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Wang M, Li Q, Liu L. Factors and Methods for the Detection of Gene Expression Regulation. Biomolecules 2023; 13:biom13020304. [PMID: 36830673 PMCID: PMC9953580 DOI: 10.3390/biom13020304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Gene-expression regulation involves multiple processes and a range of regulatory factors. In this review, we describe the key factors that regulate gene expression, including transcription factors (TFs), chromatin accessibility, histone modifications, DNA methylation, and RNA modifications. In addition, we also describe methods that can be used to detect these regulatory factors.
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Chang W, Zhao Y, Rayêe D, Xie Q, Suzuki M, Zheng D, Cvekl A. Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation. Epigenetics Chromatin 2023; 16:4. [PMID: 36698218 PMCID: PMC9875507 DOI: 10.1186/s13072-023-00478-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Cellular differentiation is marked by temporally and spatially coordinated gene expression regulated at multiple levels. DNA methylation represents a universal mechanism to control chromatin organization and its accessibility. Cytosine methylation of CpG dinucleotides regulates binding of methylation-sensitive DNA-binding transcription factors within regulatory regions of transcription, including promoters and distal enhancers. Ocular lens differentiation represents an advantageous model system to examine these processes as lens comprises only two cell types, the proliferating lens epithelium and postmitotic lens fiber cells all originating from the epithelium. RESULTS Using whole genome bisulfite sequencing (WGBS) and microdissected lenses, we investigated dynamics of DNA methylation and chromatin changes during mouse lens fiber and epithelium differentiation between embryos (E14.5) and newborns (P0.5). Histone H3.3 variant chromatin landscapes were also generated for both P0.5 lens epithelium and fibers by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Tissue-specific features of DNA methylation patterns are demonstrated via comparative studies with embryonic stem (ES) cells and neural progenitor cells (NPCs) at Nanog, Pou5f1, Sox2, Pax6 and Six3 loci. Comparisons with ATAC-seq and RNA-seq data demonstrate that reduced methylation is associated with increased expression of fiber cell abundant genes, including crystallins, intermediate filament (Bfsp1 and Bfsp2) and gap junction proteins (Gja3 and Gja8), marked by high levels of histone H3.3 within their transcribed regions. Interestingly, Pax6-binding sites exhibited predominantly DNA hypomethylation in lens chromatin. In vitro binding of Pax6 proteins showed Pax6's ability to interact with sites containing one or two methylated CpG dinucleotides. CONCLUSIONS Our study has generated the first data on methylation changes between two different stages of mammalian lens development and linked these data with chromatin accessibility maps, presence of histone H3.3 and gene expression. Reduced DNA methylation correlates with expression of important genes involved in lens morphogenesis and lens fiber cell differentiation.
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Affiliation(s)
- William Chang
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Yilin Zhao
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Danielle Rayêe
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Qing Xie
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Masako Suzuki
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Deyou Zheng
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ales Cvekl
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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Retinal Pigment Epithelium Cell Development: Extrapolating Basic Biology to Stem Cell Research. Biomedicines 2023; 11:biomedicines11020310. [PMID: 36830851 PMCID: PMC9952929 DOI: 10.3390/biomedicines11020310] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
The retinal pigment epithelium (RPE) forms an important cellular monolayer, which contributes to the normal physiology of the eye. Damage to the RPE leads to the development of degenerative diseases, such as age-related macular degeneration (AMD). Apart from acting as a physical barrier between the retina and choroidal blood vessels, the RPE is crucial in maintaining photoreceptor (PR) and visual functions. Current clinical intervention to treat early stages of AMD includes stem cell-derived RPE transplantation, which is still in its early stages of evolution. Therefore, it becomes essential to derive RPEs which are functional and exhibit features as observed in native human RPE cells. The conventional strategy is to use the knowledge obtained from developmental studies using various animal models and stem cell-based exploratory studies to understand RPE biogenies and developmental trajectory. This article emphasises such studies and aims to present a comprehensive understanding of the basic biology, including the genetics and molecular pathways of RPE development. It encompasses basic developmental biology and stem cell-based developmental studies to uncover RPE differentiation. Knowledge of the in utero developmental cues provides an inclusive methodology required for deriving RPEs using stem cells.
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Akinmusola RY, Wilkins CA, Doughty J. DDM1-Mediated TE Silencing in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:437. [PMID: 36771522 PMCID: PMC9919755 DOI: 10.3390/plants12030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic modifications are indispensable for regulating gene bodies and TE silencing. DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeller involved in histone modifications and DNA methylation. Apart from maintaining the epigenome, DDM1 also maintains key plant traits such as flowering time and heterosis. The role of DDM1 in epigenetic regulation is best characterised in plants, especially arabidopsis, rice, maize and tomato. The epigenetic changes induced by DDM1 establish the stable inheritance of many plant traits for at least eight generations, yet DDM1 does not methylate protein-coding genes. The DDM1 TE silencing mechanism is distinct and has evolved independently of other silencing pathways. Unlike the RNA-directed DNA Methylation (RdDM) pathway, DDM1 does not depend on siRNAs to enforce the heterochromatic state of TEs. Here, we review DDM1 TE silencing activity in the RdDM and non-RdDM contexts. The DDM1 TE silencing machinery is strongly associated with the histone linker H1 and histone H2A.W. While the linker histone H1 excludes the RdDM factors from methylating the heterochromatin, the histone H2A.W variant prevents TE mobility. The DDM1-H2A.W strategy alone silences nearly all the mobile TEs in the arabidopsis genome. Thus, the DDM1-directed TE silencing essentially preserves heterochromatic features and abolishes mobile threats to genome stability.
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Characterizing crosstalk in epigenetic signaling to understand disease physiology. Biochem J 2023; 480:57-85. [PMID: 36630129 PMCID: PMC10152800 DOI: 10.1042/bcj20220550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Epigenetics, the inheritance of genomic information independent of DNA sequence, controls the interpretation of extracellular and intracellular signals in cell homeostasis, proliferation and differentiation. On the chromatin level, signal transduction leads to changes in epigenetic marks, such as histone post-translational modifications (PTMs), DNA methylation and chromatin accessibility to regulate gene expression. Crosstalk between different epigenetic mechanisms, such as that between histone PTMs and DNA methylation, leads to an intricate network of chromatin-binding proteins where pre-existing epigenetic marks promote or inhibit the writing of new marks. The recent technical advances in mass spectrometry (MS) -based proteomic methods and in genome-wide DNA sequencing approaches have broadened our understanding of epigenetic networks greatly. However, further development and wider application of these methods is vital in developing treatments for disorders and pathologies that are driven by epigenetic dysregulation.
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56
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Kumar A, Maurya P, Hayes JJ. Post-Translation Modifications and Mutations of Human Linker Histone Subtypes: Their Manifestation in Disease. Int J Mol Sci 2023; 24:ijms24021463. [PMID: 36674981 PMCID: PMC9860689 DOI: 10.3390/ijms24021463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Linker histones (LH) are a critical component of chromatin in addition to the canonical histones (H2A, H2B, H3, and H4). In humans, 11 subtypes (7 somatic and 4 germinal) of linker histones have been identified, and their diverse cellular functions in chromatin structure, DNA replication, DNA repair, transcription, and apoptosis have been explored, especially for the somatic subtypes. Delineating the unique role of human linker histone (hLH) and their subtypes is highly tedious given their high homology and overlapping expression patterns. However, recent advancements in mass spectrometry combined with HPLC have helped in identifying the post-translational modifications (PTMs) found on the different LH subtypes. However, while a number of PTMs have been identified and their potential nuclear and non-nuclear functions explored in cellular processes, there are very few studies delineating the direct relevance of these PTMs in diseases. In addition, recent whole-genome sequencing of clinical samples from cancer patients and individuals afflicted with Rahman syndrome have identified high-frequency mutations and therefore broadened the perspective of the linker histone mutations in diseases. In this review, we compile the identified PTMs of hLH subtypes, current knowledge of the relevance of hLH PTMs in human diseases, and the correlation of PTMs coinciding with mutations mapped in diseases.
