174 DOI: 10.1007/s00018-017-2700-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 10/17/2017] [Accepted: 10/26/2017] [Indexed: 12/14/2022]
Abstract
Chemical modifications of RNA have been attracting increasing interest because of their impact on RNA fate and function. Therefore, the characterization of enzymes catalyzing such modifications is of great importance. The RNA cytosine methyltransferase NSUN3 was recently shown to generate 5-methylcytosine in the anticodon loop of mitochondrial tRNAMet. Further oxidation of this position is required for normal mitochondrial translation and function in human somatic cells. Because embryonic stem cells (ESCs) are less dependent on oxidative phosphorylation than somatic cells, we examined the effects of catalytic inactivation of Nsun3 on self-renewal and differentiation potential of murine ESCs. We demonstrate that Nsun3-mutant cells show strongly reduced mt-tRNAMet methylation and formylation as well as reduced mitochondrial translation and respiration. Despite the lower dependence of ESCs on mitochondrial activity, proliferation of mutant cells was reduced, while pluripotency marker gene expression was not affected. By contrast, ESC differentiation was skewed towards the meso- and endoderm lineages at the expense of neuroectoderm. Wnt3 was overexpressed in early differentiating mutant embryoid bodies and in ESCs, suggesting that impaired mitochondrial function disturbs normal differentiation programs by interfering with cellular signalling pathways. Interestingly, basal levels of reactive oxygen species (ROS) were not altered in ESCs, but Nsun3 inactivation attenuated induction of mitochondrial ROS upon stress, which may affect gene expression programs upon differentiation. Our findings not only characterize Nsun3 as an important regulator of stem cell fate but also provide a model system to study the still incompletely understood interplay of mitochondrial function with stem cell pluripotency and differentiation.
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Affiliation(s)
- Lukas Trixl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Thomas Amort
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Alexandra Wille
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Manuela Zinni
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Susanne Ebner
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant, and Thoracic Surgery, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Clara Hechenberger
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Felix Eichin
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Hanna Gabriel
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ines Schoberleitner
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Anming Huang
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | | | - Roxana Nat
- Institute for Neuroscience, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Jakob Troppmair
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant, and Thoracic Surgery, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria.
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16
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Rüthemann P, Balbo Pogliano C, Codilupi T, Garajovà Z, Naegeli H. Chromatin remodeler CHD1 promotes XPC-to-TFIIH handover of nucleosomal UV lesions in nucleotide excision repair. EMBO J 2017; 36:3372-3386. [PMID: 29018037 DOI: 10.15252/embj.201695742] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 08/10/2017] [Accepted: 09/08/2017] [Indexed: 12/27/2022] Open
Abstract
Ultraviolet (UV) light induces mutagenic cyclobutane pyrimidine dimers (CPDs) in nucleosomal DNA that is tightly wrapped around histone octamers. How global-genome nucleotide excision repair (GG-NER) processes CPDs despite that this chromatin arrangement is poorly understood. An increased chromatin association of CHD1 (chromodomain helicase DNA-binding 1) upon UV irradiation indicated possible roles of this chromatin remodeler in the UV damage response. Immunoprecipitation of chromatin fragments revealed that CHD1 co-localizes in part with GG-NER factors. Chromatin fractionation showed that the UV-dependent recruitment of CHD1 occurs to UV lesions in histone-assembled nucleosomal DNA and that this CHD1 relocation requires the lesion sensor XPC (xeroderma pigmentosum group C). In situ immunofluorescence analyses further demonstrate that CHD1 facilitates substrate handover from XPC to the downstream TFIIH (transcription factor IIH). Consequently, CHD1 depletion slows down CPD excision and sensitizes cells to UV-induced cytotoxicity. The finding of a CHD1-driven lesion handover between sequentially acting GG-NER factors on nucleosomal histone octamers suggests that chromatin provides a recognition scaffold enabling the detection of a subset of CPDs.
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Affiliation(s)
- Peter Rüthemann
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Chiara Balbo Pogliano
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Tamara Codilupi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Zuzana Garajovà
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
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17
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Hota SK, Bruneau BG. ATP-dependent chromatin remodeling during mammalian development. Development 2017; 143:2882-97. [PMID: 27531948 DOI: 10.1242/dev.128892] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Precise gene expression ensures proper stem and progenitor cell differentiation, lineage commitment and organogenesis during mammalian development. ATP-dependent chromatin-remodeling complexes utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression. These complexes contain diverse subunits that together provide a multitude of functions, from early embryogenesis through cell differentiation and development into various adult tissues. Here, we review the functions of chromatin remodelers and their different subunits during mammalian development. We discuss the mechanisms by which chromatin remodelers function and highlight their specificities during mammalian cell differentiation and organogenesis.
