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Schneps CM, Dunleavy R, Crane BR. Dissecting the Interaction between Cryptochrome and Timeless Reveals Underpinnings of Light-Dependent Recognition. Biochemistry 2024:10.1021/acs.biochem.3c00630. [PMID: 38294880 PMCID: PMC11289166 DOI: 10.1021/acs.biochem.3c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Circadian rhythms are determined by cell-autonomous transcription-translation feedback loops that entrain to environmental stimuli. In the model circadian clock of Drosophila melanogaster, the clock is set by the light-induced degradation of the core oscillator protein timeless (TIM) by the principal light-sensor cryptochrome (CRY). The cryo-EM structure of CRY bound to TIM revealed that within the extensive CRY:TIM interface, the TIM N-terminus binds into the CRY FAD pocket, in which FAD and the associated phosphate-binding loop (PBL) undergo substantial rearrangement. The TIM N-terminus involved in CRY binding varies in isoforms that facilitate the adaptation of flies to different light environments. Herein, we demonstrate, through peptide binding assays and pulsed-dipolar electron spin resonance (ESR) spectroscopy, that the TIM N-terminal peptide alone exhibits light-dependent binding to CRY and that the affinity of the interaction depends on the initiating methionine residue. Extensions to the TIM N-terminus that mimic less light-sensitive variants have substantially reduced interactions with CRY. Substitutions of CRY residues that couple to the flavin rearrangement in the CRY:TIM complex have dramatic effects on CRY light activation. CRY residues Arg237 on α8, Asn253, and Gln254 on the PBL are critical for the release of the CRY autoinhibitory C-terminal tail (CTT) and subsequent TIM binding. These key light-responsive elements of CRY are well conserved throughout Type I cryptochromes of invertebrates but not by cryptochromes of chordates and plants, which likely utilize a distinct light-activation mechanism.
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Affiliation(s)
| | - Robert Dunleavy
- Cornell University, Department of Chemistry & Chemical Biology, Ithaca, NY 14853
| | - Brian R. Crane
- Cornell University, Department of Chemistry & Chemical Biology, Ithaca, NY 14853
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2
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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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3
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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.
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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
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4
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García-Giménez JL, Garcés C, Romá-Mateo C, Pallardó FV. Oxidative stress-mediated alterations in histone post-translational modifications. Free Radic Biol Med 2021; 170:6-18. [PMID: 33689846 DOI: 10.1016/j.freeradbiomed.2021.02.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022]
Abstract
Epigenetic regulation of gene expression provides a finely tuned response capacity for cells when undergoing environmental changes. However, in the context of human physiology or disease, any cellular imbalance that modulates homeostasis has the potential to trigger molecular changes that result either in physiological adaptation to a new situation or pathological conditions. These effects are partly due to alterations in the functionality of epigenetic regulators, which cause long-term and often heritable changes in cell lineages. As such, free radicals resulting from unbalanced/extended oxidative stress have been proved to act as modulators of epigenetic agents, resulting in alterations of the epigenetic landscape. In the present review we will focus on the particular effect that oxidative stress and free radicals produce in histone post-translational modifications that contribute to altering the histone code and, consequently, gene expression. The pathological consequences of the changes in this epigenetic layer of regulation of gene expression are thoroughly evidenced by data gathered in many physiological adaptive processes and in human diseases that range from age-related neurodegenerative pathologies to cancer, and that include respiratory syndromes, infertility, and systemic inflammatory conditions like sepsis.
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Affiliation(s)
- José-Luis García-Giménez
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Concepción Garcés
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain
| | - Carlos Romá-Mateo
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Federico V Pallardó
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
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5
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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.
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6
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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.
