1
|
García‐Gomis D, López J, Calderón A, Andrés M, Ponte I, Roque A. Proteasome-dependent degradation of histone H1 subtypes is mediated by its C-terminal domain. Protein Sci 2024; 33:e4970. [PMID: 38591484 PMCID: PMC11002908 DOI: 10.1002/pro.4970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/29/2024] [Accepted: 03/10/2024] [Indexed: 04/10/2024]
Abstract
Histone H1 is involved in chromatin compaction and dynamics. In human cells, the H1 complement is formed by different amounts of somatic H1 subtypes, H1.0-H1.5 and H1X. The amount of each variant depends on the cell type, the cell cycle phase, and the time of development and can be altered in disease. However, the mechanisms regulating H1 protein levels have not been described. We have analyzed the contribution of the proteasome to the degradation of H1 subtypes in human cells using two different inhibitors: MG132 and bortezomib. H1 subtypes accumulate upon treatment with both drugs, indicating that the proteasome is involved in the regulation of H1 protein levels. Proteasome inhibition caused a global increase in cytoplasmatic H1, with slight changes in the composition of H1 bound to chromatin and chromatin accessibility and no alterations in the nucleosome repeat length. The analysis of the proteasome degradation pathway showed that H1 degradation is ubiquitin-independent. The whole protein and its C-terminal domain can be degraded directly by the 20S proteasome in vitro. Partial depletion of PA28γ revealed that this regulatory subunit contributes to H1 degradation within the cell. Our study shows that histone H1 protein levels are under tight regulation to prevent its accumulation in the nucleus. We revealed a new regulatory mechanism for histone H1 degradation, where the C-terminal disordered domain is responsible for its targeting and degradation by the 20S proteasome, a process enhanced by the regulatory subunit PA28γ.
Collapse
Affiliation(s)
- D. García‐Gomis
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - J. López
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - A. Calderón
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - M. Andrés
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - I. Ponte
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - A. Roque
- Biochemistry and Molecular Biology Department, Biosciences FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| |
Collapse
|
2
|
Suárez R, Chapela SP, Álvarez-Córdova L, Bautista-Valarezo E, Sarmiento-Andrade Y, Verde L, Frias-Toral E, Sarno G. Epigenetics in Obesity and Diabetes Mellitus: New Insights. Nutrients 2023; 15:nu15040811. [PMID: 36839169 PMCID: PMC9963127 DOI: 10.3390/nu15040811] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/08/2023] Open
Abstract
A long-term complication of obesity is the development of type 2 diabetes (T2D). Patients with T2D have been described as having epigenetic modifications. Epigenetics is the post-transcriptional modification of DNA or associated factors containing genetic information. These environmentally-influenced modifications, maintained during cell division, cause stable changes in gene expression. Epigenetic modifications of T2D are DNA methylation, acetylation, ubiquitylation, SUMOylation, and phosphorylation at the lysine residue at the amino terminus of histones, affecting DNA, histones, and non-coding RNA. DNA methylation has been shown in pancreatic islets, adipose tissue, skeletal muscle, and the liver. Furthermore, epigenetic changes have been observed in chronic complications of T2D, such as diabetic nephropathy, diabetic retinopathy, and diabetic neuropathy. Recently, a new drug has been developed which acts on bromodomains and extraterminal (BET) domain proteins, which operate like epigenetic readers and communicate with chromatin to make DNA accessible for transcription by inhibiting them. This drug (apabetalone) is being studied to prevent major adverse cardiovascular events in people with T2D, low HDL cholesterol, chronic kidney failure, and recent coronary events. This review aims to describe the relationship between obesity, long-term complications such as T2D, and epigenetic modifications and their possible treatments.