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Affiliation(s)
- Swetansu K Hota
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Department of Pediatrics, University of California, San Francisco, CA 94143, USA Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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18
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Lim CY, Knowles BB, Solter D, Messerschmidt DM. Epigenetic Control of Early Mouse Development. Curr Top Dev Biol 2016; 120:311-60. [PMID: 27475856 DOI: 10.1016/bs.ctdb.2016.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Although the genes sequentially transcribed in the mammalian embryo prior to implantation have been identified, understanding of the molecular processes ensuring this transcription is still in development. The genomes of the sperm and egg are hypermethylated, hence transcriptionally silent. Their union, in the prepared environment of the egg, initiates their epigenetic genomic reprogramming into a totipotent zygote, in which the genome gradually becomes transcriptionally activated. During gametogenesis, sex-specific processes result in sperm and eggs with disparate epigenomes, both of which require drastic reprogramming to establish the totipotent genome of the zygote and the pluripotent inner cell mass of the blastocyst. Herein, we describe the factors, DNA and histone modifications, activation and repression of retrotransposons, and cytoplasmic localizations, known to influence the activation of the mammalian genome at the initiation of new life.
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Affiliation(s)
- C Y Lim
- Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - B B Knowles
- Emerita, The Jackson Laboratory, Bar Harbor, ME, United States; Siriraj Center of Excellence for Stem Cell Research, Mahidol University, Bangkok, Thailand
| | - D Solter
- Siriraj Center of Excellence for Stem Cell Research, Mahidol University, Bangkok, Thailand; Emeritus, Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - D M Messerschmidt
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
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19
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Wille A, Amort T, Singewald N, Sartori SB, Lusser A. Dysregulation of select ATP-dependent chromatin remodeling factors in high trait anxiety. Behav Brain Res 2016; 311:141-146. [PMID: 27208790 DOI: 10.1016/j.bbr.2016.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/18/2016] [Accepted: 05/16/2016] [Indexed: 01/01/2023]
Abstract
Enhanced anxiety is a salient feature of a number of psychiatric disorders including anxiety disorders, trauma-related disorders and depression. Although aberrant expression of various genes has been detected in patients suffering from persistent high anxiety as well as in high anxiety rodent models, the molecular mechanisms responsible for altered transcription regulation have been poorly addressed. Transcription regulation intimately involves the contribution of chromatin modifying processes, such as histone modification and ATP-dependent chromatin remodeling, yet their role in pathological anxiety is not known. Here, we investigated for the first time if altered levels of several ATP-dependent chromatin remodeling factors (ChRFs) and histone deacetylases (HDACs) may be linked to high trait anxiety in mice. While we found protein levels of the ChRFs SNF2H, ATRX, CHD1, CHD3 and CHD5 and of HDACs 1-3 and 6 to be similar in most of the tested brain areas of mice with high (HAB) versus normal (NAB) anxiety-related behavior, we observed distinctly altered regulation of SNF2H in the amygdala, and of CHD3 and CHD5 in the ventral hippocampus. In particular, CHD3 and CHD5 exhibited altered expression of protein but not of mRNA in HAB mice. Since both proteins are components of NuRD-like complexes, these results may indicate an impaired equilibrium between different NuRD-like complexes in the ventral hippocampus. Overall, our data provide novel evidence for localized differences of specific ATP-dependent chromatin remodeling factors in mice with high trait anxiety that may ultimately contribute to altered transcriptional programs resulting in the manifestation of pathological anxiety.