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7
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Soler-Ventura A, Gay M, Jodar M, Vilanova M, Castillo J, Arauz-Garofalo G, Villarreal L, Ballescà JL, Vilaseca M, Oliva R. Characterization of Human Sperm Protamine Proteoforms through a Combination of Top-Down and Bottom-Up Mass Spectrometry Approaches. J Proteome Res 2019; 19:221-237. [PMID: 31703166 DOI: 10.1021/acs.jproteome.9b00499] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Protamine 1 (P1) and protamine 2 (P2) family are extremely basic, sperm-specific proteins, packing 85-95% of the paternal DNA. P1 is synthesized as a mature form, whereas P2 components (HP2, HP3, and HP4) arise from the proteolysis of the precursor (pre-P2). Due to the particular protamine physical-chemical properties, their identification by standardized bottom-up mass spectrometry (MS) strategies is not straightforward. Therefore, the aim of this study was to identify the sperm protamine proteoforms profile, including their post-translational modifications, in normozoospermic individuals using two complementary strategies, a top-down MS approach and a proteinase-K-digestion-based bottom-up MS approach. By top-down MS, described and novel truncated P1 and pre-P2 proteoforms were identified. Intact P1, pre-P2, and P2 mature proteoforms and their phosphorylation pattern were also detected. Additionally, a +61 Da modification in different proteoforms was observed. By the bottom-up MS approach, phosphorylated residues for pre-P2, as well as the new P2 isoform 2, which is not annotated in the UniProtKB database, were revealed. Implementing these strategies in comparative studies of different infertile phenotypes, together with the evaluation of P1/P2 and pre-P2/P2 MS-derived ratios, would permit determining specific alterations in the protamine proteoforms and elucidate the role of phosphorylation/dephosphorylation dynamics in male fertility.
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Affiliation(s)
- Ada Soler-Ventura
- EUGIN-UB Research Excellence Program, Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica (FCRB), Faculty of Medicine and Health Sciences , University of Barcelona , 08036 Barcelona , Spain
| | - Marina Gay
- EUGIN-UB Research Excellence Program, Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Baldiri Reixac, 10 , 08028 Barcelona , Spain
| | - Meritxell Jodar
- EUGIN-UB Research Excellence Program, Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica (FCRB), Faculty of Medicine and Health Sciences , University of Barcelona , 08036 Barcelona , Spain
| | - Mar Vilanova
- EUGIN-UB Research Excellence Program, Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Baldiri Reixac, 10 , 08028 Barcelona , Spain
| | - Judit Castillo
- EUGIN-UB Research Excellence Program, Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica (FCRB), Faculty of Medicine and Health Sciences , University of Barcelona , 08036 Barcelona , Spain
| | - Gianluca Arauz-Garofalo
- EUGIN-UB Research Excellence Program, Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Baldiri Reixac, 10 , 08028 Barcelona , Spain
| | - Laura Villarreal
- EUGIN-UB Research Excellence Program, Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Baldiri Reixac, 10 , 08028 Barcelona , Spain
| | | | - Marta Vilaseca
- EUGIN-UB Research Excellence Program, Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Baldiri Reixac, 10 , 08028 Barcelona , Spain
| | - Rafael Oliva
- EUGIN-UB Research Excellence Program, Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica (FCRB), Faculty of Medicine and Health Sciences , University of Barcelona , 08036 Barcelona , Spain
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8
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Mezquita-Pla J. Gordon H. Dixon's trace in my personal career and the quantic jump experienced in regulatory information. Syst Biol Reprod Med 2018; 64:448-468. [PMID: 30136864 DOI: 10.1080/19396368.2018.1503752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Even before Rosalin Franklin had discovered the DNA double helix, in her impressive X-ray diffraction image pattern, Erwin Schröedinger, described, in his excellent book, What is Life, how the finding of aperiodic crystals in biological systems surprised him (an aperiodic crystal, which, in my opinion is the material carrier of life). In the 21st century and still far from being able to define life, we are attending to a quick acceleration of knowledge on regulatory information. With the discovery of new codes and punctuation marks, we will greatly increase our understanding in front of an impressive avalanche of genomic sequences. Trifonov et al. defined a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology. These patterns are largely captured in transcribed messages that give meaning and identity to the particular cells. In this review, I will go through my personal career in and after my years of work in the laboratory of Gordon H. Dixon, extending toward the impressive acquisition of new knowledge on regulatory information and genetic codes provided by remarkable scientists in the field. Abbreviations: CA II: carbonic anhydridase II (chicken); Car2: carbonic anhydridase 2 (mouse); CpG islands: short (>0.5 