Collapse
Affiliation(s)
- Rosario Suárez
- School of Medicine, Universidad Técnica Particular de Loja, Calle París, San Cayetano Alto, Loja 110101, Ecuador
| | - Sebastián P. Chapela
- Departamento de Bioquímica Humana, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABE, Argentina
- Hospital Británico de Buenos Aires, Equipo de Soporte Nutricional, Buenos Aires C1280AEB, Argentina
- Correspondence: ; Tel.: +54-91168188308
| | - Ludwig Álvarez-Córdova
- School of Medicine, Universidad Católica Santiago de Guayaquil, Av. Pdte. Carlos Julio Arosemena Tola, Guayaquil 090615, Ecuador
- Carrera de Nutrición y Dietética, Facultad de Ciencias Médicas, Universidad Católica De Santiago de Guayaquil, Av. Pdte. Carlos Julio Arosemena Tola, Guayaquil 090615, Ecuador
| | - Estefanía Bautista-Valarezo
- School of Medicine, Universidad Técnica Particular de Loja, Calle París, San Cayetano Alto, Loja 110101, Ecuador
| | - Yoredy Sarmiento-Andrade
- School of Medicine, Universidad Técnica Particular de Loja, Calle París, San Cayetano Alto, Loja 110101, Ecuador
| | - Ludovica Verde
- Centro Italiano per la Cura e il Benessere del Paziente con Obesità (C.I.B.O), Department of Clinical Medicine and Surgery, Endocrinology Unit, University Medical School of Naples, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Evelyn Frias-Toral
- School of Medicine, Universidad Católica Santiago de Guayaquil, Av. Pdte. Carlos Julio Arosemena Tola, Guayaquil 090615, Ecuador
| | - Gerardo Sarno
- “San Giovanni di Dio e Ruggi D’Aragona” University Hospital, Scuola Medica Salernitana, 84131 Salerno, Italy
| |
Collapse
|
3
|
Hao F, Mishra LN, Jaya P, Jones R, Hayes JJ. Identification and Analysis of Six Phosphorylation Sites Within the Xenopus laevis Linker Histone H1.0 C-Terminal Domain Indicate Distinct Effects on Nucleosome Structure. Mol Cell Proteomics 2022; 21:100250. [PMID: 35618225 PMCID: PMC9243160 DOI: 10.1016/j.mcpro.2022.100250] [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: 11/13/2021] [Revised: 05/01/2022] [Accepted: 05/20/2022] [Indexed: 11/25/2022] Open
Abstract
As a key structural component of the chromatin of higher eukaryotes, linker histones (H1s) are involved in stabilizing the folding of extended nucleosome arrays into higher-order chromatin structures and function as a gene-specific regulator of transcription in vivo. The H1 C-terminal domain (CTD) is essential for high-affinity binding of linker histones to chromatin and stabilization of higher-order chromatin structure. Importantly, the H1 CTD is an intrinsically disordered domain that undergoes a drastic condensation upon binding to nucleosomes. Moreover, although phosphorylation is a prevalent post-translational modification within the H1 CTD, exactly where this modification is installed and how phosphorylation influences the structure of the H1 CTD remains unclear for many H1s. Using novel mass spectrometry techniques, we identified six phosphorylation sites within the CTD of the archetypal linker histone Xenopus H1.0. We then analyzed nucleosome-dependent CTD condensation and H1-dependent linker DNA organization for H1.0 in which the phosphorylated serine residues were replaced by glutamic acid residues (phosphomimics) in six independent mutants. We find that phosphomimetics at residues S117E, S155E, S181E, S188E, and S192E resulted in a significant reduction in nucleosome-bound H1.0 CTD condensation compared with unphosphorylated H1.0, whereas S130E did not alter CTD structure. Furthermore, we found distinct effects among the phosphomimetics on H1-dependent linker DNA trajectory, indicating unique mechanisms by which this modification can influence H1 CTD condensation. These results bring to light a novel role for linker histone phosphorylation in directly altering the structure of nucleosome-bound H1 and a potential novel mechanism for its effects on chromatin structure and function.
Collapse
Affiliation(s)
- Fanfan Hao
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA
| | - Laxmi N Mishra
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA
| | - Prasoon Jaya
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA; Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA.
| |
Collapse
|
4
|
Lai S, Jia J, Cao X, Zhou PK, Gao S. Molecular and Cellular Functions of the Linker Histone H1.2. Front Cell Dev Biol 2022; 9:773195. [PMID: 35087830 PMCID: PMC8786799 DOI: 10.3389/fcell.2021.773195] [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: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 01/14/2023] Open
Abstract
Linker histone H1.2, which belongs to the linker histone family H1, plays a crucial role in the maintenance of the stable higher-order structures of chromatin and nucleosomes. As a critical part of chromatin structure, H1.2 has an important function in regulating chromatin dynamics and participates in multiple other cellular processes as well. Recent work has also shown that linker histone H1.2 regulates the transcription levels of certain target genes and affects different processes as well, such as cancer cell growth and migration, DNA duplication and DNA repair. The present work briefly summarizes the current knowledge of linker histone H1.2 modifications. Further, we also discuss the roles of linker histone H1.2 in the maintenance of genome stability, apoptosis, cell cycle regulation, and its association with disease.