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Affiliation(s)
- Alexandra Wille
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Thomas Amort
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology, Institute Pharmacy, Center for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Simone B Sartori
- Department of Pharmacology and Toxicology, Institute Pharmacy, Center for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
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20
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Boltengagen M, Huang A, Boltengagen A, Trixl L, Lindner H, Kremser L, Offterdinger M, Lusser A. A novel role for the histone acetyltransferase Hat1 in the CENP-A/CID assembly pathway in Drosophila melanogaster. Nucleic Acids Res 2015; 44:2145-59. [PMID: 26586808 PMCID: PMC4797270 DOI: 10.1093/nar/gkv1235] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022] Open
Abstract
The incorporation of CENP-A into centromeric chromatin is an essential prerequisite for kinetochore formation. Yet, the molecular mechanisms governing this process are surprisingly divergent in different organisms. While CENP-A loading mechanisms have been studied in some detail in mammals, there are still large gaps to our understanding of CENP-A/Cid loading pathways in Drosophila. Here, we report on the characterization and delineation of at least three different CENP-A preloading complexes in Drosophila. Two complexes contain the CENP-A chaperones CAL1, FACT and/or Caf1/Rbap48. Notably, we identified a novel complex consisting of the histone acetyltransferase Hat1, Caf1 and CENP-A/H4. We show that Hat1 is required for proper CENP-A loading into chromatin, since knock-down in S2 cells leads to reduced incorporation of newly synthesized CENP-A. In addition, we demonstrate that CENP-A/Cid interacts with the HAT1 complex via an N-terminal region, which is acetylated in cytoplasmic but not in nuclear CENP-A. Since Hat1 is not responsible for acetylation of CENP-A/Cid, these results suggest a histone acetyltransferase activity-independent escort function for Hat1. Thus, our results point toward intriguing analogies between the complex processing pathways of newly synthesized CENP-A and canonical histones.
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Affiliation(s)
- Mark Boltengagen
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anming Huang
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anastasiya Boltengagen
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas Trixl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Martin Offterdinger
- Division of Neurobiochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
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21
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Wille A, Maurer V, Piatti P, Whittle N, Rieder D, Singewald N, Lusser A. Impaired Contextual Fear Extinction Learning is Associated with Aberrant Regulation of CHD-Type Chromatin Remodeling Factors. Front Behav Neurosci 2015; 9:313. [PMID: 26635563 PMCID: PMC4649039 DOI: 10.3389/fnbeh.2015.00313] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/03/2015] [Indexed: 02/04/2023] Open
Abstract
Successful attenuation of fearful memories is a cognitive process requiring initiation of highly coordinated transcription programs. Chromatin-modulating mechanisms such as DNA methylation and histone modifications, including acetylation, are key regulators of these processes. However, knowledge concerning the role of ATP-dependent chromatin remodeling factors (ChRFs) being required for successful fear extinction is lacking. Underscoring the potential importance of these factors that alter histone-DNA contacts within nucleosomes are recent genome-wide association studies linking several ChRFs to various human cognitive and psychiatric disorders. To better understand the role of ChRFs in the brain, and since to date little is known about ChRF expression in the brain, we performed a comprehensive survey of expression levels of 24 ATP-dependent remodelers across different brain areas, and we identified several distinct high molecular weight complexes by chromatographic methods. We next aimed to gain novel insight into the potential regulation of ChRFs in different brain regions in association with normal and impaired fear extinction learning. To this end, we established the 129S1/SvImJ (S1) laboratory mouse strain as a model for compromised contextual fear extinction learning that can be rescued by dietary zinc restriction (ZnR). Using this model along with genetically related but fear extinction-competent 129S6/SvEv (S6) mice as controls, we found that impaired fear extinction in S1 was associated with enhanced ventral hippocampal expression of CHD1 and reduced expression of CHD5 that was normalized following successful rescue of impaired fear extinction. Moreover, a select reduction in CHD3 expression was observed in the ventral hippocampus (vHC) following successful rescue of fear extinction in S1 mice. Taken together, these data provide novel insight into the regulation of specific ChRFs following an impaired cognitive process and its rescue, and they suggest that imbalance of CHD-type remodeler levels, which consequently may lead to changes of transcriptional programs, may be an underlying mechanism involved in impaired fear extinction learning and its therapeutic rescue.
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Affiliation(s)
- Alexandra Wille
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck Innsbruck, Austria
| | - Verena Maurer
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, Institute of Chemistry and Pharmacy, Leopold-Franzens University of Innsbruck Innsbruck, Austria
| | - Paolo Piatti
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck Innsbruck, Austria
| | - Nigel Whittle
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, Institute of Chemistry and Pharmacy, Leopold-Franzens University of Innsbruck Innsbruck, Austria
| | - Dietmar Rieder
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck Innsbruck, Austria
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, Institute of Chemistry and Pharmacy, Leopold-Franzens University of Innsbruck Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck Innsbruck, Austria
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