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Affiliation(s)
- Ashok Kumar
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
- Correspondence:
| | - Preeti Maurya
- Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY 14642, USA
| | - Jeffrey J. Hayes
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
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Löffler T, Krüger A, Zirak P, Winterhalder MJ, Müller AL, Fischbach A, Mangerich A, Zumbusch A. Influence of chain length and branching on poly(ADP-ribose)-protein interactions. Nucleic Acids Res 2023; 51:536-552. [PMID: 36625274 PMCID: PMC9881148 DOI: 10.1093/nar/gkac1235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/16/2022] [Accepted: 12/10/2022] [Indexed: 01/11/2023] Open
Abstract
Hundreds of proteins interact with poly(ADP-ribose) (PAR) via multiple PAR interaction motifs, thereby regulating their physico-chemical properties, sub-cellular localizations, enzymatic activities, or protein stability. Here, we present a targeted approach based on fluorescence correlation spectroscopy (FCS) to characterize potential structure-specific interactions of PAR molecules of defined chain length and branching with three prime PAR-binding proteins, the tumor suppressor protein p53, histone H1, and the histone chaperone APLF. Our study reveals complex and structure-specific PAR-protein interactions. Quantitative Kd values were determined and binding affinities for all three proteins were shown to be in the nanomolar range. We report PAR chain length dependent binding of p53 and H1, yet chain length independent binding of APLF. For all three PAR binders, we found a preference for linear over hyperbranched PAR. Importantly, protein- and PAR-structure-specific binding modes were revealed. Thus, while the H1-PAR interaction occurred largely on a bi-molecular 1:1 basis, p53-and potentially also APLF-can form complex multivalent PAR-protein structures. In conclusion, our study gives detailed and quantitative insight into PAR-protein interactions in a solution-based setting at near physiological buffer conditions. The results support the notion of protein and PAR-structure-specific binding modes that have evolved to fit the purpose of the respective biochemical functions and biological contexts.
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Affiliation(s)
| | | | - Peyman Zirak
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | | | - Anna-Lena Müller
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | - Arthur Fischbach
- Department of Biology, Universität Konstanz, Konstanz D-78457, Germany
| | - Aswin Mangerich
- To whom correspondence should be addressed. Tel: +49 33200 88 5301;
| | - Andreas Zumbusch
- Correspondence may also be addressed to Andreas Zumbusch. Tel: +49 7531 882027;
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Song L, Soomro MA, Wang L, Song Y, Hu G. Identification and functional analysis of histone 1.2-like in red sea bream (Pagrus major). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 138:104529. [PMID: 36087785 DOI: 10.1016/j.dci.2022.104529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Histone H1 acts as an essential chromatin component and participates in the formation of higher chromatin structures together with core histones. In addition, H1 also has important functions in physiological processes such as gene expression regulation, DNA repair, and the immune response. In this study, the histone homologous protein Pm-H1.2-like was identified from the transcriptome database of Pagrus major we studied previously. Conservatism of evolution was investigated by sequence alignment and phylogenetic analysis. Transcripts of Pm-H1.2-like were detected in P. major tissues. The highest expression level was found in gill and skin tissues. Consistent with the data from the transcriptome database, we observed that the expression of Pm-H1.2-like was rapidly induced in nonspecific cytotoxic cells (NCCs) infected with inactivated Vibrio anguillarum. Gene silencing of Pm-H1.2-like by RNAi significantly suppressed the expression of NK-lysin and GZMB in NCCs at 12 h after pathogen stimulation, but had no significant effect on IFN-γ expression. Next, we obtained the fusion proteins rPm-H1.2-like and rPm-H1.2-like (36-80) through prokaryotic expression. ELISA showed that rPm-H1.2-like bound to oligonucleotide (ODN) in a concentration-dependent manner, while no binding activity of rPm-H1.2-like (36-80) with ODN was observed. This study confirmed that Pm-H1.2-like actively participates in the immune response of NCCs to bacterial infection, deepening the understanding of the immune features of histone H1 in fish.
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Affiliation(s)
- Lianfei Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Maqsood Ahmed Soomro
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Lingshu Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Yuting Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Guobin Hu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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59
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Ayala-Guerrero L, Claudio-Galeana S, Furlan-Magaril M, Castro-Obregón S. Chromatin Structure from Development to Ageing. Subcell Biochem 2023; 102:7-51. [PMID: 36600128 DOI: 10.1007/978-3-031-21410-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Nuclear structure influences genome architecture, which contributes to determine patterns of gene expression. Global changes in chromatin dynamics are essential during development and differentiation, and are one of the hallmarks of ageing. This chapter describes the molecular dynamics of chromatin structure that occur during development and ageing. In the first part, we introduce general information about the nuclear lamina, the chromatin structure, and the 3D organization of the genome. Next, we detail the molecular hallmarks found during development and ageing, including the role of DNA and histone modifications, 3D genome dynamics, and changes in the nuclear lamina. Within the chapter we discuss the implications that genome structure has on the mechanisms that drive development and ageing, and the physiological consequences when these mechanisms fail.
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Affiliation(s)
- Lorelei Ayala-Guerrero
- Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico
| | - Sherlyn Claudio-Galeana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico
| | - Mayra Furlan-Magaril
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
| | - Susana Castro-Obregón
- Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
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Whiwon L, Salma S, Daniel A, Stephanie L, Marc C, Cherith S, Abby T, Angela S, Robin H, Yvonne B. Patient-facing digital tools for delivering genetic services: a systematic review. J Med Genet 2023; 60:1-10. [PMID: 36137613 DOI: 10.1136/jmg-2022-109085] [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: 04/20/2022] [Accepted: 07/19/2022] [Indexed: 01/24/2023]
Abstract
This study systematically reviewed the literature on the impact of digital genetics tools on patient care and system efficiencies. MEDLINE and Embase were searched for articles published between January 2010 and March 2021. Studies evaluating the use of patient-facing digital tools in the context of genetic service delivery were included. Two reviewers screened and extracted patient-reported and system-focused outcomes from each study. Data were synthesised using a descriptive approach. Of 3226 unique studies identified, 87 were included. A total of 70 unique digital tools were identified. As a result of using digital tools, 84% of studies reported a positive outcome in at least one of the following patient outcomes: knowledge, psychosocial well-being, behavioural/management changes, family communication, decision-making or level of engagement. Digital tools improved workflow and efficiency for providers and reduced the amount of time they needed to spend with patients. However, we identified a misalignment between study purpose and patient-reported outcomes measured and a lack of tools that encompass the entire genetic counselling and testing trajectory. Given increased demand for genetic services and the shift towards virtual care, this review provides evidence that digital tools can be used to efficiently deliver patient-centred care. Future research should prioritise development, evaluation and implementation of digital tools that can support the entire patient trajectory across a range of clinical settings. PROSPERO registration numberCRD42020202862.
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Affiliation(s)
- Lee Whiwon
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shickh Salma
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Assamad Daniel
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Luca Stephanie
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Clausen Marc
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Somerville Cherith
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Tafler Abby
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shaw Angela
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Hayeems Robin
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Bombard Yvonne
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
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61
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Frederick MA, Williamson KE, Fernandez Garcia M, Ferretti MB, McCarthy RL, Donahue G, Luzete Monteiro E, Takenaka N, Reynaga J, Kadoch C, Zaret KS. A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling. Nat Struct Mol Biol 2023; 30:31-37. [PMID: 36536103 PMCID: PMC10004348 DOI: 10.1038/s41594-022-00886-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
To determine how different pioneer transcription factors form a targeted, accessible nucleosome within compacted chromatin and collaborate with an ATP-dependent chromatin remodeler, we generated nucleosome arrays in vitro with a central nucleosome containing binding sites for the hematopoietic E-Twenty Six (ETS) factor PU.1 and Basic Leucine Zipper (bZIP) factors C/EBPα and C/EBPβ. Our long-read sequencing reveals that each factor can expose a targeted nucleosome on linker histone-compacted arrays, but with different nuclease sensitivity patterns. The DNA binding domain of PU.1 binds mononucleosomes, but requires an additional intrinsically disordered domain to bind and open compacted chromatin. The canonical mammalian SWI/SNF (cBAF) remodeler was unable to act upon two forms of locally open chromatin unless cBAF was enabled by a separate transactivation domain of PU.1. cBAF potentiates the PU.1 DNA binding domain to weakly open chromatin in the absence of the PU.1 disordered domain. Our findings reveal a hierarchy by which chromatin is opened and show that pioneer factors can provide specificity for action by nucleosome remodelers.