Collapse
Affiliation(s)
- Shuting Lai
- Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, China.,Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jin Jia
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China.,School of Medicine, University of South China, Hengyang, China
| | - Xiaoyu Cao
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China.,School of Life Sciences, Hebei University, Baoding, China
| | - Ping-Kun Zhou
- Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, China.,Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Shanshan Gao
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| |
Collapse
|
5
|
Mimura M, Tomita S, Sugai H, Shinkai Y, Ishihara S, Kurita R. Uncharged Components of Single-Stranded DNA Modulate Liquid-Liquid Phase Separation With Cationic Linker Histone H1. Front Cell Dev Biol 2021; 9:710729. [PMID: 34422830 PMCID: PMC8371396 DOI: 10.3389/fcell.2021.710729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/14/2021] [Indexed: 11/15/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of proteins and DNAs has been recognized as a fundamental mechanism for the formation of intracellular biomolecular condensates. Here, we show the role of the constituent DNA components, i.e., the phosphate groups, deoxyribose sugars, and nucleobases, in LLPS with a polycationic peptide, linker histone H1, a known key regulator of chromatin condensation. A comparison of the phase behavior of mixtures of H1 and single-stranded DNA-based oligomers in which one or more of the constituent moieties of DNA were removed demonstrated that not only the electrostatic interactions between the anionic phosphate groups of the oligomers and the cationic residues of H1, but also the interactions involving nucleobases and deoxyriboses (i) promoted the generation of spherical liquid droplets via LLPS as well as (ii) increased the density of DNA and decreased its fluidity within the droplets under low-salt conditions. Furthermore, we found the formation of non-spherical assemblies with both mobile and immobile fractions at relatively higher concentrations of H1 for all the oligomers. The roles of the DNA components that promote phase separation and modulate droplet characteristics revealed in this study will facilitate our understanding of the formation processes of the various biomolecular condensates containing nucleic acids, such as chromatin organization.
Collapse
Affiliation(s)
- Masahiro Mimura
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Shunsuke Tomita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hiroka Sugai
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yoichi Shinkai
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Sayaka Ishihara
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ryoji Kurita
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| |
Collapse
|
6
|
Zheng HT, Zhuang ZX, Chen CJ, Liao HY, Chen HL, Hsueh HC, Chen CF, Chen SE, Huang SY. Effects of acute heat stress on protein expression and histone modification in the adrenal gland of male layer-type country chickens. Sci Rep 2021; 11:6499. [PMID: 33753796 PMCID: PMC7985386 DOI: 10.1038/s41598-021-85868-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/08/2021] [Indexed: 01/31/2023] Open
Abstract
The adrenal gland responds to heat stress by epinephrine and glucocorticoid release to alleviate the adverse effects. This study investigated the effect of acute heat stress on the protein profile and histone modification in the adrenal gland of layer-type country chickens. A total of 192 roosters were subject to acute heat stress and thereafter classified into a resistant or susceptible group according to body temperature change. The iTRAQ analysis identified 80 differentially expressed proteins, in which the resistant group had a higher level of somatostatin and hydroxy-δ-5-steroid dehydrogenase but a lower parathymosin expression in accordance with the change of serum glucocorticoid levels. Histone modification analysis identified 115 histone markers. The susceptible group had a higher level of tri-methylation of histone H3 lysine 27 (H3K27me3) and showed a positive crosstalk with K36me and K37me in the H3 tails. The differential changes of body temperature projected in physiological regulation at the hypothalamus-pituitary-adrenal axis suggest the genetic heterogeneity in basic metabolic rate and efficiency for heat dissipation to acclimate to thermal stress and maintain body temperature homeostasis. The alteration of adrenal H3K27me3 level was associated with the endocrine function of adrenal gland and may contribute to the thermotolerance of chickens.
