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Yao W, Hu X, Wang X. Crossing epigenetic frontiers: the intersection of novel histone modifications and diseases. Signal Transduct Target Ther 2024; 9:232. [PMID: 39278916 PMCID: PMC11403012 DOI: 10.1038/s41392-024-01918-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/11/2024] [Accepted: 06/30/2024] [Indexed: 09/18/2024] Open
Abstract
Histone post-translational modifications (HPTMs), as one of the core mechanisms of epigenetic regulation, are garnering increasing attention due to their close association with the onset and progression of diseases and their potential as targeted therapeutic agents. Advances in high-throughput molecular tools and the abundance of bioinformatics data have led to the discovery of novel HPTMs which similarly affect gene expression, metabolism, and chromatin structure. Furthermore, a growing body of research has demonstrated that novel histone modifications also play crucial roles in the development and progression of various diseases, including various cancers, cardiovascular diseases, infectious diseases, psychiatric disorders, and reproductive system diseases. This review defines nine novel histone modifications: lactylation, citrullination, crotonylation, succinylation, SUMOylation, propionylation, butyrylation, 2-hydroxyisobutyrylation, and 2-hydroxybutyrylation. It comprehensively introduces the modification processes of these nine novel HPTMs, their roles in transcription, replication, DNA repair and recombination, metabolism, and chromatin structure, as well as their involvement in promoting the occurrence and development of various diseases and their clinical applications as therapeutic targets and potential biomarkers. Moreover, this review provides a detailed overview of novel HPTM inhibitors targeting various targets and their emerging strategies in the treatment of multiple diseases while offering insights into their future development prospects and challenges. Additionally, we briefly introduce novel epigenetic research techniques and their applications in the field of novel HPTM research.
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Affiliation(s)
- Weiyi Yao
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Xinting Hu
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Taishan Scholars Program of Shandong Province, Jinan, Shandong, 250021, China.
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2
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Selvam K, Wyrick JJ, Parra MA. DNA Repair in Nucleosomes: Insights from Histone Modifications and Mutants. Int J Mol Sci 2024; 25:4393. [PMID: 38673978 PMCID: PMC11050016 DOI: 10.3390/ijms25084393] [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: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
DNA repair pathways play a critical role in genome stability, but in eukaryotic cells, they must operate to repair DNA lesions in the compact and tangled environment of chromatin. Previous studies have shown that the packaging of DNA into nucleosomes, which form the basic building block of chromatin, has a profound impact on DNA repair. In this review, we discuss the principles and mechanisms governing DNA repair in chromatin. We focus on the role of histone post-translational modifications (PTMs) in repair, as well as the molecular mechanisms by which histone mutants affect cellular sensitivity to DNA damage agents and repair activity in chromatin. Importantly, these mechanisms are thought to significantly impact somatic mutation rates in human cancers and potentially contribute to carcinogenesis and other human diseases. For example, a number of the histone mutants studied primarily in yeast have been identified as candidate oncohistone mutations in different cancers. This review highlights these connections and discusses the potential importance of DNA repair in chromatin to human health.
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Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Michael A. Parra
- Department of Chemistry, Susquehanna University, Selinsgrove, PA 17870, USA
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3
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Lian T, Guan R, Zhou BR, Bai Y. Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα. Nat Struct Mol Biol 2024; 31:633-643. [PMID: 38267599 DOI: 10.1038/s41594-023-01189-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 11/23/2023] [Indexed: 01/26/2024]
Abstract
Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA targets remains elusive. Here we report the structures of the nucleosome containing the mouse genomic CX3CR1 enhancer DNA and its complexes with PU.1 alone and with both PU.1 and the C/EBPα DNA binding domain. Our structures reveal that PU.1 binds the DNA motif at the exit linker, shifting 17 bp of DNA into the core region through interactions with H2A, unwrapping ~20 bp of nucleosomal DNA. C/EBPα binding, aided by PU.1's repositioning, unwraps ~25 bp of entry DNA. The PU.1 Q218H mutation, linked to acute myeloid leukemia, disrupts PU.1-H2A interactions. PU.1 and C/EBPα jointly displace linker histone H1 and open the H1-condensed nucleosome array. Our study unveils how two pioneer factors can work cooperatively to open closed chromatin by altering DNA positioning in the nucleosome.
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Affiliation(s)
- Tengfei Lian
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ruifang Guan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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4
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Suganuma T, Workman JL. Chromatin balances cell redox and energy homeostasis. Epigenetics Chromatin 2023; 16:46. [PMID: 38017471 PMCID: PMC10683155 DOI: 10.1186/s13072-023-00520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Chromatin plays a central role in the conversion of energy in cells: alteration of chromatin structure to make DNA accessible consumes energy, and compaction of chromatin preserves energy. Alteration of chromatin structure uses energy sources derived from carbon metabolism such as ATP and acetyl-CoA; conversely, chromatin compaction and epigenetic modification feedback to metabolism and energy homeostasis by controlling gene expression and storing metabolites. Coordination of these dual chromatin events must be flexibly modulated in response to environmental changes such as during development and exposure to stress. Aging also alters chromatin structure and the coordination of metabolism, chromatin dynamics, and other cell processes. Noncoding RNAs and other RNA species that associate directly with chromatin or with chromatin modifiers contribute to spatiotemporal control of transcription and energy conversion. The time required for generating the large amounts of RNAs and chromatin modifiers observed in super-enhancers may be critical for regulation of transcription and may be impacted by aging. Here, taking into account these factors, we review alterations of chromatin that are fundamental to cell responses to metabolic changes due to stress and aging to maintain redox and energy homeostasis. We discuss the relationship between spatiotemporal control of energy and chromatin function, as this emerging concept must be considered to understand how cell homeostasis is maintained.
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Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA.
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
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5
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Lian T, Guan R, Zhou BR, Bai Y. Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554718. [PMID: 37790476 PMCID: PMC10542146 DOI: 10.1101/2023.08.25.554718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA targets remain elusive. Here we report the structures of the nucleosome containing the mouse genomic CX3CR1 enhancer DNA and its complexes with PU.1 alone and with both PU.1 and the C/EBPα DNA binding domain. Our structures reveal that PU.1 binds the DNA motif at the exit linker, shifting 17 bp of DNA into the core region through interactions with H2A, unwrapping ~20 bp of nucleosomal DNA. C/EBPα binding, aided by PU.1's repositioning, unwraps ~25 bp entry DNA. The PU.1 Q218H mutation, linked to acute myeloid leukemia, disrupts PU.1-H2A interactions. PU.1 and C/EBPα jointly displace linker histone H1 and open the H1-condensed nucleosome array. Our study unveils how two pioneer factors can work cooperatively to open closed chromatin by altering DNA positioning in the nucleosome.
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Affiliation(s)
- Tengfei Lian
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- These authors equally contributed to this work
| | - Ruifang Guan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- These authors equally contributed to this work
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Hong ZZ, Yu RR, Zhang X, Webb AM, Burge NL, Poirier MG, Ottesen JJ. Development of Convergent Hybrid Phase Ligation for Efficient and Convenient Total Synthesis of Proteins. Pept Sci (Hoboken) 2023; 115:e24323. [PMID: 37692919 PMCID: PMC10488053 DOI: 10.1002/pep2.24323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/16/2023] [Indexed: 09/12/2023]
Abstract
Simple and efficient total synthesis of homogeneous and chemically modified protein samples remains a significant challenge. Here, we report development of a convergent hybrid phase native chemical ligation (CHP-NCL) strategy for facile preparation of proteins. In this strategy, proteins are split into ~100-residue blocks, and each block is assembled on solid support from synthetically accessible peptide fragments before ligated together into full-length protein in solution. With the new method, we increase the yield of CENP-A synthesis by 2.5-fold compared to the previous hybrid phase ligation approach. We further extend the new strategy to the total chemical synthesis of 212-residue linker histone H1.2 in unmodified, phosphorylated, and citrullinated forms, each from eight peptide segments with only one single purification. We demonstrate that fully synthetic H1.2 replicates the binding interactions of linker histones to intact mononucleosomes, as a proxy for the essential function of linker histones in the formation and regulation of higher order chromatin structure.