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Affiliation(s)
- Megan A Frederick
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kaylyn E Williamson
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Meilin Fernandez Garcia
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Max B Ferretti
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan L McCarthy
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Greg Donahue
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edgar Luzete Monteiro
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Naomi Takenaka
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Janice Reynaga
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Previously Unidentified Histone H1-Like Protein Is Involved in Cell Division and Ribosome Biosynthesis in Toxoplasma gondii. mSphere 2022; 7:e0040322. [PMID: 36468865 PMCID: PMC9769792 DOI: 10.1128/msphere.00403-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromatin dynamics can regulate all DNA-dependent processes. Access to DNA within chromatin is orchestrated mainly by histones and their posttranslational modifications (PTMs). Like other eukaryotes, the apicomplexan parasite Toxoplasma gondii encodes four canonical histones and five histone variants. In contrast, the linker histone (H1) has never been identified in apicomplexan parasites. In other eukaryotes, histone H1 compacts the chromatin by linking the nucleosome and increasing the DNA compaction. H1 is a multifunctional protein and can be involved in different steps of DNA metabolism or associated with protein complexes related to distinct biological processes. We have identified a novel protein in T. gondii ("TgH1-like") that, although lacking the globular domain of mammalian H1, is remarkably like the H1-like proteins of bacteria and trypanosomatids. Our results demonstrate that TgH1-like is a nuclear protein associated with chromatin and other histones. Curiously, TgH1-like is also in the nucleolus and associated with ribosomal proteins, indicating a versatile function in this parasite. Although knockout of the tgh1-like gene does not affect the cell cycle, it causes endopolygeny and asynchronous division. Interestingly, mutation of posttranslationally modified amino acids results in defects in cell division like those in the Δtgh1-like mutant, showing that these sites are important for protein function. Furthermore, in the bradyzoite stage, this protein is expressed only in dividing parasites, reinforcing its importance in cell division. Indeed, the absence of TgH1-like decreases compaction of peripheral chromatin, confirming its role in the chromatin modulation in T. gondii. IMPORTANCE Histone H1, or linker histone, is an important protein that binds to the nucleosome, aiding chromatin compaction. Here, we characterize for the first time a linker histone in T. gondii, named TgH1-like. It is a small and basic protein that corresponds only to the C-terminal portion of the human H1 but is similar to histone H1 from trypanosomatids and bacteria. TgH1-like is located in the nucleus, interacts with nucleosome histones, and acts in chromatin structure and cell division. Our findings show for the first time the presence of a histone H1 protein in an apicomplexan parasite and will provide new insights into cell division and chromatin dynamics in T. gondii and related parasites.
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63
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Kloc M, Kubiak JZ, Zdanowski R, Ghobrial RM. Memory Macrophages. Int J Mol Sci 2022; 24:ijms24010038. [PMID: 36613481 PMCID: PMC9819859 DOI: 10.3390/ijms24010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Immunological memory is a crucial part of the immune defense that allows organisms to respond against previously encountered pathogens or other harmful factors. Immunological memory is based on the establishment of epigenetic modifications of the genome. The ability to memorize encounters with pathogens and other harmful factors and mount enhanced defense upon subsequent encounters is an evolutionarily ancient mechanism operating in all animals and plants. However, the term immunological memory is usually restricted to the organisms (invertebrates and vertebrates) possessing the immune system. The mammalian immune system, with innate and adaptive branches, is the most sophisticated among vertebrates. The concept of innate memory and memory macrophages is relatively new and thus understudied. We introduce the concept of immunological memory and describe types of memory in different species and their evolutionary status. We discuss why the traditional view of innate immune cells as the first-line defenders is too restrictive and how the innate immune cells can accumulate and retain immunologic memory. We describe how the initial priming leads to chromatin remodeling and epigenetic changes, which allow memory macrophage formation. We also summarize what is currently known about the mechanisms underlying development of memory macrophages; their molecular and metabolic signature and surface markers; and how they may contribute to immune defense, diseases, and organ transplantation.
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Affiliation(s)
- Malgorzata Kloc
- The Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
- Correspondence:
| | - Jacek Z. Kubiak
- Dynamics and Mechanics of Epithelia Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, University of Rennes, CNRS, UMR 6290, 35043 Rennes, France
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, Szaserow 128, 04-141 Warsaw, Poland
| | - Robert Zdanowski
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, Szaserow 128, 04-141 Warsaw, Poland
| | - Rafik M. Ghobrial
- The Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX 77030, USA
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64
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Nunez-Vazquez R, Desvoyes B, Gutierrez C. Histone variants and modifications during abiotic stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:984702. [PMID: 36589114 PMCID: PMC9797984 DOI: 10.3389/fpls.2022.984702] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/28/2022] [Indexed: 06/17/2023]
Abstract
Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.
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65
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Azumamides A-E: Isolation, Synthesis, Biological Activity, and Structure-Activity Relationship. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238438. [PMID: 36500529 PMCID: PMC9737774 DOI: 10.3390/molecules27238438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/16/2022] [Accepted: 11/29/2022] [Indexed: 12/09/2022]
Abstract
Cyclic peptides are one of the important chemical groups in the HDAC inhibitor family. Following the success of romidepsin in the clinic, naturally occurring cyclic peptides with a hydrophilic moiety have been intensively studied to test their function as HDAC inhibitors. Azumamides A-E, isolated from Mycale izuensis, are one of the powerful HDAC inhibitor classes. Structurally, azumamides A-E consist of three D-α-amino acids and unnatural β-amino acids such as 3-amino-2-methyl-5-nonenedioic acid-9-amide (Amnna) and 3-amino-2-methyl-5-nonenoic-1,9-diacid (Amnda). Moreover, azumamides have a retro-arrangement peptide backbone, unlike other naturally occurring cyclopeptide HDAC inhibitors, owing to the D-configuration of all residues. This review summarizes the currently available synthetic methods of azumamides A-E focusing on the synthesis of β-amino acids and macrocyclization. In addition, we overview the structure-activity relationship of azumamides A-E based on reported analogs. Collectively, this review highlights the potentiality of azumamides A-E as an HDAC inhibitor and provides further developmental insight into naturally occurring cyclic peptides in HDAC inhibition.
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66
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Recillas-Targa F. Cancer Epigenetics: An Overview. Arch Med Res 2022; 53:732-740. [PMID: 36411173 DOI: 10.1016/j.arcmed.2022.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/18/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
Cancer is a complex disease caused by genetic and epigenetic alterations in the control of cell division. Findings from the field of cancer genomics and epigenomics have increased our understanding of the origin and evolution of tumorigenic processes, greatly advancing our knowledge of the molecular etiology of cancer. Consequently, any contemporary view of cancer research must consider tumorigenesis as a cellular phenomenon that is a result of the interplay between genetic and epigenetic mutations and their interaction with environmental factors, including our microbiome, that influences cellular metabolism and proliferation rates. The integration and better knowledge of these processes will help us to improve diagnosis, prognosis, and future genetic and epigenetic therapies. Here, I present an overview of the epigenetic processes that are affected in cancer and how they contribute to the onset and progression of the disease. Finally, I discuss how the development of sophisticated experimental approaches and computational tools, including novel ways to exploit large data sets, could contribute to the better understanding and treatment of cancer.
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Affiliation(s)
- Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México.
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67
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Zhou JJ, Cho KWY. Epigenomic dynamics of early Xenopus Embryos. Dev Growth Differ 2022; 64:508-516. [PMID: 36168140 PMCID: PMC10550391 DOI: 10.1111/dgd.12813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 12/31/2022]
Abstract
How the embryonic genome regulates accessibility to transcription factors is one of the major questions in understanding the spatial and temporal dynamics of gene expression during embryogenesis. Epigenomic analyses of embryonic chromatin provide molecular insights into cell-specific gene activities and genomic architectures. In recent years, significant advances have been made to elucidate the dynamic changes behind the activation of the zygotic genome in various model organisms. Here we provide an overview of the recent epigenomic studies pertaining to early Xenopus development.
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Affiliation(s)
- Jeff Jiajing Zhou
- Developmental and Cell Biology, University of California, Irvine, California, USA
| | - Ken W Y Cho
- Developmental and Cell Biology, University of California, Irvine, California, USA
- Center for Complex Biological Systems, University of California, Irvine, California, USA
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68
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
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Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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69
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Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1. Nat Commun 2022; 13:7287. [PMID: 36435862 PMCID: PMC9701232 DOI: 10.1038/s41467-022-35003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/15/2022] [Indexed: 11/28/2022] Open
Abstract
In chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in the chromatosome has remained enigmatic. Here we report the cryo-electron microscopy (cryo-EM) structures of transcribing RNAPII-chromatosome complexes (forms I and II), in which RNAPII is paused at the entry linker DNA region of the chromatosome due to H1 binding. In the form I complex, the H1 bound to the nucleosome restricts the linker DNA orientation, and the exit linker DNA is captured by the RNAPII DNA binding cleft. In the form II complex, the RNAPII progresses a few bases ahead by releasing the exit linker DNA from the RNAPII cleft, and directly clashes with the H1 bound to the nucleosome. The transcription elongation factor Spt4/5 masks the RNAPII DNA binding region, and drastically reduces the H1-mediated RNAPII pausing.