Collapse
Affiliation(s)
- Hao-Teng Zheng
- grid.260542.70000 0004 0532 3749Department of Animal Science, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan
| | - Zi-Xuan Zhuang
- grid.260542.70000 0004 0532 3749Department of Animal Science, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan
| | - Chao-Jung Chen
- grid.411508.90000 0004 0572 9415Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, 2 Yude Road, Taichung, 40447 Taiwan ,grid.254145.30000 0001 0083 6092Graduate Institute of Integrated Medicine, China Medical University, 91 Hsueh–Shih Road, Taichung, 40402 Taiwan
| | - Hsin-Yi Liao
- grid.411508.90000 0004 0572 9415Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, 2 Yude Road, Taichung, 40447 Taiwan
| | - Hung-Lin Chen
- grid.260542.70000 0004 0532 3749Department of Animal Science, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan
| | - Huang-Chun Hsueh
- grid.260542.70000 0004 0532 3749Department of Animal Science, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan
| | - Chih-Feng Chen
- grid.260542.70000 0004 0532 3749Department of Animal Science, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan ,grid.260542.70000 0004 0532 3749The iEGG and Animal Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan
| | - Shuen-Ei Chen
- grid.260542.70000 0004 0532 3749Department of Animal Science, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan ,grid.260542.70000 0004 0532 3749The iEGG and Animal Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan ,grid.260542.70000 0004 0532 3749Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan ,grid.260542.70000 0004 0532 3749Research Center for Sustainable Energy and Nanotechnology, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan
| | - San-Yuan Huang
- grid.260542.70000 0004 0532 3749Department of Animal Science, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan ,grid.260542.70000 0004 0532 3749The iEGG and Animal Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan ,grid.260542.70000 0004 0532 3749Research Center for Sustainable Energy and Nanotechnology, National Chung Hsing University, 145 Xingda Road, Taichung, 40227 Taiwan
| |
Collapse
|
7
|
Histone H1 Post-Translational Modifications: Update and Future Perspectives. Int J Mol Sci 2020; 21:ijms21165941. [PMID: 32824860 PMCID: PMC7460583 DOI: 10.3390/ijms21165941] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022] Open
Abstract
Histone H1 is the most variable histone and its role at the epigenetic level is less characterized than that of core histones. In vertebrates, H1 is a multigene family, which can encode up to 11 subtypes. The H1 subtype composition is different among cell types during the cell cycle and differentiation. Mass spectrometry-based proteomics has added a new layer of complexity with the identification of a large number of post-translational modifications (PTMs) in H1. In this review, we summarize histone H1 PTMs from lower eukaryotes to humans, with a particular focus on mammalian PTMs. Special emphasis is made on PTMs, whose molecular function has been described. Post-translational modifications in H1 have been associated with the regulation of chromatin structure during the cell cycle as well as transcriptional activation, DNA damage response, and cellular differentiation. Additionally, PTMs in histone H1 that have been linked to diseases such as cancer, autoimmune disorders, and viral infection are examined. Future perspectives and challenges in the profiling of histone H1 PTMs are also discussed.
Collapse
|
8
|
Demetriadou C, Koufaris C, Kirmizis A. Histone N-alpha terminal modifications: genome regulation at the tip of the tail. Epigenetics Chromatin 2020; 13:29. [PMID: 32680559 PMCID: PMC7367250 DOI: 10.1186/s13072-020-00352-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/09/2020] [Indexed: 01/07/2023] Open
Abstract
Histone proteins are decorated with numerous post-(PTMs) or co-(CTMs) translational modifications mainly on their unstructured tails, but also on their globular domain. For many decades research on histone modifications has been focused almost solely on the biological role of modifications occurring at the side-chain of internal amino acid residues. In contrast, modifications on the terminal N-alpha amino group of histones-despite being highly abundant and evolutionarily conserved-have been largely overlooked. This oversight has been due to the fact that these marks were being considered inert until recently, serving no regulatory functions. However, during the past few years accumulating evidence has drawn attention towards the importance of chemical marks added at the very N-terminal tip of histones and unveiled their role in key biological processes including aging and carcinogenesis. Further elucidation of the molecular mechanisms through which these modifications are regulated and by which they act to influence chromatin dynamics and DNA-based processes like transcription is expected to enlighten our understanding of their emerging role in controlling cellular physiology and contribution to human disease. In this review, we clarify the difference between N-alpha terminal (Nt) and internal (In) histone modifications; provide an overview of the different types of known histone Nt-marks and the associated histone N-terminal transferases (NTTs); and explore how they function to shape gene expression, chromatin architecture and cellular phenotypes.