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Affiliation(s)
- Ziyong Z. Hong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Ruixuan R. Yu
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
| | - Xiaoyu Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Allison M. Webb
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Nathaniel L. Burge
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
| | - Michael G. Poirier
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
- Department of Physics, Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Jennifer J. Ottesen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
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7
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Guan R, Lian T, Zhou BR, Wheeler D, Bai Y. Structural mechanism of LIN28B nucleosome targeting by OCT4. Mol Cell 2023; 83:1970-1982.e6. [PMID: 37327775 PMCID: PMC10276192 DOI: 10.1016/j.molcel.2023.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/31/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin.
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Affiliation(s)
- Ruifang Guan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tengfei Lian
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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8
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Suzuki S, Nakajima Y, Kamo N, Osakabe A, Okamoto A, Hayashi G, Murakami H. Thiocholine-Mediated One-Pot Peptide Ligation and Desulfurization. Molecules 2023; 28:molecules28093655. [PMID: 37175065 PMCID: PMC10179797 DOI: 10.3390/molecules28093655] [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: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Thiol catalysts are essential in native chemical ligation (NCL) to increase the reaction efficiency. In this paper, we report the use of thiocholine in chemical protein synthesis, including NCL-based peptide ligation and metal-free desulfurization. Evaluation of thiocholine peptide thioester in terms of NCL and hydrolysis kinetics revealed its practical utility, which was comparable to that of other alkyl thioesters. Importantly, thiocholine showed better reactivity as a thiol additive in desulfurization, which is often used in chemical protein synthesis to convert Cys residues to more abundant Ala residues. Finally, we achieved chemical synthesis of two differently methylated histone H3 proteins via one-pot NCL and desulfurization with thiocholine.
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Affiliation(s)
- Sae Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yuya Nakajima
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Naoki Kamo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akihisa Osakabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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9
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Chio US, Rechiche O, Bryll AR, Zhu J, Leith EM, Feldman JL, Peterson CL, Tan S, Armache JP. Cryo-EM structure of the human Sirtuin 6-nucleosome complex. SCIENCE ADVANCES 2023; 9:eadf7586. [PMID: 37058572 PMCID: PMC10104460 DOI: 10.1126/sciadv.adf7586] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo-electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56.
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Affiliation(s)
- Un Seng Chio
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94152, USA
| | - Othman Rechiche
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Alysia R. Bryll
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Medical Scientist Training Program, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jiang Zhu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Erik M. Leith
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jessica L. Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jean-Paul Armache
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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10
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Chio US, Rechiche O, Bryll AR, Zhu J, Feldman JL, Peterson CL, Tan S, Armache JP. Cryo-EM structure of the human Sirtuin 6-nucleosome complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533206. [PMID: 36993468 PMCID: PMC10055229 DOI: 10.1101/2023.03.17.533206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo-electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56. Teaser The structure of the SIRT6 deacetylase/nucleosome complex suggests how the enzyme acts on both histone H3 K9 and K56 residues.
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Affiliation(s)
- Un Seng Chio
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94152, USA
| | - Othman Rechiche
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Alysia R. Bryll
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Medical Scientist Training Program, University of Massachusetts Medical School, Worcester, MA 01605
| | - Jiang Zhu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jessica L. Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jean-Paul Armache
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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11
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Funamoto M, Imanishi M, Tsuchiya K, Ikeda Y. Roles of histone acetylation sites in cardiac hypertrophy and heart failure. Front Cardiovasc Med 2023; 10:1133611. [PMID: 37008337 PMCID: PMC10050342 DOI: 10.3389/fcvm.2023.1133611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/24/2023] [Indexed: 03/17/2023] Open
Abstract
Heart failure results from various physiological and pathological stimuli that lead to cardiac hypertrophy. This pathological process is common in several cardiovascular diseases and ultimately leads to heart failure. The development of cardiac hypertrophy and heart failure involves reprogramming of gene expression, a process that is highly dependent on epigenetic regulation. Histone acetylation is dynamically regulated by cardiac stress. Histone acetyltransferases play an important role in epigenetic remodeling in cardiac hypertrophy and heart failure. The regulation of histone acetyltransferases serves as a bridge between signal transduction and downstream gene reprogramming. Investigating the changes in histone acetyltransferases and histone modification sites in cardiac hypertrophy and heart failure will provide new therapeutic strategies to treat these diseases. This review summarizes the association of histone acetylation sites and histone acetylases with cardiac hypertrophy and heart failure, with emphasis on histone acetylation sites.
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Affiliation(s)
- Masafumi Funamoto
- Department of Pharmacology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
- Correspondence: Masafumi Funamoto Yasumasa Ikeda
| | - Masaki Imanishi
- Department of Medical Pharmacology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Koichiro Tsuchiya
- Department of Medical Pharmacology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yasumasa Ikeda
- Department of Pharmacology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
- Correspondence: Masafumi Funamoto Yasumasa Ikeda
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12
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Donovan BT, Luo Y, Meng Z, Poirier MG. The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics. Nucleic Acids Res 2023; 51:1139-1153. [PMID: 36688297 PMCID: PMC9943653 DOI: 10.1093/nar/gkac1267] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 11/27/2022] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
Transcription factors (TF) require access to target sites within nucleosomes to initiate transcription. The target site position within the nucleosome significantly influences TF occupancy, but how is not quantitatively understood. Using ensemble and single-molecule fluorescence measurements, we investigated the targeting and occupancy of the transcription factor, Gal4, at different positions within the nucleosome. We observe a dramatic decrease in TF occupancy to sites extending past 30 base pairs (bp) into the nucleosome which cannot be explained by changes in the TF dissociation rate or binding site orientation. Instead, the nucleosome unwrapping free energy landscape is the primary determinant of Gal4 occupancy by reducing the Gal4 binding rate. The unwrapping free energy landscape defines two distinct regions of accessibility and kinetics with a boundary at 30 bp into the nucleosome where the inner region is over 100-fold less accessible. The Gal4 binding rate in the inner region no longer depends on its concentration because it is limited by the nucleosome unwrapping rate, while the frequency of nucleosome rewrapping decreases because Gal4 exchanges multiple times before the nucleosome rewraps. Our findings highlight the importance of the nucleosome unwrapping free energy landscape on TF occupancy and dynamics that ultimately influences transcription initiation.
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Affiliation(s)
- Benjamin T Donovan
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi Luo
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Zhiyuan Meng
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43214, USA
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13
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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14
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Frigerio C, Di Nisio E, Galli M, Colombo CV, Negri R, Clerici M. The Chromatin Landscape around DNA Double-Strand Breaks in Yeast and Its Influence on DNA Repair Pathway Choice. Int J Mol Sci 2023; 24:ijms24043248. [PMID: 36834658 PMCID: PMC9967470 DOI: 10.3390/ijms24043248] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/21/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
DNA double-strand breaks (DSBs) are harmful DNA lesions, which elicit catastrophic consequences for genome stability if not properly repaired. DSBs can be repaired by either non-homologous end joining (NHEJ) or homologous recombination (HR). The choice between these two pathways depends on which proteins bind to the DSB ends and how their action is regulated. NHEJ initiates with the binding of the Ku complex to the DNA ends, while HR is initiated by the nucleolytic degradation of the 5'-ended DNA strands, which requires several DNA nucleases/helicases and generates single-stranded DNA overhangs. DSB repair occurs within a precisely organized chromatin environment, where the DNA is wrapped around histone octamers to form the nucleosomes. Nucleosomes impose a barrier to the DNA end processing and repair machinery. Chromatin organization around a DSB is modified to allow proper DSB repair either by the removal of entire nucleosomes, thanks to the action of chromatin remodeling factors, or by post-translational modifications of histones, thus increasing chromatin flexibility and the accessibility of repair enzymes to the DNA. Here, we review histone post-translational modifications occurring around a DSB in the yeast Saccharomyces cerevisiae and their role in DSB repair, with particular attention to DSB repair pathway choice.
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Affiliation(s)
- Chiara Frigerio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Elena Di Nisio
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Michela Galli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Chiara Vittoria Colombo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, 00185 Rome, Italy
- Correspondence: (R.N.); (M.C.)
| | - Michela Clerici
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
- Correspondence: (R.N.); (M.C.)