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70
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The Oocyte-Specific Linker Histone H1FOO Is Not Essential for Mouse Oogenesis and Fertility. Cells 2022; 11:cells11223706. [PMID: 36429134 PMCID: PMC9688445 DOI: 10.3390/cells11223706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Meiosis is a highly conserved specialized cell division process that generates haploid gametes. Many of its events are associated with dynamically regulated chromosomal structures and chromatin remodeling, which are mainly modulated by histone modifications. Histone H1 is a linker histone essential for packing the nucleosome into higher-order structures, and H1FOO (H1 histone family, member O, oocyte-specific) is a H1 variant whose expression pattern is restricted to growing oocytes and zygotes. To further explore the function of H1FOO, we generated mice lacking the H1foo gene by the CRISPR/Cas9 technique. Herein, we combine mouse genetics and cellular studies to show that H1foo-null mutants have no overt phenotype, with both males and females being fertile and presenting no gross defects in meiosis progression nor in synapsis dynamics. Accordingly, the histological sections show a normal development of gametes in both male and female mice. Considering the important role of oocyte constituents in enhancing mammalian somatic cell reprogramming, we analyzed iPSCs generation in H1foo mutant MEFs and observed no differences in the absence of H1FOO. Taken all together, in this work we present the first in vivo evidence of H1FOO dispensability for mouse fertility, clarifying the debate in the field surrounding its essentiality in meiosis.
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71
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Torres-Arciga K, Flores-León M, Ruiz-Pérez S, Trujillo-Pineda M, González-Barrios R, Herrera LA. Histones and their chaperones: Adaptive remodelers of an ever-changing chromatinic landscape. Front Genet 2022; 13:1057846. [PMID: 36468032 PMCID: PMC9709290 DOI: 10.3389/fgene.2022.1057846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/02/2022] [Indexed: 07/29/2023] Open
Abstract
Chromatin maintenance and remodeling are processes that take place alongside DNA repair, replication, or transcription to ensure the survival and adaptability of a cell. The environment and the needs of the cell dictate how chromatin is remodeled; particularly where and which histones are deposited, thus changing the canonical histone array to regulate chromatin structure and gene expression. Chromatin is highly dynamic, and histone variants and their chaperones play a crucial role in maintaining the epigenetic regulation at different genomic regions. Despite the large number of histone variants reported to date, studies on their roles in physiological processes and pathologies are emerging but continue to be scarce. Here, we present recent advances in the research on histone variants and their chaperones, with a focus on their importance in molecular mechanisms such as replication, transcription, and DNA damage repair. Additionally, we discuss the emerging role they have in transposable element regulation, aging, and chromatin remodeling syndromes. Finally, we describe currently used methods and their limitations in the study of these proteins and highlight the importance of improving the experimental approaches to further understand this epigenetic machinery.
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Affiliation(s)
- Karla Torres-Arciga
- Doctorado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Manuel Flores-León
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Samuel Ruiz-Pérez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Magalli Trujillo-Pineda
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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72
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Robusti G, Vai A, Bonaldi T, Noberini R. Investigating pathological epigenetic aberrations by epi-proteomics. Clin Epigenetics 2022; 14:145. [PMID: 36371348 PMCID: PMC9652867 DOI: 10.1186/s13148-022-01371-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetics includes a complex set of processes that alter gene activity without modifying the DNA sequence, which ultimately determines how the genetic information common to all the cells of an organism is used to generate different cell types. Dysregulation in the deposition and maintenance of epigenetic features, which include histone posttranslational modifications (PTMs) and histone variants, can result in the inappropriate expression or silencing of genes, often leading to diseased states, including cancer. The investigation of histone PTMs and variants in the context of clinical samples has highlighted their importance as biomarkers for patient stratification and as key players in aberrant epigenetic mechanisms potentially targetable for therapy. Mass spectrometry (MS) has emerged as the most powerful and versatile tool for the comprehensive, unbiased and quantitative analysis of histone proteoforms. In recent years, these approaches-which we refer to as "epi-proteomics"-have demonstrated their usefulness for the investigation of epigenetic mechanisms in pathological conditions, offering a number of advantages compared with the antibody-based methods traditionally used to profile clinical samples. In this review article, we will provide a critical overview of the MS-based approaches that can be employed to study histone PTMs and variants in clinical samples, with a strong focus on the latest advances in this area, such as the analysis of uncommon modifications and the integration of epi-proteomics data into multi-OMICs approaches, as well as the challenges to be addressed to fully exploit the potential of this novel field of research.
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Affiliation(s)
- Giulia Robusti
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Alessandro Vai
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Tiziana Bonaldi
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milan, Italy
| | - Roberta Noberini
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
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73
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Feng H, Zhou BR, Schwieters CD, Bai Y. Structural Mechanism of TAF-Iβ Chaperone Function on Linker Histone H1.10. J Mol Biol 2022; 434:167755. [PMID: 35870650 PMCID: PMC9489631 DOI: 10.1016/j.jmb.2022.167755] [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: 05/10/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022]
Abstract
Linker histone H1, facilitated by its chaperones, plays an essential role in regulating gene expression by maintaining chromatin's higher-order structure and epigenetic state. However, we know little about the structural mechanism of how the chaperones recognize linker histones and conduct their function. Here, we used biophysical and biochemical methods to investigate the recognition of human linker histone isoform H1.10 by the TAF-Iβ chaperone. Both H1.10 and TAF-Iβ proteins consist of folded cores and disordered tails. We found that H1.10 formed a complex with TAF-Iβ in a 2:2 stoichiometry. Using distance restraints obtained from methyl-TROSY NMR and spin labels, we built a structural model for the core region of the complex. In the model, the TAF-Iβ core interacts with the globular domain of H1.10 mainly through electrostatic interactions. We confirmed the interactions by measuring the effects of mutations on the binding affinity. A comparison of our structural model with the chromatosome structure shows that TAF-Iβ blocks the DNA binding sites of H1.10. Our study provides insights into the structural mechanism whereby TAF-Iβ functions as a chaperone by preventing H1.10 from interacting with DNA directly.
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Affiliation(s)
- Haniqao Feng
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles D Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Abstract
Undifferentiated small round cell sarcomas (SRCSs) of bone and soft tissue comprise a heterogeneous group of highly aggressive tumours associated with a poor prognosis, especially in metastatic disease. SRCS entities mainly occur in the third decade of life and can exhibit striking disparities regarding preferentially affected sex and tumour localization. SRCSs comprise new entities defined by specific genetic abnormalities, namely EWSR1-non-ETS fusions, CIC-rearrangements or BCOR genetic alterations, as well as EWSR1-ETS fusions in the prototypic SRCS Ewing sarcoma. These gene fusions mainly encode aberrant oncogenic transcription factors that massively rewire the transcriptome and epigenome of the as yet unknown cell or cells of origin. Additional mutations or copy number variants are rare at diagnosis and, depending on the tumour entity, may involve TP53, CDKN2A and others. Histologically, these lesions consist of small round cells expressing variable levels of CD99 and specific marker proteins, including cyclin B3, ETV4, WT1, NKX3-1 and aggrecan, depending on the entity. Besides locoregional treatment that should follow standard protocols for sarcoma management, (neo)adjuvant treatment is as yet ill-defined but generally follows that of Ewing sarcoma and is associated with adverse effects that might compromise quality of life. Emerging studies on the molecular mechanisms of SRCSs and the development of genetically engineered animal models hold promise for improvements in early detection, disease monitoring, treatment-related toxicity, overall survival and quality of life.