Collapse
Affiliation(s)
- Christina Demetriadou
- Epigenetics Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Costas Koufaris
- Epigenetics Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Antonis Kirmizis
- Epigenetics Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus.
| |
Collapse
|
9
|
Application of CE-MS for the analysis of histones and histone modifications. Methods 2020; 184:125-134. [PMID: 32014606 DOI: 10.1016/j.ymeth.2020.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/02/2019] [Accepted: 01/26/2020] [Indexed: 02/02/2023] Open
Abstract
The analysis, identification and quantification of histones and their post-translational modifications plays a central role in chromatin research and in studying epigenetic regulations during physiological processes. In the last decade analytical strategies based on mass spectrometry have been greatly improved for providing a global view of single modification abundances or to determine combinatorial patterns of modifications. Presented here is a newly developed strategy for histone protein analysis and a number of applications are illustrated with an emphasis on PTM characterization. Capillary electrophoresis is coupled to mass spectrometry (CE-MS) and has proven to be a very promising concept as it enables to study intact histones (top-down proteomics) as well as the analysis of enzymatically digested proteins (bottom-up proteomics). This technology combines highly efficient low-flow CE separations with ionization in a single device and offers an orthogonal separation principle to conventional LC-MS analysis, thus expanding the existing analytical repertoire in a perfect manner.
Collapse
|
10
|
Chikhirzhina E, Starkova T, Polyanichko A. The Role of Linker Histones in Chromatin Structural Organization. 1. H1 Family Histones. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918060064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
11
|
Ribas TFA, Nagamachi CY, Aleixo A, Pinheiro MLS, O´Brien PCM, Ferguson-Smith MA, Yang F, Suarez P, Pieczarka JC. Chromosome painting in Glyphorynchus spirurus (Vieillot, 1819) detects a new fission in Passeriformes. PLoS One 2018; 13:e0202040. [PMID: 30138388 PMCID: PMC6107148 DOI: 10.1371/journal.pone.0202040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 07/26/2018] [Indexed: 11/18/2022] Open
Abstract
Glyphorynchus spirurus (GSP), also called the Wedge-billed Woodcreeper (Furnariidae) has an extensive distribution in the Americas, including the Atlantic coast of Brazil. Nevertheless, there is no information about its karyotype or genome organization. To contribute to the knowledge of chromosomal evolution in Passeriformes we analysed the karyotype of Glyphorynchus spirurus by classic and molecular cytogenetics methods. We show that Glyphorynchus spirurus has a 2n = 80 karyotype with a fundamental number (FN) of 84, similar to the avian putative ancestral karyotype (PAK). Glyphorynchus spirurus pair 1 was heteromorphic in the Tapajós population whereby the short arms varied in sizes, possibly due to a pericentric inversion, as described in other Furnariidae birds. FISH with the Histone H5 probe revealed a signal in the pericentromeric region of G. spirurus chromosome 5 and rDNA 18S showed interstitial signal in GSP-1. Chromosome painting with Gallus gallus (GGA) macrochromosomes 1-9 probes showed disruption of chromosome syntenies of GGA-1, 2 and 4 by fission in Glyphorynchus spirurus. Our results confirm that the GGA1 centric fission is a synapomorphic character for the phylogenetic branch composed of Strigiformes, Passeriformes, Columbiformes and Falconiformes. On the other hand, the GGA-2 fission is reported here for the first time in Passeriformes. Chromosome painting with BOE whole chromosome probes confirmed these rearrangements in Glyphorynchus spirurus revealed by Gallus gallus 1-9 probes, in addition to enabling the establishment of genome-wide homology map.