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15
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Yang Y, Yan C, Yu L, Zhang X, Shang J, Fan J, Zhang R, Ren J, Duan X. The star target in SLE: IL-17. Inflamm Res 2023; 72:313-328. [PMID: 36538077 DOI: 10.1007/s00011-022-01674-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/30/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The purpose of this review is to discuss the significance of IL-17 in SLE and the potential of IL-17-targeted therapy. BACKGROUND Systemic lupus erythematosus (SLE) is an autoimmune disease that can affect many organs and tissues throughout the body. It is characterized by overactive B and T cells and loss of immune tolerance to autoantigens. Interleukin-17 (IL-17) is a cytokine that promotes inflammation and has been implicated in the pathogenesis of several autoimmune diseases as well as inflammatory diseases. In in vitro cellular experiments in lupus susceptible mice or SLE patients, there is substantial evidence that IL-17 is a highly promising therapeutic target. METHODS We searched papers from PubMed database using the search terms, such as interleukin-17, systemic lupus erythematosus, treatment targets, T cells, lupus nephritis, and other relevant terms. RESULTS We discuss in this paper the molecular mechanisms of IL-17 expression, Th17 cell proliferation, and the relationship between IL-17 and Th17. The significance of IL-17 in SLE and the potential of IL-17-targeted therapy are further discussed in detail. CONCLUSION IL-17 has a very high potential for the development as a star target in SLE.
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Affiliation(s)
- Yi Yang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chen Yan
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Le Yu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiuling Zhang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jingjing Shang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jie Fan
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Rongwei Zhang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jie Ren
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xinwang Duan
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Nanchang University, Nanchang, China.
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16
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Guan R, Lian T, Zhou BR, Bai Y. Structural mechanism of LIN28B nucleosome targeting by OCT4 for pluripotency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522631. [PMID: 36789416 PMCID: PMC9928048 DOI: 10.1101/2023.01.03.522631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA motifs. Two use their POUS domains by forming extensive hydrogen bonds. The other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Our study suggests a mechanism whereby OCT4s target the LIN28B nucleosome by forming multivalent interactions with nucleosomal motifs, unwrapping nucleosomal DNA, evicting H1, and cooperatively open closed chromatin to initiate cell reprogramming.
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Affiliation(s)
- Ruifang Guan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.,These authors equally contributed to this work
| | - Tengfei Lian
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.,These authors equally contributed to this work
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.,Correspondence:
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17
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Hammonds EF, Morrison EA. Nucleosome Core Particle Reconstitution with Recombinant Histones and Widom 601 DNA. Methods Mol Biol 2023; 2599:177-190. [PMID: 36427150 DOI: 10.1007/978-1-0716-2847-8_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Reconstitution of nucleosomes from recombinant histones and DNA is a widely used tool for studying nucleosome structure, dynamics, and interactions. Preparation of reconstituted nucleosomes allows for the study of nucleosomes with defined compositions. Here, we describe methods for refolding recombinant human histones, reconstituting nucleosome core particles with 147 bp Widom 601 DNA, and purification via sucrose gradient.
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Affiliation(s)
- Erin F Hammonds
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Emma A Morrison
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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18
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Afonso CF, Marques MC, António JPM, Cordeiro C, Gois PMP, Cal PMSD, Bernardes GJL. Cysteine-Assisted Click-Chemistry for Proximity-Driven, Site-Specific Acetylation of Histones. Angew Chem Int Ed Engl 2022; 61:e202208543. [PMID: 36124857 PMCID: PMC9828500 DOI: 10.1002/anie.202208543] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 01/12/2023]
Abstract
Post-translational modifications of histones are essential in the regulation of chromatin structure and function. Among these modifications, lysine acetylation is one of the most established. Earlier studies relied on the use of chromatin containing heterogeneous mixtures of histones acetylated at multiple sites. Differentiating the individual contribution of single acetylation events towards chromatin regulation is thus of great relevance. However, it is difficult to access homogeneous samples of histones, with a single acetylation, in sufficient quantities for such studies. By engineering histone H3 with a cysteine in proximity of the lysine of interest, we demonstrate that conjugation with maleimide-DBCO followed by a strain-promoted alkyne-azide cycloaddition reaction results in the acetylation of a single lysine in a controlled, site-specific manner. The chemical precision offered by our click-to-acetylate approach will facilitate access to and the study of acetylated histones.
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Affiliation(s)
- Cláudia F. Afonso
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - Marta C. Marques
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - João P. M. António
- Research Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | - Carlos Cordeiro
- Laboratório de FT-ICR e Espectrometria de Massa EstruturalFaculdade de CiênciasUniversidade de LisboaCampo Grande1749-016LisboaPortugal
| | - Pedro M. P. Gois
- Research Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | - Pedro M. S. D. Cal
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - Gonçalo J. L. Bernardes
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal,Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
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19
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HIV-1 Preintegration Complex Preferentially Integrates the Viral DNA into Nucleosomes Containing Trimethylated Histone 3-Lysine 36 Modification and Flanking Linker DNA. J Virol 2022; 96:e0101122. [PMID: 36094316 PMCID: PMC9517705 DOI: 10.1128/jvi.01011-22] [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] [Indexed: 01/11/2023] Open
Abstract
HIV-1 DNA is preferentially integrated into chromosomal hot spots by the preintegration complex (PIC). To understand the mechanism, we measured the DNA integration activity of PICs-extracted from infected cells-and intasomes, biochemically assembled PIC substructures using a number of relevant target substrates. We observed that PIC-mediated integration into human chromatin is preferred compared to genomic DNA. Surprisingly, nucleosomes lacking histone modifications were not preferred integration compared to the analogous naked DNA. Nucleosomes containing the trimethylated histone 3 lysine 36 (H3K36me3), an epigenetic mark linked to active transcription, significantly stimulated integration, but the levels remained lower than the naked DNA. Notably, H3K36me3-modified nucleosomes with linker DNA optimally supported integration mediated by the PIC but not by the intasome. Interestingly, optimal intasome-mediated integration required the cellular cofactor LEDGF. Unexpectedly, LEDGF minimally affected PIC-mediated integration into naked DNA but blocked integration into nucleosomes. The block for the PIC-mediated integration was significantly relieved by H3K36me3 modification. Mapping the integration sites in the preferred substrates revealed that specific features of the nucleosome-bound DNA are preferred for integration, whereas integration into naked DNA was random. Finally, biochemical and genetic studies demonstrate that DNA condensation by the H1 protein dramatically reduces integration, providing further evidence that features inherent to the open chromatin are preferred for HIV-1 integration. Collectively, these results identify the optimal target substrate for HIV-1 integration, report a mechanistic link between H3K36me3 and integration preference, and importantly, reveal distinct mechanisms utilized by the PIC for integration compared to the intasomes. IMPORTANCE HIV-1 infection is dependent on integration of the viral DNA into the host chromosomes. The preintegration complex (PIC) containing the viral DNA, the virally encoded integrase (IN) enzyme, and other viral/host factors carries out HIV-1 integration. HIV-1 integration is not dependent on the target DNA sequence, and yet the viral DNA is selectively inserted into specific "hot spots" of human chromosomes. A growing body of literature indicates that structural features of the human chromatin are important for integration targeting. However, the mechanisms that guide the PIC and enable insertion of the PIC-associated viral DNA into specific hot spots of the human chromosomes are not fully understood. In this study, we describe a biochemical mechanism for the preference of the HIV-1 DNA integration into open chromatin. Furthermore, our study defines a direct role for the histone epigenetic mark H3K36me3 in HIV-1 integration preference and identify an optimal substrate for HIV-1 PIC-mediated viral DNA integration.
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20
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Millán-Zambrano G, Burton A, Bannister AJ, Schneider R. Histone post-translational modifications - cause and consequence of genome function. Nat Rev Genet 2022; 23:563-580. [PMID: 35338361 DOI: 10.1038/s41576-022-00468-7] [Citation(s) in RCA: 327] [Impact Index Per Article: 163.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2022] [Indexed: 12/16/2022]
Abstract
Much has been learned since the early 1960s about histone post-translational modifications (PTMs) and how they affect DNA-templated processes at the molecular level. This understanding has been bolstered in the past decade by the identification of new types of histone PTM, the advent of new genome-wide mapping approaches and methods to deposit or remove PTMs in a locally and temporally controlled manner. Now, with the availability of vast amounts of data across various biological systems, the functional role of PTMs in important processes (such as transcription, recombination, replication, DNA repair and the modulation of genomic architecture) is slowly emerging. This Review explores the contribution of histone PTMs to the regulation of genome function by discussing when these modifications play a causative (or instructive) role in DNA-templated processes and when they are deposited as a consequence of such processes, to reinforce and record the event. Important advances in the field showing that histone PTMs can exert both direct and indirect effects on genome function are also presented.