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75
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Oliveira IH, Kjeldsen F, Melo-Braga MN, Verano-Braga T, de Andrade HM. Assessing the effects of Leishmania (Leishmania) infantum and L. (L.) amazonensis infections in macrophages using a quantitative proteome approach. Exp Parasitol 2022; 243:108413. [DOI: 10.1016/j.exppara.2022.108413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 11/30/2022]
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Portillo-Ledesma S, Wagley M, Schlick T. Chromatin transitions triggered by LH density as epigenetic regulators of the genome. Nucleic Acids Res 2022; 50:10328-10342. [PMID: 36130289 PMCID: PMC9561278 DOI: 10.1093/nar/gkac757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/26/2022] [Accepted: 09/02/2022] [Indexed: 11/14/2022] Open
Abstract
Motivated by experiments connecting linker histone (LH) deficiency to lymphoma progression and retinal disorders, we study by mesoscale chromatin modeling how LH density (ρ) induces gradual, as well sudden, changes in chromatin architecture and how the process depends on DNA linker length, LH binding dynamics and binding mode, salt concentration, tail modifications, and combinations of ρ and linker DNA length. We show that ρ tightly regulates the overall shape and compaction of the fiber, triggering a transition from an irregular disordered state to a compact and ordered structure. Such a structural transition, resembling B to A compartment transition connected with lymphoma of B cells, appears to occur around ρ = 0.5. The associated mechanism is DNA stem formation by LH binding, which is optimal when the lengths of the DNA linker and LH C-terminal domain are similar. Chromatin internal and external parameters are key regulators, promoting or impeding the transition. The LH density thus emerges as a critical tunable variable in controlling cellular functions through structural transitions of the genome.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Meghna Wagley
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai 200062, China.,Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, NY 10012, USA.,Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003 USA
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77
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Fernández-Justel JM, Santa-María C, Martín-Vírgala S, Ramesh S, Ferrera-Lagoa A, Salinas-Pena M, Isoler-Alcaraz J, Maslon MM, Jordan A, Cáceres JF, Gómez M. Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner. Cell Rep 2022; 40:111329. [PMID: 36103831 PMCID: PMC7613722 DOI: 10.1016/j.celrep.2022.111329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/04/2022] [Accepted: 08/17/2022] [Indexed: 12/24/2022] Open
Abstract
Linker histones are highly abundant chromatin-associated proteins with well-established structural roles in chromatin and as general transcriptional repressors. In addition, it has been long proposed that histone H1 exerts context-specific effects on gene expression. Here, we identify a function of histone H1 in chromatin structure and transcription using a range of genomic approaches. In the absence of histone H1, there is an increase in the transcription of non-coding RNAs, together with reduced levels of m6A modification leading to their accumulation on chromatin and causing replication-transcription conflicts. This strongly suggests that histone H1 prevents non-coding RNA transcription and regulates non-coding transcript turnover on chromatin. Accordingly, altering the m6A RNA methylation pathway rescues the replicative phenotype of H1 loss. This work unveils unexpected regulatory roles of histone H1 on non-coding RNA turnover and m6A deposition, highlighting the intimate relationship between chromatin conformation, RNA metabolism, and DNA replication to maintain genome performance.
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Affiliation(s)
- José Miguel Fernández-Justel
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Cristina Santa-María
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Sara Martín-Vírgala
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Shreya Ramesh
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Alberto Ferrera-Lagoa
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Mónica Salinas-Pena
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Javier Isoler-Alcaraz
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe South Road, Edinburgh EH4 2XU, UK
| | - Albert Jordan
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe South Road, Edinburgh EH4 2XU, UK
| | - María Gómez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain.
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78
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Zhang H, Huo QY, Gao YQ. DNA Sequence-Dependent Binding of Linker Histone gH1 Regulates Nucleosome Conformations. J Phys Chem B 2022; 126:6771-6779. [PMID: 36062461 DOI: 10.1021/acs.jpcb.2c03785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence-dependent binding between DNA and proteins in chromatin is an essential part of gene expression. Linker histone H1 is an important protein in the regulation of chromatin compartmentalization and compaction, and its binding with the nucleosome is sensitive to the DNA sequence. Although the interactions of H1 and DNA have been widely investigated, the mechanism of nucleosome conformation changes induced by the DNA-sequence-dependent binding with gH1 (globular H1.0) remains largely unclear at the atomic level. In the present molecular dynamics simulations, both linker and dyad DNAs were mutated to investigate the conformational changes of the nucleosome induced by the sequence-dependent binding of gH1 based on the on-dyad binding mode. Our results indicate that gH1 is insensitive to the DNA sequence of the dyad DNA but presents an apparent preference to linker DNA with an AT-rich sequence. Moreover, this specific binding induces the entry/exit region of a nucleosome to a tight conformation and regulates the accessibility of core histones. Considering that the entry/exit region of the nucleosome is a crucial binding site for many functional proteins related to gene expression, the conformational change at this region could represent an important gene regulation signal.
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Affiliation(s)
- Hong Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qin Yuan Huo
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
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79
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Jiang XC, Tu FH, Wei LY, Wang BZ, Yuan H, Yuan JM, Rao Y, Huang SL, Li QJ, Ou TM, Wang HG, Tan JH, Chen SB, Huang ZS. Discovery of a Novel G-Quadruplex and Histone Deacetylase (HDAC) Dual-Targeting Agent for the Treatment of Triple-Negative Breast Cancer. J Med Chem 2022; 65:12346-12366. [PMID: 36053318 DOI: 10.1021/acs.jmedchem.2c01058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of triple-negative breast cancer (TNBC) is highly associated with G-quadruplex (G4); thus, targeting G4 is a potential strategy for TNBC therapy. Because concomitant histone deacetylases (HDAC) inhibition could amplify the impact of G4-targeting compounds, we designed and synthesized two novel series of G4/HDAC dual-targeting compounds by connecting the zinc-binding pharmacophore of HDAC inhibitors to the G4-targeting isaindigotone scaffold (1). Among the new compounds, a6 with the potent HDAC inhibitory and G4 stabilizing activity could induce more DNA G4 formation than SAHA and 1 in TNBC cells. Remarkably, a6 caused more G4-related DNA damage and G4-related differentially expressed genes, consistent with its effect on disrupting the cell cycle, invasion, and glycolysis. Furthermore, a6 significantly suppresses the proliferation of various TNBC cells and the MDA-MB-231 xenograft model without evident toxicity. Our study suggests a novel strategy for TNBC therapeutics through dual-targeting HDAC and G4.
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Affiliation(s)
- Xin-Chen Jiang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Fang-Hai Tu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Li-Yuan Wei
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Bo-Zheng Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jing-Mei Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Yong Rao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shi-Liang Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Qing-Jiang Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hong-Gen Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
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80
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Bernués J, Izquierdo-Boulstridge A, Reina O, Castejón L, Fernández-Castañer E, Leal N, Guerrero-Pepinosa N, Bonet-Costa C, Vujatovic O, Climent-Cantó P, Azorín F. Lysine 27 dimethylation of Drosophila linker histone dH1 contributes to heterochromatin organization independently of H3K9 methylation. Nucleic Acids Res 2022; 50:9212-9225. [PMID: 36039761 PMCID: PMC9458452 DOI: 10.1093/nar/gkac716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 08/01/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Post-translational modifications (PTMs) of core histones are important epigenetic determinants that correlate with functional chromatin states. However, despite multiple linker histone H1s PTMs have been identified, little is known about their genomic distribution and contribution to the epigenetic regulation of chromatin. Here, we address this question in Drosophila that encodes a single somatic linker histone, dH1. We previously reported that dH1 is dimethylated at K27 (dH1K27me2). Here, we show that dH1K27me2 is a major PTM of Drosophila heterochromatin. At mitosis, dH1K27me2 accumulates at pericentromeric heterochromatin, while, in interphase, it is also detected at intercalary heterochromatin. ChIPseq experiments show that >98% of dH1K27me2 enriched regions map to heterochromatic repetitive DNA elements, including transposable elements, simple DNA repeats and satellite DNAs. Moreover, expression of a mutated dH1K27A form, which impairs dH1K27me2, alters heterochromatin organization, upregulates expression of heterochromatic transposable elements and results in the accumulation of RNA:DNA hybrids (R-loops) in heterochromatin, without affecting H3K9 methylation and HP1a binding. The pattern of dH1K27me2 is H3K9 methylation independent, as it is equally detected in flies carrying a H3K9R mutation, and is not affected by depletion of Su(var)3-9, HP1a or Su(var)4-20. Altogether these results suggest that dH1K27me2 contributes to heterochromatin organization independently of H3K9 methylation.
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Affiliation(s)
- Jordi Bernués
- To whom correspondence should be addressed. Tel: +34 934034960;
| | - Andrea Izquierdo-Boulstridge
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lucía Castejón
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Elena Fernández-Castañer
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Núria Leal
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Nancy Guerrero-Pepinosa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Carles Bonet-Costa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Olivera Vujatovic
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Paula Climent-Cantó
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
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81
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Chen JJ, Stermer D, Tanny JC. Decoding histone ubiquitylation. Front Cell Dev Biol 2022; 10:968398. [PMID: 36105353 PMCID: PMC9464978 DOI: 10.3389/fcell.2022.968398] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Histone ubiquitylation is a critical part of both active and repressed transcriptional states, and lies at the heart of DNA damage repair signaling. The histone residues targeted for ubiquitylation are often highly conserved through evolution, and extensive functional studies of the enzymes that catalyze the ubiquitylation and de-ubiquitylation of histones have revealed key roles linked to cell growth and division, development, and disease in model systems ranging from yeast to human cells. Nonetheless, the downstream consequences of these modifications have only recently begun to be appreciated on a molecular level. Here we review the structure and function of proteins that act as effectors or “readers” of histone ubiquitylation. We highlight lessons learned about how ubiquitin recognition lends specificity and function to intermolecular interactions in the context of transcription and DNA repair, as well as what this might mean for how we think about histone modifications more broadly.