Collapse
Affiliation(s)
- Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- CNPq Researcher, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasilia, Brazil
| | - Alexandre Aleixo
- Department of Zoology, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - Melquizedec Luiz Silva Pinheiro
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Patricia Caroline Mary O´Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Pablo Suarez
- Instituto de Biología Subtropical (IBS), CONICET-UNaM, Puerto Iguazú, Misiones, Argentina
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- CNPq Researcher, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasilia, Brazil
| |
Collapse
|
12
|
Öztürk MA, Cojocaru V, Wade RC. Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification. Biophys J 2018; 114:2363-2375. [PMID: 29759374 PMCID: PMC6129471 DOI: 10.1016/j.bpj.2018.04.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/18/2018] [Accepted: 04/09/2018] [Indexed: 12/20/2022] Open
Abstract
Linker histone (LH) proteins play a key role in higher-order structuring of chromatin for the packing of DNA in eukaryotic cells and in the regulation of genomic function. The common fruit fly (Drosophila melanogaster) has a single somatic isoform of the LH (H1). It is thus a useful model organism for investigating the effects of the LH on nucleosome compaction and the structure of the chromatosome, the complex formed by binding of an LH to a nucleosome. The structural and mechanistic details of how LH proteins bind to nucleosomes are debated. Here, we apply Brownian dynamics simulations to compare the nucleosome binding of the globular domain of D. melanogaster H1 (gH1) and the corresponding chicken (Gallus gallus) LH isoform, gH5, to identify residues in the LH that critically affect the structure of the chromatosome. Moreover, we investigate the effects of posttranslational modifications on the gH1 binding mode. We find that certain single-point mutations and posttranslational modifications of the LH proteins can significantly affect chromatosome structure. These findings indicate that even subtle differences in LH sequence can significantly shift the chromatosome structural ensemble and thus have implications for chromatin structure and transcriptional regulation.
Collapse
Affiliation(s)
- Mehmet Ali Öztürk
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany; The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, Heidelberg University, Heidelberg, Germany
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg, Germany.
| |
Collapse
|
13
|
Ye X, Feng C, Gao T, Mu G, Zhu W, Yang Y. Linker Histone in Diseases. Int J Biol Sci 2017; 13:1008-1018. [PMID: 28924382 PMCID: PMC5599906 DOI: 10.7150/ijbs.19891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/30/2017] [Indexed: 01/21/2023] Open
Abstract
The linker histone is a protein that binds with the nucleosome, which is generally considered to achieve chromatin condensation in the nucleus. Accumulating evidences suggest that the linker histone is essential in the pathogenesis of several diseases. In this review, we briefly introduce the current knowledge of the linker histone, including its structure, characteristics and functions. Also, we move forward to present the advances of the linker histone's association with certain diseases, such as cancer, Alzheimer's disease, infection, male infertility and aberrant immunity situations, focusing on the alteration of the linker histone under certain pathological conditions and its role in developing each disease.
Collapse
Affiliation(s)
- Xin Ye
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - ChuanLin Feng
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - Tian Gao
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - Guanqun Mu
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - Weiguo Zhu
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| | - Yang Yang
- Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xueyuan Road, Beijing 100191, China
| |
Collapse
|
14
|
Ponte I, Romero D, Yero D, Suau P, Roque A. Complex Evolutionary History of the Mammalian Histone H1.1-H1.5 Gene Family. Mol Biol Evol 2017; 34:545-558. [PMID: 28100789 PMCID: PMC5400378 DOI: 10.1093/molbev/msw241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
H1 is involved in chromatin higher-order structure and gene regulation. H1 has a tripartite structure. The central domain is stably folded in solution, while the N- and C-terminal domains are intrinsically disordered. The terminal domains are encoded by DNA of low sequence complexity, and are thus prone to short insertions/deletions (indels). We have examined the evolution of the H1.1-H1.5 gene family from 27 mammalian species. Multiple sequence alignment has revealed a strong preferential conservation of the number and position of basic residues among paralogs, suggesting that overall H1 basicity is under a strong purifying selection. The presence of a conserved pattern of indels, ancestral to the splitting of mammalian orders, in the N- and C-terminal domains of the paralogs, suggests that slippage may have favored the rapid divergence of the subtypes and that purifying selection has maintained this pattern because it is associated with function. Evolutionary analyses have found evidences of positive selection events in H1.1, both before and after the radiation of mammalian orders. Positive selection ancestral to mammalian radiation involved changes at specific sites that may have contributed to the low relative affinity of H1.1 for chromatin. More recent episodes of positive selection were detected at codon positions encoding amino acids of the C-terminal domain of H1.1, which may modulate the folding of the CTD. The detection of putative recombination points in H1.1-H1.5 subtypes suggests that this process may has been involved in the acquisition of the tripartite H1 structure.