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Affiliation(s)
- Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Adam Burton
- Institute of Epigenetics and Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Center Munich, Munich, Germany.
- Faculty of Biology, Ludwig Maximilian University (LMU) of Munich, Munich, Germany.
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21
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Isbel L, Grand RS, Schübeler D. Generating specificity in genome regulation through transcription factor sensitivity to chromatin. Nat Rev Genet 2022; 23:728-740. [PMID: 35831531 DOI: 10.1038/s41576-022-00512-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 12/11/2022]
Abstract
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA sequence motifs embedded in chromatin. Understanding how motifs are accessed in chromatin is crucial to comprehend differential transcriptional responses and the phenotypic impact of sequence variation. Chromatin obstacles to TF binding range from DNA methylation to restriction of DNA access by nucleosomes depending on their position, composition and modification. In vivo and in vitro approaches now enable the study of TF binding in chromatin at unprecedented resolution. Emerging insights suggest that TFs vary in their ability to navigate chromatin states. However, it remains challenging to link binding and transcriptional outcomes to molecular characteristics of TFs or the local chromatin substrate. Here, we discuss our current understanding of how TFs access DNA in chromatin and novel techniques and directions towards a better understanding of this critical step in genome regulation.
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Affiliation(s)
- Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,Faculty of Sciences, University of Basel, Basel, Switzerland.
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22
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The deacetylase SIRT2 contributes to autoimmune disease pathogenesis by modulating IL-17A and IL-2 transcription. Cell Mol Immunol 2022; 19:738-750. [PMID: 35523941 DOI: 10.1038/s41423-022-00874-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/13/2022] [Indexed: 12/14/2022] Open
Abstract
Aberrant IL-17A expression together with reduced IL-2 production by effector CD4+ T cells contributes to the pathogenesis of systemic lupus erythematosus (SLE). Here, we report that Sirtuin 2 (SIRT2), a member of the family of NAD+-dependent histone deacetylases, suppresses IL-2 production by CD4+ T cells while promoting their differentiation into Th17 cells. Mechanistically, we show that SIRT2 is responsible for the deacetylation of p70S6K, activation of the mTORC1/HIF-1α/RORγt pathway and induction of Th17-cell differentiation. Additionally, SIRT2 was shown to be responsible for the deacetylation of c-Jun and histones at the Il-2 gene, resulting in decreased IL-2 production. We found that the transcription factor inducible cAMP early repressor (ICER), which is overexpressed in T cells from people with SLE and lupus-prone mice, bound directly to the Sirt2 promoter and promoted its transcription. AK-7, a SIRT2 inhibitor, limited the ability of adoptively transferred antigen-specific CD4+ T cells to cause autoimmune encephalomyelitis in mice and limited disease in lupus-prone MRL/lpr mice. Finally, CD4+ T cells from SLE patients exhibited increased expression of SIRT2, and pharmacological inhibition of SIRT2 in primary CD4+ T cells from patients with SLE attenuated the ability of these cells to differentiate into Th17 cells and promoted the generation of IL-2-producing T cells. Collectively, these results suggest that SIRT2-mediated deacetylation is essential in the aberrant expression of IL-17A and IL-2 and that SIRT2 may be a promising molecular target for new SLE therapies.
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23
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Dong J, He J, Zhang Z, Zhang W, Li Y, Li D, Xie H, Zuo W, Tang J, Zeng Z, Cai W, Lai L, Yun M, Shen L, Yin L, Tang D, Dai Y. Identification of lysine acetylome of oral squamous cell carcinoma by label-free quantitative proteomics. J Proteomics 2022; 262:104598. [PMID: 35489685 DOI: 10.1016/j.jprot.2022.104598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
Abstract
Lysine acetylation (Kac) on histone promotes relaxation of the chromatin conformation and favors gene transcription to regulate oncogenesis, whereas the total acetylation profiling of oral squamous cell carcinoma (OSCC) is unknown. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was utilised to investigate lysine acetylation features of tumor tissues and adjacent normal tissues from 9 patients with OCSS. 282 upregulated Kac sites in 234 proteins and 235 downregulated Kac sites in 162 proteins between OSCC tissues and paired adjacent normal tissues were identified. Different acetylation proteins (DAPs) were analyzed through KEGG-based and MCODE. These DAPs are enriched in the ribosome biogenesis pathway. Survival Analysis of hub genes with TCGA database was performed. In addition, IPA software was used to explore the connection between 9 core DAPs (RPS3, RPL24, RPL19, EIF4A2, RPL12, MYBPC1, RPS6, ARCN1, and TMEM9) and the different expression of KATs and KDACs identified in our proteomic. The study is the first comparative study of Kac modification on oral squamous cell carcinoma. We propose to put forward the hypothesis that the dysfunction of ribosome biogenesis caused by the change of Lysine acetylation, especially downregulated acetylation on RPS6 and RPS3 may associated with the pathogenesis of OSCC. SIGNIFICANCE: The study is the first comparative study of Kac modification on oral squamous cell carcinoma through LC-MS/MS-based modified proteomic. These DAPs are high enriched in the ribosome biogenesis pathway. Used MCODE and survival analysis, 9 core DAPs (RPS3, RPL24, RPL19, EIF4A2, RPL12, MYBPC1, RPS6, ARCN1, and TMEM9) were screened. IPA software was used to explore the connection between 9 core DAPs and the different expression of KATs and KDACs identified in our proteomic. In addition, we propose to put forward the hypothesis that the dysfunction of ribosome biogenesis caused by the change of Lysine acetylation, especially downregulated acetylation on RPS6 and RPS3 may associated with the pathogenesis of OSCC.
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Affiliation(s)
- Jingjing Dong
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China; Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Jingquan He
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Zeyu Zhang
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Wei Zhang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Yixi Li
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Dandan Li
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Hongliang Xie
- Stomatology Department, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Wenxin Zuo
- Stomatology Department, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Jianming Tang
- Stomatology Department, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Zhipeng Zeng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Wanxia Cai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Liusheng Lai
- Guangxi Key Laboratory of Metabolic Diseases Research, Affiliated No. 924 Hospital, Southern Medical University, Guilin 541002, Guangxi, China
| | - Manhua Yun
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Lingjun Shen
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Lianghong Yin
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China.
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China.
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China; Guangxi Key Laboratory of Metabolic Diseases Research, Affiliated No. 924 Hospital, Southern Medical University, Guilin 541002, Guangxi, China.
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24
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Jing Y, Li X, Liu Z, Li XD. Roles of Negatively Charged Histone Lysine Acylations in Regulating Nucleosome Structure and Dynamics. Front Mol Biosci 2022; 9:899013. [PMID: 35547393 PMCID: PMC9081332 DOI: 10.3389/fmolb.2022.899013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 01/08/2023] Open
Abstract
The nucleosome, the basic repeating unit of chromatin, is a dynamic structure that consists of DNA and histones. Insights derived from biochemical and biophysical approaches have revealed that histones posttranslational modifications (PTMs) are key regulators of nucleosome structure and dynamics. Mounting evidence suggests that the newly identified negatively charged histone lysine acylations play significant roles in altering nucleosome and chromatin dynamics, subsequently affecting downstream DNA-templated processes including gene transcription and DNA damage repair. Here, we present an overview of the dynamic changes of nucleosome and chromatin structures in response to negatively charged histone lysine acylations, including lysine malonylation, lysine succinylation, and lysine glutarylation.