kb) stretches of DNA with a G+C content ≥55%; DNMT1: DNA methyltransferases 1; DNMT3b: DNA methyltransferases 3B; DSB: double-strand DNA breaks; ERT: endogenous retrotransposon; ERV: endogenous retroviruses; ES cells: embryonic stem cells; GAPDH: glyceraldehide phosphate dehydrogenase; H1: histone H1; HATs: histone acetyltransferases; HDACs: histone deacetylases; H3K4me3: histone 3 trimethylated at lys 4; H3K79me2: histone 3 dimethylated at lys 79; HMG: high mobility group proteins; HMT: histone methyltransferase; HP1: heterochromatin protein 1; HR: homologous recombination; HSE: heat-shock element; ICRs: imprinted control regions; IRF: interferon regulatory factor; LDH-A/-B: lactate dehydrogenase A/B; LTR: long terminal repeats; MeCP2: methyl CpG binding protein 2; OCT4: octamer-binding transcription factor 4; PAF1: RNA Polymerase II associated factor 1; piRNA: PIWI-interacting RNA; poly(A) tails: poly-adenine tails; PRC2: polycomb repressive complex 2; PTMs: post-translational modifications; SIRT 1: sirtuin 1, silent information regulator; STAT3: signal transducer and activator of transcription; tRNAs: transfer RNA; tRFs: tRNA-derived fragments; TSS: transcription start site; TE: transposable elements; UB I: polyubiquitin I; UB II: polyubiquitin II; UBE 2N: ubiquitin conjugating enzyme E2N; 5'-UTR: 5'-untranslated sequences; 3'-UTR: 3'-untranslated sequences.
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Affiliation(s)
- Jovita Mezquita-Pla
- a Molecular Genetics and Control of Pluripotency Laboratory, Department of Biomedicine, IDIBAPS, Faculty of Medicine , University of Barcelona , Catalonia , Spain
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9
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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.
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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.
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10
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Emerging roles of linker histones in regulating chromatin structure and function. Nat Rev Mol Cell Biol 2017; 19:192-206. [PMID: 29018282 DOI: 10.1038/nrm.2017.94] [Citation(s) in RCA: 276] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Together with core histones, which make up the nucleosome, the linker histone (H1) is one of the five main histone protein families present in chromatin in eukaryotic cells. H1 binds to the nucleosome to form the next structural unit of metazoan chromatin, the chromatosome, which may help chromatin to fold into higher-order structures. Despite their important roles in regulating the structure and function of chromatin, linker histones have not been studied as extensively as core histones. Nevertheless, substantial progress has been made recently. The first near-atomic resolution crystal structure of a chromatosome core particle and an 11 Å resolution cryo-electron microscopy-derived structure of the 30 nm nucleosome array have been determined, revealing unprecedented details about how linker histones interact with the nucleosome and organize higher-order chromatin structures. Moreover, several new functions of linker histones have been discovered, including their roles in epigenetic regulation and the regulation of DNA replication, DNA repair and genome stability. Studies of the molecular mechanisms of H1 action in these processes suggest a new paradigm for linker histone function beyond its architectural roles in chromatin.
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11
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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.
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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
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12
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Iwasaki YW, Murano K, Ishizu H, Shibuya A, Iyoda Y, Siomi MC, Siomi H, Saito K. Piwi Modulates Chromatin Accessibility by Regulating Multiple Factors Including Histone H1 to Repress Transposons. Mol Cell 2016; 63:408-19. [PMID: 27425411 DOI: 10.1016/j.molcel.2016.06.008] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 05/13/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
Abstract
PIWI-interacting RNAs (piRNAs) mediate transcriptional and post-transcriptional silencing of transposable element (TE) in animal gonads. In Drosophila ovaries, Piwi-piRNA complexes (Piwi-piRISCs) repress TE transcription by modifying the chromatin state, such as by H3K9 trimethylation. Here, we demonstrate that Piwi physically interacts with linker histone H1. Depletion of Piwi decreases H1 density at a subset of TEs, leading to their derepression. Silencing at these loci separately requires H1 and H3K9me3 and heterochromatin protein 1a (HP1a). Loss of H1 increases target loci chromatin accessibility without affecting H3K9me3 density at these loci, while loss of HP1a does not impact H1 density. Thus, Piwi-piRISCs require both H1 and HP1a to repress TEs, and the silencing is correlated with the chromatin state rather than H3K9me3 marks. These findings suggest that Piwi-piRISCs regulate the interaction of chromatin components with target loci to maintain silencing of TEs through the modulation of chromatin accessibility.