Collapse
Affiliation(s)
- Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Devani Romero
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Daniel Yero
- Instituto de Biotecnología y de Biomedicina (IBB) y Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| |
Collapse
|
15
|
Kowalski A. A heterogeneity of the pheasant (Phasianus colchicus L.) erythrocyte histone H1 subtype H5. C R Biol 2016; 339:357-63. [DOI: 10.1016/j.crvi.2016.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 01/29/2023]
|
16
|
Kowalski A, Pałyga J. Modulation of chromatin function through linker histone H1 variants. Biol Cell 2016; 108:339-356. [PMID: 27412812 DOI: 10.1111/boc.201600007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022]
Abstract
In this review, the structural aspects of linker H1 histones are presented as a background for characterization of the factors influencing their function in animal and human chromatin. The action of H1 histone variants is largely determined by dynamic alterations of their intrinsically disordered tail domains, posttranslational modifications and allelic diversification. The interdependent effects of these factors can establish dynamic histone H1 states that may affect the organization and function of chromatin regions.
Collapse
Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| | - Jan Pałyga
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| |
Collapse
|
17
|
Hergeth SP, Schneider R. The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle. EMBO Rep 2015; 16:1439-53. [PMID: 26474902 DOI: 10.15252/embr.201540749] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/14/2015] [Indexed: 12/21/2022] Open
Abstract
The linker histone H1 family members are a key component of chromatin and bind to the nucleosomal core particle around the DNA entry and exit sites. H1 can stabilize both nucleosome structure and higher-order chromatin architecture. In general, H1 molecules consist of a central globular domain with more flexible tail regions at both their N- and C-terminal ends. The existence of multiple H1 subtypes and a large variety of posttranslational modifications brings about a considerable degree of complexity and makes studying this protein family challenging. Here, we review recent progress in understanding the function of linker histones and their subtypes beyond their role as merely structural chromatin components. We summarize current findings on the role of H1 in heterochromatin formation, transcriptional regulation and embryogenesis with a focus on H1 subtypes and their specific modifications.
Collapse
Affiliation(s)
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, Inserm U964, Université de Strasbourg, Illkirch, France
| |
Collapse
|
18
|
Roque A, Ponte I, Suau P. Interplay between histone H1 structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:444-54. [PMID: 26415976 DOI: 10.1016/j.bbagrm.2015.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/21/2015] [Accepted: 09/22/2015] [Indexed: 01/10/2023]
Abstract
H1 linker histones are involved both in the maintenance of higher-order chromatin structure and in gene regulation. Histone H1 exists in multiple isoforms, is evolutionarily variable and undergoes a large variety of post-translational modifications. We review recent progress in the understanding of the folding and structure of histone H1 domains with an emphasis on the interactions with DNA. The importance of intrinsic disorder and hydrophobic interactions in the folding and function of the carboxy-terminal domain (CTD) is discussed. The induction of a molten globule-state in the CTD by macromolecular crowding is also considered. The effects of phosphorylation by cyclin-dependent kinases on the structure of the CTD, as well as on chromatin condensation and oligomerization, are described. We also address the extranuclear functions of histone H1, including the interaction with the β-amyloid peptide.
Collapse
Affiliation(s)
- Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Spain
| | - Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Spain.
| |
Collapse
|
19
|
Izzo A, Schneider R. The role of linker histone H1 modifications in the regulation of gene expression and chromatin dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:486-95. [PMID: 26348411 DOI: 10.1016/j.bbagrm.2015.09.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/07/2015] [Accepted: 09/02/2015] [Indexed: 12/27/2022]
Abstract
BACKGROUND Linker histone H1 is a structural component of chromatin. It exists as a family of related proteins known as variants and/or subtypes. H1.1, H1.2, H1.3, H1.4 and H1.5 are present in most somatic cells, whereas other subtypes are mainly expressed in more specialized cells. SCOPE OF REVIEW H1 subtypes have been shown to have unique functions in chromatin structure and dynamics. This can occur at least in part via specific post-translational modifications of distinct H1 subtypes. However, while core histone modifications have been extensively studied, our knowledge of H1 modifications and their molecular functions has remained for a long time limited to phosphorylation. In this review we discuss the current state of knowledge of linker histone H1 modifications and where possible highlight functional differences in the modifications of distinct H1 subtypes. MAJOR CONCLUSIONS AND GENERAL SIGNIFICANCE H1 histones are intensely post-translationally modified. These modifications are located in the N- and C-terminal tails as well as within the globular domain. Recently, advanced mass spectrometrical analysis revealed a large number of novel histone H1 subtype specific modification sites and types. H1 modifications include phosphorylation, acetylation, methylation, ubiquitination, and ADP ribosylation. They are involved in the regulation of all aspects of linker histone functions, however their mechanism of action is often only poorly understood. Therefore systematic functional characterization of H1 modifications will be necessary in order to better understand their role in gene regulation as well as in higher-order chromatin structure and dynamics.