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Affiliation(s)
- Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen, China
- *Correspondence: Xiang David Li, ; Yihang Jing,
| | - Xin Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen, China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Xiang David Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen, China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
- *Correspondence: Xiang David Li, ; Yihang Jing,
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25
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Burge N, Thuma JL, Hong ZZ, Jamison KB, Ottesen JJ, Poirier MG. H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes. Biochemistry 2022; 61:625-638. [PMID: 35377618 PMCID: PMC9022651 DOI: 10.1021/acs.biochem.2c00001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/24/2022] [Indexed: 12/25/2022]
Abstract
The linker histone H1 is a highly prevalent protein that compacts chromatin and regulates DNA accessibility and transcription. However, the mechanisms behind H1 regulation of transcription factor (TF) binding within nucleosomes are not well understood. Using in vitro fluorescence assays, we positioned fluorophores throughout human H1 and the nucleosome, then monitored the distance changes between H1 and the histone octamer, H1 and nucleosomal DNA, or nucleosomal DNA and the histone octamer to monitor the H1 movement during TF binding. We found that H1 remains bound to the nucleosome dyad, while the C terminal domain (CTD) releases the linker DNA during nucleosome partial unwrapping and TF binding. In addition, mutational studies revealed that a small 16 amino acid region at the beginning of the H1 CTD is largely responsible for altering nucleosome wrapping and regulating TF binding within nucleosomes. We then investigated physiologically relevant post-translational modifications (PTMs) in human H1 by preparing fully synthetic H1 using convergent hybrid phase native chemical ligation. Both individual PTMs and combinations of phosphorylation and citrullination of H1 had no detectable influence on nucleosome binding and nucleosome wrapping, and had only a minor impact on H1 regulation of TF occupancy within nucleosomes. This suggests that these H1 PTMs function by other mechanisms. Our results highlight the importance of the H1 CTD, in particular, the first 16 amino acids, in regulating nucleosome linker DNA dynamics and TF binding within the nucleosome.
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Affiliation(s)
- Nathaniel
L. Burge
- Ohio
State Biochemistry Program, The Ohio State
University, Columbus, Ohio 43210, United States
| | - Jenna L. Thuma
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ziyong Z. Hong
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Kevin B. Jamison
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jennifer J. Ottesen
- Ohio
State Biochemistry Program, The Ohio State
University, Columbus, Ohio 43210, United States
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Michael G. Poirier
- Ohio
State Biochemistry Program, The Ohio State
University, Columbus, Ohio 43210, United States
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
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26
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Histone Chaperone Nrp1 Mutation Affects the Acetylation of H3K56 in Tetrahymena thermophila. Cells 2022; 11:cells11030408. [PMID: 35159218 PMCID: PMC8833950 DOI: 10.3390/cells11030408] [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: 11/23/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Histone modification and nucleosome assembly are mainly regulated by various histone-modifying enzymes and chaperones. The roles of histone-modification enzymes have been well analyzed, but the molecular mechanism of histone chaperones in histone modification and nucleosome assembly is incompletely understood. We previously found that the histone chaperone Nrp1 is localized in the micronucleus (MIC) and the macronucleus (MAC) and involved in the chromatin stability and nuclear division of Tetrahymena thermophila. In the present work, we found that truncated C-terminal mutant HA-Nrp1TrC abnormally localizes in the cytoplasm. The truncated-signal-peptide mutants HA-Nrp1TrNLS1 and HA-Nrp1TrNLS2 are localized in the MIC and MAC. Overexpression of Nrp1TrNLS1 inhibited cellular proliferation and disrupted micronuclear mitosis during the vegetative growth stage. During sexual development, Nrp1TrNLS1 overexpression led to abnormal bouquet structures and meiosis arrest. Furthermore, Histone H3 was not transported into the nucleus; instead, it formed an abnormal speckled cytoplastic distribution in the Nrp1TrNLS1 mutants. The acetylation level of H3K56 in the mutants also decreased, leading to significant changes in the transcription of the genome of the Nrp1TrNLS1 mutants. The histone chaperone Nrp1 regulates the H3 nuclear import and acetylation modification of H3K56 and affects chromatin stability and genome transcription in Tetrahymena.
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27
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Jing Y, Tian G, Qin X, Liu Z, Li XD. Lysine succinylation on non-histone chromosomal protein HMG-17 (HMGN2) regulates nucleosomal DNA accessibility by disrupting the HMGN2-nucleosome association. RSC Chem Biol 2021; 2:1257-1262. [PMID: 34458839 PMCID: PMC8341127 DOI: 10.1039/d1cb00070e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 02/01/2023] Open
Abstract
Lysine succinylation (Ksucc) is a novel posttranslational modification that frequently occurs on chromatin proteins including histones and non-histone proteins. Histone Ksucc affects nucleosome dynamics by increasing the DNA unwrapping rate and accessibility. However, very little is known about the regulation and functions of Ksucc located on non-histone chromosomal proteins. Here, we site-specifically installed a succinyl lysine analogue (Kcsucc) onto the non-histone chromosomal protein HMG-17 (HMGN2) to mimic the natural succinylated protein. We found that the incorporation of Kcsucc into HMGN2 at the K30 site (HMGN2Kc30succ), which is located within the nucleosome-binding domain (NBD), leads to significantly decreased HMGN2 binding to the mononucleosome. HMGN2Kc30succ also increased the nucleosomal DNA accessibility by promoting nucleosomal DNA unwrapping in the entry/exit region. This study reveals a novel mechanism of non-histone protein succinylation on altering chromatin recruitment, which can further affect nucleosome and chromatin dynamics. Succinylated HMGN2, prepared by a ‘thiol–ene reaction’, disrupted the association of HMGN2 with the nucleosome and increased nucleosomal DNA accessibility.![]()
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Affiliation(s)
- Yihang Jing
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Xiaoyu Qin
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
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28
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Systematic Analysis of the Lysine Crotonylome and Multiple Posttranslational Modification Analysis (Acetylation, Succinylation, and Crotonylation) in Candida albicans. mSystems 2021; 6:6/1/e01316-20. [PMID: 33500332 PMCID: PMC7842366 DOI: 10.1128/msystems.01316-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Candida albicans is an opportunistic pathogen that causes lethal fungal infections in immunocompromised patients. Lysine crotonylation is a newly discovered PTM (posttranslational modification) epigenetic type that may play a critical role in regulating gene expression. In this study, we used an antibody-enrichment approach along with LC-MS/MS to carry out a quantitative crotonylome analysis in C. albicans We found a total of 5,242 crotonylation sites and 1,584 crotonylated proteins among 9,038 proteins in this organism. Of these crotonylated proteins, a few unique crotonylated motifs are noted such as D and E in positions +1, +2, or +3 or K and R in positions +5 or +6, while A, E, F, G, P, W, and Y are in the -1 position or A, K, and R are found in positions -5, -6, -7, or -8. Functional analysis has shown that a majority of the crotonylated proteins are related to biosynthetic events and carbon metabolism. When combined with previously collected data on acetylation and succinylation, PPI (protein-protein interaction network) analysis reveals that proteins with functions in ribosomal biogenesis, oxidative phosphorylation, nucleus activity, and proteasome formation are heavily modified by these three PTM types. To the best of our knowledge, this is the first crotonylome study carried out in C. albicans and is an important step to a better understanding of the biological and pathogenic impact of PTM in C. albicans IMPORTANCE C. albicans is a kind of pathogen of fungal infections that is found worldwide. Lysine crotonylation of proteins as a recently discovered PTM (posttranslational modification) may have a critical role in regulating cells. We first carried out large-scale analysis of crotonylated proteome and multiple PTM analysis (acetylation, succinylation, and crotonylation), then drew a diagram to show multiple PTM sites on histones in C. albicans of our study. This study about crotonylome in human pathogenic fungi is a milestone that first and deeply investigates the functional analysis of crotonylated proteins in C. albicans, which marks an important start for further research.