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Affiliation(s)
- Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hirotsugu Ishizu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Aoi Shibuya
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yumiko Iyoda
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Kuniaki Saito
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan.
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13
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Kavi H, Emelyanov AV, Fyodorov DV, Skoultchi AI. Independent Biological and Biochemical Functions for Individual Structural Domains of Drosophila Linker Histone H1. J Biol Chem 2016; 291:15143-55. [PMID: 27226620 DOI: 10.1074/jbc.m116.730705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Indexed: 12/20/2022] Open
Abstract
Linker histone H1 is among the most abundant components of chromatin. H1 has profound effects on chromosome architecture. H1 also helps to tether DNA- and histone-modifying enzymes to chromatin. Metazoan linker histones have a conserved tripartite structure comprising N-terminal, globular, and long, unstructured C-terminal domains. Here we utilize truncated Drosophila H1 polypeptides in vitro and H1 mutant transgenes in vivo to interrogate the roles of these domains in multiple biochemical and biological activities of H1. We demonstrate that the globular domain and the proximal part of the C-terminal domain are essential for H1 deposition into chromosomes and for the stability of H1-chromatin binding. The two domains are also essential for fly viability and the establishment of a normal polytene chromosome structure. Additionally, through interaction with the heterochromatin-specific histone H3 Lys-9 methyltransferase Su(var)3-9, the H1 C-terminal domain makes important contributions to formation and H3K9 methylation of heterochromatin as well as silencing of transposons in heterochromatin. Surprisingly, the N-terminal domain does not appear to be required for any of these functions. However, it is involved in the formation of a single chromocenter in polytene chromosomes. In summary, we have discovered that linker histone H1, similar to core histones, exerts its multiple biological functions through independent, biochemically separable activities of its individual structural domains.
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Affiliation(s)
- Harsh Kavi
- From the Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Alexander V Emelyanov
- From the Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Dmitry V Fyodorov
- From the Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Arthur I Skoultchi
- From the Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
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14
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Noberini R, Sigismondo G, Bonaldi T. The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics 2016; 8:429-45. [DOI: 10.2217/epi.15.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin is a macromolecular complex composed of DNA and histones that regulate gene expression and nuclear architecture. The concerted action of DNA methylation, histone post-translational modifications and chromatin-associated proteins control the epigenetic regulation of the genome, ultimately determining cell fate and the transcriptional outputs of differentiated cells. Deregulation of this complex machinery leads to disease states, and exploiting epigenetic drugs is becoming increasingly attractive for therapeutic intervention. Mass spectrometry (MS)-based proteomics emerged as a powerful tool complementary to genomic approaches for epigenetic research, allowing the unbiased and comprehensive analysis of histone post-translational modifications and the characterization of chromatin constituents and chromatin-associated proteins. Furthermore, MS holds great promise for epigenetic biomarker discovery and represents a useful tool for deconvolution of epigenetic drug targets. Here, we will provide an overview of the applications of MS-based proteomics in various areas of chromatin biology.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, via Adamello 16, Milano, Italy
| | - Gianluca Sigismondo
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
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15
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Yu Y, Chen J, Gao Y, Gao J, Liao R, Wang Y, Oyang C, Li E, Zeng C, Zhou S, Yang P, Jin H, Yi W. Quantitative Profiling of Combinational K27/K36 Modifications on Histone H3 Variants in Mouse Organs. J Proteome Res 2016; 15:1070-9. [PMID: 26799478 DOI: 10.1021/acs.jproteome.5b01164] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The coexisting post-translational modifications (PTMs) on histone H3 N-terminal tails were known to crosstalk between each other, indicating their interdependency in the epigenetic regulation pathways. H3K36 methylation, an important activating mark, was recently reported to antagonize with PRC2-mediated H3K27 methylation with possible crosstalk mechanism during transcription regulation process. On the basis of our previous studies, we further integrated RP/HILIC liquid chromatography with MRM mass spectrometry to quantify histone PTMs from various mouse organs, especially the combinatorial K27/K36 marks for all three major histone H3 variants. Despite their subtle difference in physicochemical properties, we successfully obtained decent separation and high detection sensitivity for both histone H3.3 specific peptides and histone H3.1/3.2 specific peptides. In addition, the overall abundance of H3.3 can be quantified simultaneously. We applied this method to investigate the pattern of the combinatorial K27/K36 marks for all three major histone H3 variants across five mouse organs. Intriguing distribution differences were observed not only between different H3 variants but also between different organs. Our data shed the new insights into histone codes functions in epigenetic regulation during cell differentiation and developmental process.