Collapse
Affiliation(s)
- Annalisa Izzo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404 Illkirch, France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404 Illkirch, France.
| |
Collapse
|
20
|
Chen J, Gao J, Peng M, Wang Y, Yu Y, Yang P, Jin H. In-gel NHS-propionate derivatization for histone post-translational modifications analysis in Arabidopsis thaliana. Anal Chim Acta 2015; 886:107-13. [PMID: 26320642 DOI: 10.1016/j.aca.2015.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/26/2015] [Accepted: 06/04/2015] [Indexed: 11/16/2022]
Abstract
Post-translational modifications (PTMs) on histone are highly correlated with genetic and epigenetic regulation of gene expression from chromatin. Mass spectrometry (MS) has developed to be an optimal tool for the identification and quantification of histone PTMs. Derivatization of histones with chemicals such as propionic anhydride, N-hydroxysuccinimide ester (NHS-propionate) has been widely used in histone PTMs analysis in bottom-up MS strategy, which requires high purity for histone samples. However, biological samples are not always prepared with high purity, containing detergents or other interferences in most cases. As an alternative approach, an adaptation of in gel derivatization method, termed In-gel NHS, is utilized for a broader application in histone PTMs analysis and it is shown to be a more time-saving preparation method. The proposed method was optimized for a better derivatization efficiency and displayed high reproducibility, indicating quantification of histone PTMs based on In-gel NHS was achievable. Without any traditional fussy histone purification procedures, we succeeded to quantitatively profile the histone PTMs from Arabidopsis with selective knock down of CLF (clf-29) and the original parental (col) with In-gel NHS method in a rapid way, which indicated the high specificity of CLF on H3K27me3 in Arabidopsis. In-gel NHS quantification results also suggest distinctive histone modification patterns in plants, which is invaluable foundation for future studies on histone modifications in plants.
Collapse
Affiliation(s)
- Jiajia Chen
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Jun Gao
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China; China Novartis Institutes for BioMedical Research Co. Ltd., Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Maolin Peng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yi Wang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yanyan Yu
- China Novartis Institutes for BioMedical Research Co. Ltd., Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Pengyuan Yang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
| | - Hong Jin
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
| |
Collapse
|
21
|
Lopez R, Sarg B, Lindner H, Bartolomé S, Ponte I, Suau P, Roque A. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation. Nucleic Acids Res 2015; 43:4463-76. [PMID: 25870416 PMCID: PMC4482070 DOI: 10.1093/nar/gkv304] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 03/27/2015] [Indexed: 11/29/2022] Open
Abstract
Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation.
Collapse
Affiliation(s)
- Rita Lopez
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Bettina Sarg
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, A-6020, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, A-6020, Innsbruck, Austria
| | - Salvador Bartolomé
- Laboratorio de Luminiscencia y Espectroscopia de Biomoléculas, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| |
Collapse
|
22
|
Sarg B, Lopez R, Lindner H, Ponte I, Suau P, Roque A. Sequence conservation of linker histones between chicken and mammalian species. Data Brief 2014. [PMID: 26217688 PMCID: PMC4459761 DOI: 10.1016/j.dib.2014.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The percent identity matrices of two sequence multiple alignments between linker histones from chicken and mammalian species are described. Linker histone protein sequences for chicken, mouse, rat and humans, available on public databases were used. This information is related to the research article entitled "Identification of novel post-translational modifications in linker histones from chicken erythrocytes"published in the Journal of Proteomics [1].
Collapse
Affiliation(s)
- Bettina Sarg
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Rita Lopez
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Bellaterra, Barcelona, Spain
- Correspondance author.
| |
Collapse
|