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29
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Okimune KI, Nagy SK, Hataya S, Endo Y, Takasuka TE. Reconstitution of Drosophila and human chromatins by wheat germ cell-free co-expression system. BMC Biotechnol 2020; 20:62. [PMID: 33261588 PMCID: PMC7708258 DOI: 10.1186/s12896-020-00655-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Elaboration of the epigenetic regulation of chromatin is a long-standing aim in molecular and cellular biology. Hence, there is a great demand for the development of in vitro methods to reconstitute chromatin that can be used directly for biochemical assays. The widely used wheat germ cell-free protein expression method provides broad applications to investigate the function and structure of eukaryotic proteins. Such advantages, including high translation efficiency, flexibility, and possible automatization, are beneficial for achieving native-like chromatin substrates for in vitro studies. RESULTS We describe a novel, single-step in vitro chromatin assembly method by using the wheat germ cell-free protein synthesis. We demonstrated that both Drosophila and human chromatins can be reconstituted in the course of the in vitro translation of core histones by the addition of chromatin assembly factors, circular plasmid, and topoisomerase I in an ATP-dependent manner. Drosophila chromatin assembly was performed in 4 h at 26 °C, in the presence of premixed mRNAs encoding the core histones, dAcf1/dISWI chromatin remodeling complex, and nucleosome assembly protein, dNAP1. Similarly, the human chromatin was assembled by co-expressing the human core histones with Drosophila chromatin remodeling factor, dISWI, and chromatin chaperone, dNLP, for 6 h at 26 °C. The presence of reconstituted chromatin was monitored by DNA supercoiling assay, also the regular spacing of nucleosomes was assessed by Micrococcal nuclease assay. Furthermore, Drosophila linker histone H1-containing chromatin was reconstituted, affirming that the in vitro assembled chromatin is suitable for downstream applications. CONCLUSIONS The method described in this study allows the assembly of Drosophila and human chromatins, possibly in native-like form, by using a wheat germ cell-free protein expression. Although both chromatins were reconstituted successfully, there were unexpected differences with respect to the required ratio of histone-coding mRNAs and the reaction time. Overall, our new in vitro chromatin reconstitution method will aid to characterize the unrevealed structure, function, and regulation of chromatin dynamics.
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Affiliation(s)
- Kei-Ichi Okimune
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan
| | - Szilvia K Nagy
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Shogo Hataya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yaeta Endo
- Proteo-Science Center of Ehime University, Matsuyama, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan. .,Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan. .,GI-CORE, Hokkaido University, Sapporo, 060-8589, Japan.
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30
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Jing Y, Ding D, Tian G, Kwan KCJ, Liu Z, Ishibashi T, Li XD. Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility. Nucleic Acids Res 2020; 48:9538-9549. [PMID: 32766790 PMCID: PMC7515725 DOI: 10.1093/nar/gkaa663] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 01/06/2023] Open
Abstract
Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and function in chromatin remain poorly understood. Here, we utilized an expressed protein ligation (EPL) strategy to synthesize histone H4 with site-specific succinylation at K77 residue (H4K77succ), an evolutionarily conserved succinylation site at the nucleosomal DNA-histone interface. We then assembled mononucleosomes with the semisynthetic H4K77succ in vitro. We demonstrated that this succinylation impacts nucleosome dynamics and promotes DNA unwrapping from the histone surface, which allows proteins such as transcription factors to rapidly access buried regions of the nucleosomal DNA. In budding yeast, a lysine-to-glutamic acid mutation, which mimics Ksucc, at the H4K77 site reduced nucleosome stability and led to defects in DNA damage repair and telomere silencing in vivo. Our findings revealed this uncharacterized histone modification has important roles in nucleosome and chromatin dynamics.
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Affiliation(s)
- Yihang Jing
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dongbo Ding
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ka Chun Jonathan Kwan
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Toyotaka Ishibashi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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31
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Nakatsu K, Hayashi G, Okamoto A. Toolbox for chemically synthesized histone proteins. Curr Opin Chem Biol 2020; 58:10-19. [DOI: 10.1016/j.cbpa.2020.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 01/28/2023]
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32
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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33
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Nakatsu K, Yanase M, Hayashi G, Okamoto A. Fmoc-Compatible and C-terminal-Sequence-Independent Peptide Alkyl Thioester Formation Using Cysteinylprolyl Imide. Org Lett 2020; 22:4670-4674. [PMID: 32484687 DOI: 10.1021/acs.orglett.0c01450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report an Fmoc-compatible and external-thiol-free method of peptide C-terminus thioesterification with cysteinylprolyl imide. The newly synthesized structure, i.e., cysteinylprolyl-thiazolidinone, provided high conversion and sequence-independent fast kinetics (90 min) in the diketopiperazine thioester formation under relatively mild conditions: pH 6.0, 37 °C. Employing this thioesterification method, we synthesized histone H3.2 bearing K56 acetylation.
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Affiliation(s)
- Koki Nakatsu
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masafumi Yanase
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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34
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Wang ZA, Millard CJ, Lin CL, Gurnett JE, Wu M, Lee K, Fairall L, Schwabe JWR, Cole PA. Diverse nucleosome Site-Selectivity among histone deacetylase complexes. eLife 2020; 9:e57663. [PMID: 32501215 PMCID: PMC7316510 DOI: 10.7554/elife.57663] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Histone acetylation regulates chromatin structure and gene expression and is removed by histone deacetylases (HDACs). HDACs are commonly found in various protein complexes to confer distinct cellular functions, but how the multi-subunit complexes influence deacetylase activities and site-selectivities in chromatin is poorly understood. Previously we reported the results of studies on the HDAC1 containing CoREST complex and acetylated nucleosome substrates which revealed a notable preference for deacetylation of histone H3 acetyl-Lys9 vs. acetyl-Lys14 (Wu et al, 2018). Here we analyze the enzymatic properties of five class I HDAC complexes: CoREST, NuRD, Sin3B, MiDAC and SMRT with site-specific acetylated nucleosome substrates. Our results demonstrate that these HDAC complexes show a wide variety of deacetylase rates in a site-selective manner. A Gly13 in the histone H3 tail is responsible for a sharp reduction in deacetylase activity of the CoREST complex for H3K14ac. These studies provide a framework for connecting enzymatic and biological functions of specific HDAC complexes.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Christopher J Millard
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Chia-Liang Lin
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Jennifer E Gurnett
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - John WR Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
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35
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Zheng Y, Wu F, Ling S, Li JB, Tian C. Total chemical synthesis of bivalently modified H3 by improved three-segment native chemical ligation. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.09.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Hintzen JCJ, Poater J, Kumar K, Al Temimi AHK, Pieters BJGE, Paton RS, Bickelhaupt FM, Mecinović J. Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins. Molecules 2020; 25:molecules25081918. [PMID: 32326252 PMCID: PMC7221964 DOI: 10.3390/molecules25081918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 01/31/2023] Open
Abstract
Gaining a fundamental insight into the biomolecular recognition of posttranslationally modified histones by epigenetic reader proteins is of crucial importance to understanding the regulation of the activity of human genes. Here, we seek to establish whether trimethylthialysine, a simple trimethyllysine analogue generated through cysteine alkylation, is a good trimethyllysine mimic for studies on molecular recognition by reader proteins. Histone peptides bearing trimethylthialysine and trimethyllysine were examined for binding with five human reader proteins employing a combination of thermodynamic analyses, molecular dynamics simulations and quantum chemical analyses. Collectively, our experimental and computational findings reveal that trimethylthialysine and trimethyllysine exhibit very similar binding characteristics for the association with human reader proteins, thereby justifying the use of trimethylthialysine for studies aimed at dissecting the origin of biomolecular recognition in epigenetic processes that play important roles in human health and disease.
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Affiliation(s)
- Jordi C. J. Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jordi Poater
- ICREA and Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí I Franquès 1–11, 08028 Barcelona, Spain
| | - Kiran Kumar
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Abbas H. K. Al Temimi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6522 AJ Nijmegen, The Netherlands
| | - Bas J. G. E. Pieters
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6522 AJ Nijmegen, The Netherlands
| | - Robert S. Paton
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
- Correspondence: (R.S.P.); (F.M.B.); (J.M.); Tel.: +45-6550-3603 (J.M.)
| | - F. Matthias Bickelhaupt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6522 AJ Nijmegen, The Netherlands
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Correspondence: (R.S.P.); (F.M.B.); (J.M.); Tel.: +45-6550-3603 (J.M.)
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6522 AJ Nijmegen, The Netherlands
- Correspondence: (R.S.P.); (F.M.B.); (J.M.); Tel.: +45-6550-3603 (J.M.)
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37
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Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P. Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature 2020; 580:669-672. [PMID: 32350470 DOI: 10.1038/s41586-020-2195-y] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/18/2020] [Indexed: 02/02/2023]
Abstract
'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming1,2. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells3. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.