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82
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Li S, Shi Y, Dang Y, Hu B, Xiao L, Zhao P, Wang S, Zhang K. Linker histone H1FOO is required for bovine preimplantation development by regulating lineage specification and chromatin structure. Biol Reprod 2022; 107:1425-1438. [PMID: 36001353 DOI: 10.1093/biolre/ioac167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/11/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Linker histone H1 binds to the nucleosome and is implicated in the regulation of the chromatin structure and function. The H1 variant H1FOO is heavily expressed in oocytes and early embryos. However, given the poor homology of H1FOO among mammals, the functional role of H1FOO during preimplantation embryonic development remains largely unknown, especially in domestic animals. Here, we find that H1FOO is not only expressed in oocytes and preimplantation embryos but granulosa cells and spermatids in cattle. We then demonstrate that the interference of H1FOO results in preimplantation embryonic developmental arrest in cattle using either RNA editing or Trim-Away approach. H1FOO depletion leads to a compromised expression of critical lineage-specific genes at the morula stage and affects the establishment of cell polarity. Interestingly, H1FOO depletion causes a significant increase in the expression of genes encoding other linker H1 and core histones. Concurrently, there is an increase of H3K9me3 and H3K27me3, two markers of repressive chromatin and a decrease of H4K16ac, a marker of open chromatin. Importantly, overexpression of bovine H1FOO results in severe embryonic developmental defects. In sum, we propose that H1FOO controls the proper chromatin structure that is crucial for the fidelity of cell polarization and lineage specification during bovine preimplantation development.
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Affiliation(s)
- Shuang Li
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Shi
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yanna Dang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Bingjie Hu
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lieying Xiao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Panpan Zhao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohua Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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83
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Patra SK, Szyf M. Epigenetic perspectives of COVID-19: Virus infection to disease progression and therapeutic control. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166527. [PMID: 36002132 PMCID: PMC9393109 DOI: 10.1016/j.bbadis.2022.166527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022]
Abstract
COVID-19 has caused numerous deaths as well as imposed social isolation and upheaval world-wide. Although, the genome and the composition of the virus, the entry process and replication mechanisms are well investigated from by several laboratories across the world, there are many unknown remaining questions. For example, what are the functions of membrane lipids during entry, packaging and exit of virus particles? Also, the metabolic aspects of the infected tissue cells are poorly understood. In the course of virus replication and formation of virus particles within the host cell, the enhanced metabolic activities of the host is directly proportional to viral loads. The epigenetic landscape of the host cells is also altered, particularly the expression/repression of genes associated with cellular metabolism as well as cellular processes that are antagonistic to the virus. Metabolic pathways are enzyme driven processes and the expression profile and mechanism of regulations of the respective genes encoding those enzymes during the course of pathogen invasion might be highly informative on the course of the disease. Recently, the metabolic profile of the patients' sera have been analysed from few patients. In view of this, and to gain further insights into the roles that epigenetic mechanisms might play in this scenario in regulation of metabolic pathways during the progression of COVID-19 are discussed and summarised in this contribution for ensuring best therapy.
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Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McIntyre Medical Sciences Building, McGill University, Montreal, QC H3G 1Y6, Canada
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84
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Mitchener MM, Muir TW. Oncohistones: Exposing the nuances and vulnerabilities of epigenetic regulation. Mol Cell 2022; 82:2925-2938. [PMID: 35985302 PMCID: PMC9482148 DOI: 10.1016/j.molcel.2022.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 07/14/2022] [Indexed: 12/19/2022]
Abstract
Work over the last decade has uncovered a new layer of epigenetic dysregulation. It is now appreciated that somatic missense mutations in histones, the packaging agents of genomic DNA, are often associated with human pathologies, especially cancer. Although some of these "oncohistone" mutations are thought to be key drivers of cancer, the impacts of the majority of them on disease onset and progression remain to be elucidated. Here, we survey this rapidly expanding research field with particular emphasis on how histone mutants, even at low dosage, can corrupt chromatin states. This work is unveiling the remarkable intricacies of epigenetic control mechanisms. Throughout, we highlight how studies of oncohistones have leveraged, and in some cases fueled, the advances in our ability to manipulate and interrogate chromatin at the molecular level.
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Affiliation(s)
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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85
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He P, Zhang C, Ji Y, Ge MK, Yu Y, Zhang N, Yang S, Yu JX, Shen SM, Chen GQ. Epithelial cells-enriched lncRNA SNHG8 regulates chromatin condensation by binding to Histone H1s. Cell Death Differ 2022; 29:1569-1581. [PMID: 35140358 PMCID: PMC9345976 DOI: 10.1038/s41418-022-00944-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/12/2022] Open
Abstract
Linker histone H1 proteins contain many variants in mammalian and can stabilize the condensed state of chromatin by binding to nucleosomes and promoting a more inaccessible structure of DNA. However, it is poorly understood how the binding of histone H1s to chromatin DNA is regulated. Screened as one of a collection of epithelial cells-enriched long non-coding RNAs (lncRNAs), here we found that small nucleolar RNA host gene 8 (SNHG8) is a chromatin-localized lncRNA and presents strong interaction and phase separation with histone H1 variants. Moreover, SNHG8 presents stronger ability to bind H1s than linker DNA, and outcompetes linker DNA for H1 binding. Consequently, loss of SNHG8 increases the amount of H1s that bind to chromatin, promotes chromatin condensation, and induces an epithelial differentiation-associated gene expression pattern. Collectively, our results propose that the highly abundant SNHG8 in epithelial cells keeps histone H1 variants out of nucleosome and its loss contributes to epithelial cell differentiation.
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Affiliation(s)
- Ping He
- State Key Laboratory of Oncogenes and Related Genes, and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Renji hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200127, China
| | - Cheng Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Yan Ji
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Meng-Kai Ge
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Yun Yu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Na Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Shuo Yang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China
| | - Jian-Xiu Yu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, SJTU-SM, Shanghai, 200025, China
| | - Shao-Ming Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China.
| | - Guo-Qiang Chen
- State Key Laboratory of Oncogenes and Related Genes, and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Renji hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200127, China. .,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai, 200025, China.
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86
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Czaja AJ. Epigenetic Aspects and Prospects in Autoimmune Hepatitis. Front Immunol 2022; 13:921765. [PMID: 35844554 PMCID: PMC9281562 DOI: 10.3389/fimmu.2022.921765] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
The observed risk of autoimmune hepatitis exceeds its genetic risk, and epigenetic factors that alter gene expression without changing nucleotide sequence may help explain the disparity. Key objectives of this review are to describe the epigenetic modifications that affect gene expression, discuss how they can affect autoimmune hepatitis, and indicate prospects for improved management. Multiple hypo-methylated genes have been described in the CD4+ and CD19+ T lymphocytes of patients with autoimmune hepatitis, and the circulating micro-ribonucleic acids, miR-21 and miR-122, have correlated with laboratory and histological features of liver inflammation. Both epigenetic agents have also correlated inversely with the stage of liver fibrosis. The reduced hepatic concentration of miR-122 in cirrhosis suggests that its deficiency may de-repress the pro-fibrotic prolyl-4-hydroxylase subunit alpha-1 gene. Conversely, miR-155 is over-expressed in the liver tissue of patients with autoimmune hepatitis, and it may signify active immune-mediated liver injury. Different epigenetic findings have been described in diverse autoimmune and non-autoimmune liver diseases, and these changes may have disease-specificity. They may also be responses to environmental cues or heritable adaptations that distinguish the diseases. Advances in epigenetic editing and methods for blocking micro-ribonucleic acids have improved opportunities to prove causality and develop site-specific, therapeutic interventions. In conclusion, the role of epigenetics in affecting the risk, clinical phenotype, and outcome of autoimmune hepatitis is under-evaluated. Full definition of the epigenome of autoimmune hepatitis promises to enhance understanding of pathogenic mechanisms and satisfy the unmet clinical need to improve therapy for refractory disease.