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Affiliation(s)
- Yanyan Yu
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Jiajia Chen
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Yuan Gao
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Jun Gao
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Rijing Liao
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Yi Wang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Counde Oyang
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - En Li
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Chenhui Zeng
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
| | - Shaolian Zhou
- 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 , 220 Handan Road, Shanghai 200433, China
| | - Hong Jin
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Wei Yi
- China Novartis Institutes for BioMedical Research Co. Ltd. , Building 8, Lane 898 Halei Road, Shanghai 201203, China
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16
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Kotliński M, Rutowicz K, Kniżewski Ł, Palusiński A, Olędzki J, Fogtman A, Rubel T, Koblowska M, Dadlez M, Ginalski K, Jerzmanowski A. Histone H1 Variants in Arabidopsis Are Subject to Numerous Post-Translational Modifications, Both Conserved and Previously Unknown in Histones, Suggesting Complex Functions of H1 in Plants. PLoS One 2016; 11:e0147908. [PMID: 26820416 PMCID: PMC4731575 DOI: 10.1371/journal.pone.0147908] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/10/2016] [Indexed: 12/24/2022] Open
Abstract
Linker histones (H1s) are conserved and ubiquitous structural components of eukaryotic chromatin. Multiple non-allelic variants of H1, which differ in their DNA/nucleosome binding properties, co-exist in animal and plant cells and have been implicated in the control of genetic programs during development and differentiation. Studies in mammals and Drosophila have revealed diverse post-translational modifications of H1s, most of which are of unknown function. So far, it is not known how this pattern compares with that of H1s from other major lineages of multicellular Eukaryotes. Here, we show that the two main H1variants of a model flowering plant Arabidopsis thaliana are subject to a rich and diverse array of post-translational modifications. The distribution of these modifications in the H1 molecule, especially in its globular domain (GH1), resembles that occurring in mammalian H1s, suggesting that their functional significance is likely to be conserved. While the majority of modifications detected in Arabidopsis H1s, including phosphorylation, acetylation, mono- and dimethylation, formylation, crotonylation and propionylation, have also been reported in H1s of other species, some others have not been previously identified in histones.
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Affiliation(s)
- Maciej Kotliński
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Kinga Rutowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Łukasz Kniżewski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Antoni Palusiński
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jacek Olędzki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tymon Rubel
- Institute of Radioelectronic and Multimedia Technology, Warsaw University of Technology, Warsaw, Poland
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Andrzej Jerzmanowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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17
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Liao R, Mizzen CA. Interphase H1 phosphorylation: Regulation and functions in chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:476-85. [PMID: 26657617 DOI: 10.1016/j.bbagrm.2015.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/25/2022]
Abstract
Many metazoan cell types differentially express multiple non-allelic amino acid sequence variants of histone H1. Although early work revealed that H1 variants, collectively, are phosphorylated during interphase and mitosis, differences between individual H1 variants in the sites they possess for mitotic and interphase phosphorylation have been elucidated only relatively recently. Here, we review current knowledge on the regulation and function of interphase H1 phosphorylation, with a particular emphasis on how differences in interphase phosphorylation among the H1 variants of mammalian cells may enable them to have differential effects on transcription and other chromatin processes.
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Affiliation(s)
- Ruiqi Liao
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA
| | - Craig A Mizzen
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA; Institute for Genomic Biology, University of Illinois at Urbana Champaign, USA.