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Affiliation(s)
- Svetlana O Dodonova
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Fangjie Zhu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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38
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Brehove M, Shatoff E, Donovan BT, Jipa CM, Bundschuh R, Poirier MG. DNA sequence influences hexasome orientation to regulate DNA accessibility. Nucleic Acids Res 2019; 47:5617-5633. [PMID: 31216039 PMCID: PMC6582347 DOI: 10.1093/nar/gkz283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/03/2019] [Accepted: 04/20/2019] [Indexed: 02/02/2023] Open
Abstract
Nucleosomes, the fundamental organizing units of eukaryotic genomes, contain ∼146 base pairs of DNA wrapped around a histone H3–H4 tetramer and two histone H2A–H2B dimers. Converting nucleosomes into hexasomes by removal of a H2A–H2B dimer is an important regulatory event, but its regulation and functional consequences are not well-understood. To investigate the influence of hexasomes on DNA accessibility, we used the property of the Widom-601 Nucleosome Positioning Sequence (NPS) to form homogeneously oriented hexasomes in vitro. We find that DNA accessibility to transcription factors (TF) on the hexasome H2A–H2B distal side is identical to naked DNA, while the accessibility on the H2A–H2B proximal side is reduced by 2-fold, which is due to a 2-fold reduction in hexasome unwrapping probability. We then determined that a 23 bp region of the Widom-601 NPS is responsible for forming homogeneously oriented hexasomes. Analysis of published ChIP-exo data of hexasome containing genes identified two DNA sequence motifs that correlate with hexasome orientation in vivo, while ExoIII mapping studies of these sequences revealed they generate homogeneously oriented hexasomes in vitro. These results indicate that hexasome orientation, which is influenced by the underlying DNA sequence in vivo, is important for modulating DNA accessibility to regulate transcription.
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Affiliation(s)
- Matthew Brehove
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin T Donovan
- Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Caroline M Jipa
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Department of Physics, Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA.,Division of Hematology, Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Michael G Poirier
- Department of Physics, Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA.,Ohio State Biochemistry Program, Ohio State University, Columbus, OH 43210, USA
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39
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Zhao D, Le JV, Darcy MA, Crocker K, Poirier MG, Castro C, Bundschuh R. Quantitative Modeling of Nucleosome Unwrapping from Both Ends. Biophys J 2019; 117:2204-2216. [PMID: 31732143 DOI: 10.1016/j.bpj.2019.09.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/05/2019] [Accepted: 09/27/2019] [Indexed: 01/08/2023] Open
Abstract
In eukaryotic cells, DNA is packaged into chromatin where nucleosomes are the basic packaging unit. Important cellular processes including gene expression, DNA replication, and DNA repair require nucleosomal DNA to be unwrapped so that functional proteins can access their target sites, which otherwise are sterically occluded. A key question in this process is what the unwrapped conformations individual nucleosomes adopt within chromatin are. Here, we develop a concurrent nucleosome unwrapping model to address this question. We hypothesize that for a given end-to-end distance of the nucleosomal DNA, the nucleosomal DNA stochastically unwraps from the histone core from both ends independently and that this combination of unwrapping from both sides results in a significant increase in the average distance between the DNA extending from both sides of the nucleosomes. We test our model on recently published experiments using a DNA origami nanocaliper that quantifies nucleosome unwrapping and achieve good agreement between experiment and model prediction. We then investigate the DNA origami caliper distribution when attached to a hexasome (a nucleosome lacking an H2A/H2B dimer). A significant shift in the caliper angle distribution caused by the asymmetric structural features of the hexasome seen experimentally is consistent with the model. Our modeling approach may be more broadly useful to the interpretation of other studies of nucleosome dynamics, chromatin dynamics, and regulatory processes involving nucleosome unwrapping, as well as more generally to optimization of future DNA origami designs to probe mechanical properties of biomolecules.
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Affiliation(s)
- Dengke Zhao
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Jenny V Le
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Michael A Darcy
- Department of Physics, The Ohio State University, Columbus, Ohio
| | - Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, Ohio
| | - Michael G Poirier
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Department of Physics, The Ohio State University, Columbus, Ohio; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Carlos Castro
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio
| | - Ralf Bundschuh
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Department of Physics, The Ohio State University, Columbus, Ohio; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio; Center for RNA Biology, The Ohio State University, Columbus, Ohio.
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40
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Rodriguez Y, Horton JK, Wilson SH. Histone H3 Lysine 56 Acetylation Enhances AP Endonuclease 1-Mediated Repair of AP Sites in Nucleosome Core Particles. Biochemistry 2019; 58:3646-3655. [PMID: 31407575 DOI: 10.1021/acs.biochem.9b00433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Deciphering factors modulating DNA repair in chromatin is of great interest because nucleosomal positioning influences mutation rates. H3K56 acetylation (Ac) is implicated in chromatin landscape regulation, impacting genomic stability, yet the effect of H3K56Ac on DNA base excision repair (BER) remains unclear. We determined whether H3K56Ac plays a role in regulating AP site incision by AP endonuclease 1 (APE1), an early step in BER. Our in vitro studies of acetylated, well-positioned nucleosome core particles (H3K56Ac-601-NCPs) demonstrate APE1 strand incision is enhanced compared with that of unacetylated WT-601-NCPs. The high-mobility group box 1 protein enhances APE1 activity in WT-601-NCPs, but this effect is not observed in H3K56Ac-601-NCPs. Therefore, our results suggest APE1 activity on NCPs can be modulated by H3K56Ac.
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Affiliation(s)
- Yesenia Rodriguez
- Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States
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41
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Abstract
Repair of damaged DNA plays a crucial role in maintaining genomic integrity and normal cell function. The base excision repair (BER) pathway is primarily responsible for removing modified nucleobases that would otherwise cause deleterious and mutagenic consequences and lead to disease. The BER process is initiated by a DNA glycosylase, which recognizes and excises the target nucleobase lesion, and is completed via downstream enzymes acting in a well-coordinated manner. A majority of our current understanding about how BER enzymes function comes from in vitro studies using free duplex DNA as a simplified model. In eukaryotes, however, BER is challenged by the packaging of genomic DNA into chromatin. The fundamental structural repeating unit of chromatin is the nucleosome, which presents a more complex substrate context than free duplex DNA for repair. In this chapter, we discuss how BER enzymes, particularly glycosylases, engage in the context of packaged DNA with insights obtained from both in vivo and in vitro studies. Furthermore, we review factors and mechanisms that can modify chromatin architecture and/or influence DNA accessibility to BER machinery, such as the geometric location of the damage site, nucleosomal DNA unwrapping, histone post-translational modifications, histone variant incorporation, and chromatin remodeling.
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Affiliation(s)
- Chuxuan Li
- Department of Chemistry, Brown University, Providence, RI, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, United States.
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42
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Singh R, Bassett E, Chakravarti A, Parthun MR. Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function. Nucleic Acids Res 2019; 46:8665-8678. [PMID: 30165676 PMCID: PMC6158624 DOI: 10.1093/nar/gky768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/24/2018] [Indexed: 12/11/2022] Open
Abstract
Replication-dependent histones are expressed in a cell cycle regulated manner and supply the histones necessary to support DNA replication. In mammals, the replication-dependent histones are encoded by a family of genes that are located in several clusters. In humans, these include 16 genes for histone H2A, 22 genes for histone H2B, 14 genes for histone H3, 14 genes for histone H4 and 6 genes for histone H1. While the proteins encoded by these genes are highly similar, they are not identical. For many years, these genes were thought to encode functionally equivalent histone proteins. However, several lines of evidence have emerged that suggest that the replication-dependent histone genes can have specific functions and may constitute a novel layer of chromatin regulation. This Survey and Summary reviews the literature on replication-dependent histone isoforms and discusses potential mechanisms by which the small variations in primary sequence between the isoforms can alter chromatin function. In addition, we summarize the wealth of data implicating altered regulation of histone isoform expression in cancer.
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Affiliation(s)
- Rajbir Singh
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Emily Bassett
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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43
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Abstract
Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate DNA processes, including transcription, replication, and repair. Conformational dynamics within the nucleosome and chromatin structure play a key role in this regulatory function. Structural fluctuations continuously expose internal DNA sequences and nucleosome surfaces, thereby providing transient access for the nuclear machinery. Progress in structural studies of nucleosomes and chromatin has provided detailed insight into local chromatin organization and has set the stage for recent in-depth investigations of the structural dynamics of nucleosomes and chromatin fibers. Here, we discuss the dynamic processes observed in chromatin over different length scales and timescales and review current knowledge about the biophysics of distinct structural transitions.