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Affiliation(s)
- Albert J. Czaja
- *Correspondence: Albert J. Czaja, ; orcid.org/0000-0002-5024-3065
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87
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Yamamoto T, Schiessel H. Loop extrusion driven volume phase transition of entangled chromosomes. Biophys J 2022; 121:2742-2750. [PMID: 35706364 DOI: 10.1016/j.bpj.2022.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/26/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Experiments on reconstituted chromosomes have revealed that mitotic chromosomes are assembled even without nucleosomes. When topoisomerase II (topo II) is depleted from such reconstituted chromosomes, these chromosomes are not disentangled and form "sparklers," where DNA and linker histone are condensed in the core and condensin is localized at the periphery. To understand the mechanism of the assembly of sparklers, we here take into account the loop extrusion by condensin in an extension of the theory of entangled polymer gels. The loop extrusion stiffens an entangled DNA network because DNA segments in the elastically effective chains are translocated to loops, which are elastically ineffective. Our theory predicts that the loop extrusion by condensin drives the volume phase transition that collapses a swollen entangled DNA gel because the stiffening of the network destabilizes the swollen phase. This may be an important piece to understand the mechanism of the assembly of mitotic chromosomes.
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Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan.
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
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88
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Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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89
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Papin A, Cesarman E, Melnick A. 3D chromosomal architecture in germinal center B cells and its alterations in lymphomagenesis. Curr Opin Genet Dev 2022; 74:101915. [PMID: 35550952 DOI: 10.1016/j.gde.2022.101915] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022]
Abstract
In eukaryotic cells, the genome is three dimensionally (3D) organized with DNA interaction dynamics and topology changes that regulate gene expression and drive cell fate. Upon antigen stimulation, naive B cells are activated and form germinal centers (GC) for the generation of memory B cells and plasma cells. Thereby, terminal B-cell differentiation and associated humoral immune response require massive but rigorous 3D DNA reorganization. Here, we review the dynamics of genome reorganization during GC formation and the impact of its alterations on lymphomagenesis from the nucleosome structure to the higher order chromosome organization. We particularly discuss the identified architects of 3D DNA in GC B cells and the role of their mutations in B-cell lymphomas.
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Affiliation(s)
- Antonin Papin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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90
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Yamaguchi K, Chen X, Oji A, Hiratani I, Defossez PA. Large-Scale Chromatin Rearrangements in Cancer. Cancers (Basel) 2022; 14:cancers14102384. [PMID: 35625988 PMCID: PMC9139990 DOI: 10.3390/cancers14102384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cancers have many genetic mutations such as nucleotide changes, deletions, amplifications, and chromosome gains or losses. Some of these genetic alterations directly contribute to the initiation and progression of tumors. In parallel to these genetic changes, cancer cells acquire modifications to their chromatin landscape, i.e., to the marks that are carried by DNA and the histone proteins it is associated with. These “epimutations” have consequences for gene expression and genome stability, and also contribute to tumoral initiation and progression. Some of these chromatin changes are very local, affecting just one or a few genes. In contrast, some chromatin alterations observed in cancer are more widespread and affect a large part of the genome. In this review, we present different types of large-scale chromatin rearrangements in cancer, explain how they may occur, and why they are relevant for cancer diagnosis and treatment. Abstract Epigenetic abnormalities are extremely widespread in cancer. Some of them are mere consequences of transformation, but some actively contribute to cancer initiation and progression; they provide powerful new biological markers, as well as new targets for therapies. In this review, we examine the recent literature and focus on one particular aspect of epigenome deregulation: large-scale chromatin changes, causing global changes of DNA methylation or histone modifications. After a brief overview of the one-dimension (1D) and three-dimension (3D) epigenome in healthy cells and of its homeostasis mechanisms, we use selected examples to describe how many different events (mutations, changes in metabolism, and infections) can cause profound changes to the epigenome and fuel cancer. We then present the consequences for therapies and briefly discuss the role of single-cell approaches for the future progress of the field.
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Affiliation(s)
- Kosuke Yamaguchi
- UMR7216 Epigenetics and Cell Fate, Université Paris Cité, CNRS, F-75006 Paris, France; (K.Y.); (X.C.)
| | - Xiaoying Chen
- UMR7216 Epigenetics and Cell Fate, Université Paris Cité, CNRS, F-75006 Paris, France; (K.Y.); (X.C.)
| | - Asami Oji
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), Kobe 650-0047, Japan; (A.O.); (I.H.)
| | - Ichiro Hiratani
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), Kobe 650-0047, Japan; (A.O.); (I.H.)
| | - Pierre-Antoine Defossez
- UMR7216 Epigenetics and Cell Fate, Université Paris Cité, CNRS, F-75006 Paris, France; (K.Y.); (X.C.)
- Correspondence: ; Tel.: +33-157278916
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91
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Latham AP, Zhang B. On the stability and layered organization of protein-DNA condensates. Biophys J 2022; 121:1727-1737. [PMID: 35364104 PMCID: PMC9117872 DOI: 10.1016/j.bpj.2022.03.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/02/2021] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Multi-component phase separation is emerging as a key mechanism for the formation of biological condensates that play essential roles in signal sensing and transcriptional regulation. The molecular factors that dictate these condensates' stability and spatial organization are not fully understood, and it remains challenging to predict their microstructures. Using a near-atomistic, chemically accurate force field, we studied the phase behavior of chromatin regulators that are crucial for heterochromatin organization and their interactions with DNA. Our computed phase diagrams recapitulated previous experimental findings on different proteins. They revealed a strong dependence of condensate stability on the protein-DNA mixing ratio as a result of balancing protein-protein interactions and charge neutralization. Notably, a layered organization was observed in condensates formed by mixing HP1, histone H1, and DNA. This layered organization may be of biological relevance, as it enables cooperative DNA packaging between the two chromatin regulators: histone H1 softens the DNA to facilitate the compaction induced by HP1 droplets. Our study supports near-atomistic models as a valuable tool for characterizing the structure and stability of biological condensates.
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Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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92
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Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P. Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. Nat Struct Mol Biol 2022; 29:493-501. [PMID: 35581345 PMCID: PMC9113941 DOI: 10.1038/s41594-022-00768-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/01/2022] [Indexed: 01/17/2023]
Abstract
Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions. Cryo-EM structures of human H1-containing tetranucleosome arrays with distinct, physiological nucleosome repeat lengths reveal that nucleosomes assume a zig-zag arrangement and H1 binds to stacked nucleosomes with longer linker DNA.
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Affiliation(s)
- Marco Dombrowski
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Maik Engeholm
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Svetlana Dodonova
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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93
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Genome-wide identification of chromatin regulators in Sorghum bicolor. 3 Biotech 2022; 12:117. [PMID: 35547013 PMCID: PMC9033926 DOI: 10.1007/s13205-022-03181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/03/2022] [Indexed: 11/01/2022] Open
Abstract
Chromatin regulators play important roles in plant development and stress response. In this study, we identified totally 231 chromatin regulators including 63 histones, 29 histone chaperones, 101 histone modification enzymes, and 38 chromatin remodeling factors from Sorghum bicolor (L.) Moench. Most of these chromatin regulators are homologous to their counterparts in Arabidopsis or rice. However, sorghum genome evolves a few novel histone variants specific to some grass species and a sorghum-unique chromatin remodeling factor that contain the domains belonging to the elongation factor EF-Tu and the histone chaperone SPT16. Finally, we performed co-expression analysis for the chromatin regulator-encoding genes by clustering the expression patterns of these genes. Our results provide useful information for the future studies on the mechanism of epigenetic regulation in sorghum and its roles in development and stress response. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03181-8.
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94
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Leicher R, Osunsade A, Chua GNL, Faulkner SC, Latham AP, Watters JW, Nguyen T, Beckwitt EC, Christodoulou-Rubalcava S, Young PG, Zhang B, David Y, Liu S. Single-stranded nucleic acid binding and coacervation by linker histone H1. Nat Struct Mol Biol 2022; 29:463-471. [PMID: 35484234 PMCID: PMC9117509 DOI: 10.1038/s41594-022-00760-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/14/2022] [Indexed: 02/04/2023]
Abstract
The H1 linker histone family is the most abundant group of eukaryotic chromatin-binding proteins. However, their contribution to chromosome structure and function remains incompletely understood. Here we use single-molecule fluorescence and force microscopy to directly visualize the behavior of H1 on various nucleic acid and nucleosome substrates. We observe that H1 coalesces around single-stranded DNA generated from tension-induced DNA duplex melting. Using a droplet fusion assay controlled by optical tweezers, we find that single-stranded nucleic acids mediate the formation of gel-like H1 droplets, whereas H1-double-stranded DNA and H1-nucleosome droplets are more liquid-like. Molecular dynamics simulations reveal that multivalent and transient engagement of H1 with unpaired DNA strands drives their enhanced phase separation. Using eGFP-tagged H1, we demonstrate that inducing single-stranded DNA accumulation in cells causes an increase in H1 puncta that are able to fuse. We further show that H1 and Replication Protein A occupy separate nuclear regions, but that H1 colocalizes with the replication factor Proliferating Cell Nuclear Antigen, particularly after DNA damage. Overall, our results provide a refined perspective on the diverse roles of H1 in genome organization and maintenance, and indicate its involvement at stalled replication forks.