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18
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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: 223] [Impact Index Per Article: 24.8] [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.
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Affiliation(s)
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, Inserm U964, Université de Strasbourg, Illkirch, France
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19
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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.
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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.
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20
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Histone H1: Lessons from Drosophila. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:526-32. [PMID: 26361208 DOI: 10.1016/j.bbagrm.2015.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/28/2015] [Accepted: 09/02/2015] [Indexed: 01/02/2023]
Abstract
Eukaryotic genomes are structured in the form of chromatin with the help of a set of five small basic proteins, the histones. Four of them are highly conserved through evolution, form the basic unit of the chromatin, the nucleosome, and have been intensively studied and are well characterized. The fifth histone, histone H1, adds to this basic structure through its interaction at the entry/exit site of DNA in the nucleosome and makes an essential contribution to the higher order folding of the chromatin fiber. Histone H1 is the less conserved histone and the less known of them. Though for long time considered as a general repressor of gene expression, recent studies in Drosophila have rejected this view and have contributed to uncover important functions on genome stability and development. Here we present some of the most recent data obtained in the Drosophila model system and discuss how the lessons learnt in these studies compare and could be applied to all other eukaryotes.
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21
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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.
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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.
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22
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Chen Y, Hoover ME, Dang X, Shomo AA, Guan X, Marshall AG, Freitas MA, Young NL. Quantitative Mass Spectrometry Reveals that Intact Histone H1 Phosphorylations are Variant Specific and Exhibit Single Molecule Hierarchical Dependence. Mol Cell Proteomics 2015. [PMID: 26209608 DOI: 10.1074/mcp.m114.046441] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Breast cancer was the second leading cause of cancer related mortality for females in 2014. Recent studies suggest histone H1 phosphorylation may be useful as a clinical biomarker of breast and other cancers because of its ability to recognize proliferative cell populations. Although monitoring a single phosphorylated H1 residue is adequate to stratify high-grade breast tumors, expanding our knowledge of how H1 is phosphorylated through the cell cycle is paramount to understanding its role in carcinogenesis. H1 analysis by bottom-up MS is challenging because of the presence of highly homologous sequence variants expressed by most cells. These highly basic proteins are difficult to analyze by LC-MS/MS because of the small, hydrophilic nature of peptides produced by tryptic digestion. Although bottom-up methods permit identification of several H1 phosphorylation events, these peptides are not useful for observing the combinatorial post-translational modification (PTM) patterns on the protein of interest. To complement the information provided by bottom-up MS, we utilized a top-down MS/MS workflow to permit identification and quantitation of H1 proteoforms related to the progression of breast cells through the cell cycle. Histones H1.2 and H1.4 were observed in MDA-MB-231 metastatic breast cells, whereas an additional histone variant, histone H1.3, was identified only in nonneoplastic MCF-10A cells. Progressive phosphorylation of histone H1.4 was identified in both cell lines at mitosis (M phase). Phosphorylation occurred first at S172 followed successively by S187, T18, T146, and T154. Notably, phosphorylation at S173 of histone H1.2 and S172, S187, T18, T146, and T154 of H1.4 significantly increases during M phase relative to S phase, suggesting that these events are cell cycle-dependent and may serve as markers for proliferation. Finally, we report the observation of the H1.2 SNP variant A18V in MCF-10A cells.
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Affiliation(s)
- Yu Chen
- From the ‡Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, 32310
| | - Michael E Hoover
- §Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, College of Medicine and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, 43210
| | - Xibei Dang
- ¶Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, 32306
| | - Alan A Shomo
- ¶Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, 32306
| | - Xiaoyan Guan
- From the ‡Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, 32310
| | - Alan G Marshall
- From the ‡Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, 32310; ¶Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, 32306
| | - Michael A Freitas
- §Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, College of Medicine and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, 43210;
| | - Nicolas L Young
- From the ‡Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, 32310;
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23
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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24
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A novel approach for studying histone H1 function in vivo. Genetics 2015; 200:29-33. [PMID: 25805849 DOI: 10.1534/genetics.114.170514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/17/2015] [Indexed: 11/18/2022] Open
Abstract
In this report, we investigate the mechanisms that regulate Drosophila histone H1 expression and its association with chromatin in vivo. We show that histone H1 is subject to negative autoregulation and exploit this result to examine the effects of mutations of the main phosphorylation site of histone H1.