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Affiliation(s)
- Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Michael G. Poirier
- Department of Physics, Biophysics Graduate Program, Ohio State Biochemistry Graduate Program, and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210-1117, USA
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44
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Jbara M, Maity SK, Brik A. Examining Several Strategies for the Chemical Synthesis of Phosphorylated Histone H3 Reveals the Effectiveness of the Convergent Approach. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900257] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; 3200008 Haifa Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; 3200008 Haifa Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; 3200008 Haifa Israel
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45
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Donovan BT, Chen H, Jipa C, Bai L, Poirier MG. Dissociation rate compensation mechanism for budding yeast pioneer transcription factors. eLife 2019; 8:43008. [PMID: 30888317 PMCID: PMC6449090 DOI: 10.7554/elife.43008] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/14/2019] [Indexed: 01/06/2023] Open
Abstract
Nucleosomes restrict the occupancy of most transcription factors (TF) by reducing binding and accelerating dissociation, while a small group of TFs have high affinities to nucleosome-embedded sites and facilitate nucleosome displacement. To understand this process mechanistically, we investigated two Saccharomyces cerevisiae TFs, Reb1 and Cbf1. We show that these factors bind to their sites within nucleosomes with similar binding affinities as to naked DNA, trapping a partially unwrapped nucleosome without histone eviction. Both the binding and dissociation rates of Reb1 and Cbf1 are significantly slower at the nucleosomal sites relative to those for naked DNA, demonstrating that the high affinities are achieved by increasing the dwell time on nucleosomes in order to compensate for reduced binding. Reb1 also shows slow migration rate in the yeast nuclei. These properties are similar to those of human pioneer factors (PFs), suggesting that the mechanism of nucleosome targeting is conserved from yeast to humans.
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Affiliation(s)
- Benjamin T Donovan
- Biophysics Graduate Program, The Ohio State University, Columbus, United States
| | - Hengye Chen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States.,Center for Eukaryotic Gene Regulation, The Pennsylvania State University, State College, United States
| | - Caroline Jipa
- Department of Physics, The Ohio State University, Columbus, United States
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States.,Department of Physics, The Pennsylvania State University, State College, United States
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, United States.,Department of Physics, The Ohio State University, Columbus, United States.,Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, United States.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, United States
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46
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Nucleosome DNA unwrapping does not affect prototype foamy virus integration efficiency or site selection. PLoS One 2019; 14:e0212764. [PMID: 30865665 PMCID: PMC6415784 DOI: 10.1371/journal.pone.0212764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 02/09/2019] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic DNA binding proteins must access genomic DNA that is packaged into chromatin in vivo. During a productive infection, retroviral integrases (IN) must similarly interact with chromatin to integrate the viral cDNA genome. Here we examine the role of nucleosome DNA unwrapping in the retroviral integrase search for a target site. These studies utilized PFV intasomes that are comprised of a tetramer of PFV IN with two oligomers mimicking the viral cDNA ends. Modified recombinant human histones were used to generate nucleosomes with increased unwrapping rates at different DNA regions. These modifications included the acetylmimetic H3(K56Q) and the chemically engineered H4(K77ac, K79ac). While transcription factors and DNA damage sensors may search nucleosome bound DNA during transient unwrapping, PFV intasome mediated integration appears to be unaffected by increased nucleosome unwrapping. These studies suggest PFV intasomes do not utilize nucleosome unwrapping to search nucleosome targets.
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47
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McCullough LL, Pham TH, Parnell TJ, Connell Z, Chandrasekharan MB, Stillman DJ, Formosa T. Establishment and Maintenance of Chromatin Architecture Are Promoted Independently of Transcription by the Histone Chaperone FACT and H3-K56 Acetylation in Saccharomyces cerevisiae. Genetics 2019; 211:877-892. [PMID: 30679261 PMCID: PMC6404263 DOI: 10.1534/genetics.118.301853] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/14/2019] [Indexed: 12/16/2022] Open
Abstract
FACT (FAcilitates Chromatin Transcription/Transactions) is a histone chaperone that can destabilize or assemble nucleosomes. Acetylation of histone H3-K56 weakens a histone-DNA contact that is central to FACT activity, suggesting that this modification could affect FACT functions. We tested this by asking how mutations of H3-K56 and FACT affect nucleosome reorganization activity in vitro, and chromatin integrity and transcript output in vivo Mimics of unacetylated or permanently acetylated H3-K56 had different effects on FACT activity as expected, but the same mutations had surprisingly similar effects on global transcript levels. The results are consistent with emerging models that emphasize FACT's importance in establishing global chromatin architecture prior to transcription, promoting transitions among different states as transcription profiles change, and restoring chromatin integrity after it is disturbed. Optimal FACT activity required the availability of both modified and unmodified states of H3-K56. Perturbing this balance was especially detrimental for maintaining repression of genes with high nucleosome occupancy over their promoters and for blocking antisense transcription at the +1 nucleosome. The results reveal a complex collaboration between H3-K56 modification status and multiple FACT functions, and support roles for nucleosome reorganization by FACT before, during, and after transcription.
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Affiliation(s)
- Laura L McCullough
- Department of Biochemistry, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Trang H Pham
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Timothy J Parnell
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Zaily Connell
- Department of Biochemistry, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - David J Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Tim Formosa
- Department of Biochemistry, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
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48
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Zhou K, Gaullier G, Luger K. Nucleosome structure and dynamics are coming of age. Nat Struct Mol Biol 2018; 26:3-13. [PMID: 30532059 DOI: 10.1038/s41594-018-0166-x] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022]
Abstract
Since the first high-resolution structure of the nucleosome was reported in 1997, the available information on chromatin structure has increased very rapidly. Here, we review insights derived from cutting-edge biophysical and structural approaches applied to the study of nucleosome dynamics and nucleosome-binding factors, with a focus on the experimental advances driving the research. In addition, we highlight emerging challenges in nucleosome structural biology.
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Affiliation(s)
- Keda Zhou
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Guillaume Gaullier
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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49
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Gosavi PM, Jayachandran M, Rempillo JJL, Zozulia O, Makhlynets OV, Korendovych IV. A Designed Enzyme Promotes Selective Post-translational Acylation. Chembiochem 2018; 19:1605-1608. [PMID: 29756279 DOI: 10.1002/cbic.201800196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Indexed: 11/10/2022]
Abstract
A computationally designed, allosterically regulated catalyst (CaM M144H) produced by substituting a single residue in calmodulin, a non-enzymatic protein, is capable of efficient and site selective post-translational acylation of lysines in peptides with highly diverse sequences. Calmodulin's binding partners are involved in regulating a large number of cellular processes; this new chemical-biology tool will help to identify them and provide structural insight into their interactions with calmodulin.
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Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Megha Jayachandran
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Joel J L Rempillo
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
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50
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Sueoka T, Koyama K, Hayashi G, Okamoto A. Chemistry-Driven Epigenetic Investigation of Histone and DNA Modifications. CHEM REC 2018; 18:1727-1744. [PMID: 30070422 DOI: 10.1002/tcr.201800040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/22/2018] [Indexed: 12/26/2022]
Abstract
In the regulation processes of gene expression, genomic DNA and nuclear proteins, including histone proteins, cooperate with each other, leading to the distinctive functions of eukaryotic cells such as pluripotency and differentiation. Chemical modification of histone proteins and DNA has been revealed as one of the major driving forces in the complicated epigenetic regulation system. However, understanding of the precise molecular mechanisms is still limited. To address this issue, researchers have proposed both biological and chemical strategies for the preparation and detection of modified proteins and nucleic acids. In this review, we focus on chemical methods around the field of epigenetics. Chemical protein synthesis has enabled the preparation of site-specifically modified histones and their successful application to various in vitro assays, which have emphasized the significance of posttranslational modifications of interest. We also review the modification-specific chemical reactions against synthetic and genomic DNA, which enabled discrimination of several modified bases at single-base resolution.
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Affiliation(s)
- Takuma Sueoka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenta Koyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Gosuke Hayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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