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Affiliation(s)
- Rachel Leicher
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Adewola Osunsade
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Sarah C Faulkner
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John W Watters
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Tuan Nguyen
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Emily C Beckwitt
- Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | | | - Paul G Young
- Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA.
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA.
- Tri-Institutional MD-PhD Program, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA.
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA.
- Tri-Institutional MD-PhD Program, New York, NY, USA.
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95
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Etier A, Dumetz F, Chéreau S, Ponts N. Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism. Toxins (Basel) 2022; 14:toxins14050317. [PMID: 35622565 PMCID: PMC9145779 DOI: 10.3390/toxins14050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Chromatin structure is a major regulator of DNA-associated processes, such as transcription, DNA repair, and replication. Histone post-translational modifications, or PTMs, play a key role on chromatin dynamics. PTMs are involved in a wide range of biological processes in eukaryotes, including fungal species. Their deposition/removal and their underlying functions have been extensively investigated in yeasts but much less in other fungi. Nonetheless, the major role of histone PTMs in regulating primary and secondary metabolisms of filamentous fungi, including human and plant pathogens, has been pinpointed. In this review, an overview of major identified PTMs and their respective functions in fungi is provided, with a focus on filamentous fungi when knowledge is available. To date, most of these studies investigated histone acetylations and methylations, but the development of new methodologies and technologies increasingly allows the wider exploration of other PTMs, such as phosphorylation, ubiquitylation, sumoylation, and acylation. Considering the increasing number of known PTMs and the full range of their possible interactions, investigations of the subsequent Histone Code, i.e., the biological consequence of the combinatorial language of all histone PTMs, from a functional point of view, are exponentially complex. Better knowledge about histone PTMs would make it possible to efficiently fight plant or human contamination, avoid the production of toxic secondary metabolites, or optimize the industrial biosynthesis of certain beneficial compounds.
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96
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Gurova K. Can aggressive cancers be identified by the "aggressiveness" of their chromatin? Bioessays 2022; 44:e2100212. [PMID: 35452144 DOI: 10.1002/bies.202100212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022]
Abstract
Phenotypic plasticity is a crucial feature of aggressive cancer, providing the means for cancer progression. Stochastic changes in tumor cell transcriptional programs increase the chances of survival under any condition. I hypothesize that unstable chromatin permits stochastic transitions between transcriptional programs in aggressive cancers and supports non-genetic heterogeneity of tumor cells as a basis for their adaptability. I present a mechanistic model for unstable chromatin which includes destabilized nucleosomes, mobile chromatin fibers and random enhancer-promoter contacts, resulting in stochastic transcription. I suggest potential markers for "unsettled" chromatin in tumors associated with poor prognosis. Although many of the characteristics of unstable chromatin have been described, they were mostly used to explain changes in the transcription of individual genes. I discuss approaches to evaluate the role of unstable chromatin in non-genetic tumor cell heterogeneity and suggest using the degree of chromatin instability and transcriptional noise in tumor cells to predict cancer aggressiveness.
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Affiliation(s)
- Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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97
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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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98
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Serna-Pujol N, Salinas-Pena M, Mugianesi F, Le Dily F, Marti-Renom MA, Jordan A. Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion. Nucleic Acids Res 2022; 50:3892-3910. [PMID: 35380694 PMCID: PMC9023279 DOI: 10.1093/nar/gkac226] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022] Open
Abstract
Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.
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Affiliation(s)
- Núria Serna-Pujol
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
| | - Mónica Salinas-Pena
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
| | - Francesca Mugianesi
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - François Le Dily
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.,Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain.,Pompeu Fabra University, Doctor Aiguader 88, Barcelona 08003, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
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99
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Nothof SA, Magdinier F, Van-Gils J. Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological Implication. Genes (Basel) 2022; 13:genes13040639. [PMID: 35456445 PMCID: PMC9029427 DOI: 10.3390/genes13040639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Chromatin structure is an essential regulator of gene expression. Its state of compaction contributes to the regulation of genetic programs, in particular during differentiation. Epigenetic processes, which include post-translational modifications of histones, DNA methylation and implication of non-coding RNA, are powerful regulators of gene expression. Neurogenesis and neuronal differentiation are spatio-temporally regulated events that allow the formation of the central nervous system components. Here, we review the chromatin structure and post-translational histone modifications associated with neuronal differentiation. Studying the impact of histone modifications on neuronal differentiation improves our understanding of the pathophysiological mechanisms of chromatinopathies and opens up new therapeutic avenues. In addition, we will discuss techniques for the analysis of histone modifications on a genome-wide scale and the pathologies associated with the dysregulation of the epigenetic machinery.
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Affiliation(s)
- Sophie A. Nothof
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Frédérique Magdinier
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Julien Van-Gils
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
- Reference Center AD SOOR, AnDDI-RARE, Inserm U 1211, Medical Genetics Department, Bordeaux University, Center Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France
- Correspondence:
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100
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Reece AS, Hulse GK. Geotemporospatial and causal inferential epidemiological overview and survey of USA cannabis, cannabidiol and cannabinoid genotoxicity expressed in cancer incidence 2003-2017: part 1 - continuous bivariate analysis. Arch Public Health 2022; 80:99. [PMID: 35354487 PMCID: PMC8966217 DOI: 10.1186/s13690-022-00811-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/29/2022] [Indexed: 01/07/2023] Open
Abstract
Background The genotoxic and cancerogenic impacts of population-wide cannabinoid exposure remains an open but highly salient question. The present report examines these issues from a continuous bivariate perspective with subsequent reports continuing categorical and detailed analyses. Methods Age-standardized state census incidence of 28 cancer types (including “All (non-skin) Cancer”) was sourced using SEER*Stat software from Centres for Disease Control and National Cancer Institute across US states 2001–2017. It was joined with drug exposure data from the nationally representative National Survey of Drug Use and Health conducted annually by the Substance Abuse and Mental Health Services Administration 2003–2017, response rate 74.1%. Cannabinoid data was from Federal seizure data. Income and ethnicity data sourced from the US Census Bureau. Data was processed in R. Results Nineteen thousand eight hundred seventy-seven age-standardized cancer rates were returned. Based on these rates and state populations this equated to 51,623,922 cancer cases over an aggregated population 2003–2017 of 124,896,418,350. Regression lines were charted for cancer-substance exposures for cigarettes, alcohol use disorder (AUD), cannabis, THC, cannabidiol, cannabichromene, cannabinol and cannabigerol. In this substance series positive trends were found for 14, 9, 6, 9, 12, 6, 9 and 7 cancers; with largest minimum E-Values (mEV) of 1.76 × 109, 4.67 × 108, 2.74 × 104, 4.72, 2.34 × 1018, 2.74 × 1017, 1.90 × 107, 5.05 × 109; and total sum of exponents of mEV of 34, 32, 13, 0, 103, 58, 25, 31 indicating that cannabidiol followed by cannabichromene are the most strongly implicated in environmental carcinogenesis. Breast cancer was associated with tobacco and all cannabinoids (from mEV = 3.53 × 109); “All Cancer” (non-skin) linked with cannabidiol (mEV = 1.43 × 1011); pediatric AML linked with cannabis (mEV = 19.61); testicular cancer linked with THC (mEV = 1.33). Cancers demonstrating elevated mEV in association with THC were: thyroid, liver, pancreas, AML, breast, oropharynx, CML, testis and kidney. Cancers demonstrating elevated mEV in relation to cannabidiol: prostate, bladder, ovary, all cancers, colorectum, Hodgkins, brain, Non-Hodgkins lymphoma, esophagus, breast and stomach. Conclusion Data suggest that cannabinoids including THC and cannabidiol are important community carcinogens exceeding the effects of tobacco or alcohol. Testicular, (prostatic) and ovarian tumours indicate mutagenic corruption of the germline in both sexes; pediatric tumourigenesis confirms transgenerational oncogenesis; quantitative criteria implying causality are fulfilled. Supplementary Information The online version contains supplementary material available at 10.1186/s13690-022-00811-8.
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Affiliation(s)
- Albert Stuart Reece
- Division of Psychiatry, University of Western Australia, Crawley, WA, 6009, Australia. .,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia. .,, Brisbane, Australia.
| | - Gary Kenneth Hulse
- Division of Psychiatry, University of Western Australia, Crawley, WA, 6009, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
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