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25
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Terme JM, Millán-Ariño L, Mayor R, Luque N, Izquierdo-Bouldstridge A, Bustillos A, Sampaio C, Canes J, Font I, Sima N, Sancho M, Torrente L, Forcales S, Roque A, Suau P, Jordan A. Dynamics and dispensability of variant-specific histone H1 Lys-26/Ser-27 and Thr-165 post-translational modifications. FEBS Lett 2014; 588:2353-62. [PMID: 24873882 DOI: 10.1016/j.febslet.2014.05.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 12/31/2022]
Abstract
In mammals, the linker histone H1, involved in DNA packaging into chromatin, is represented by a family of variants. H1 tails undergo post-translational modifications (PTMs) that can be detected by mass spectrometry. We developed antibodies to analyze several of these as yet unexplored PTMs including the combination of H1.4 K26 acetylation or trimethylation and S27 phosphorylation. H1.2-T165 phosphorylation was detected at S and G2/M phases of the cell cycle and was dispensable for chromatin binding and cell proliferation; while the H1.4-K26 residue was essential for proper cell cycle progression. We conclude that histone H1 PTMs are dynamic over the cell cycle and that the recognition of modified lysines may be affected by phosphorylation of adjacent residues.
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Affiliation(s)
- Jean-Michel Terme
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Lluís Millán-Ariño
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Regina Mayor
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Neus Luque
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | | | - Alberto Bustillos
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Sampaio
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Jordi Canes
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Isaura Font
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Núria Sima
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Mónica Sancho
- Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Laura Torrente
- Institut de Medecina Predictiva i Personalitzada del Cancer, Badalona, Catalonia, Spain
| | - Sonia Forcales
- Institut de Medecina Predictiva i Personalitzada del Cancer, Badalona, Catalonia, Spain
| | - Alicia Roque
- Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Pere Suau
- Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Albert Jordan
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain.
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26
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Millán-Ariño L, Islam ABMMK, Izquierdo-Bouldstridge A, Mayor R, Terme JM, Luque N, Sancho M, López-Bigas N, Jordan A. Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2. Nucleic Acids Res 2014; 42:4474-93. [PMID: 24476918 PMCID: PMC3985652 DOI: 10.1093/nar/gku079] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Seven linker histone H1 variants are present in human somatic cells with distinct prevalence across cell types. Despite being key structural components of chromatin, it is not known whether the different variants have specific roles in the regulation of nuclear processes or are differentially distributed throughout the genome. Using variant-specific antibodies to H1 and hemagglutinin (HA)-tagged recombinant H1 variants expressed in breast cancer cells, we have investigated the distribution of six H1 variants in promoters and genome-wide. H1 is depleted at promoters depending on its transcriptional status and differs between variants. Notably, H1.2 is less abundant than other variants at the transcription start sites of inactive genes, and promoters enriched in H1.2 are different from those enriched in other variants and tend to be repressed. Additionally, H1.2 is enriched at chromosomal domains characterized by low guanine–cytosine (GC) content and is associated with lamina-associated domains. Meanwhile, other variants are associated with higher GC content, CpG islands and gene-rich domains. For instance, H1.0 and H1X are enriched at gene-rich chromosomes, whereas H1.2 is depleted. In short, histone H1 is not uniformly distributed along the genome and there are differences between variants, H1.2 being the one showing the most specific pattern and strongest correlation with low gene expression.
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Affiliation(s)
- Lluís Millán-Ariño
- Department of Molecular Genomics, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, E-08028 Spain, Research Programme on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, E-08003 Spain, Department of Genetic Engineering, Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh, Centro de Investigación Príncipe Felipe, Valencia, E-46012 Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, E-08010 Spain
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27
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Venne AS, Kollipara L, Zahedi RP. The next level of complexity: Crosstalk of posttranslational modifications. Proteomics 2014; 14:513-24. [DOI: 10.1002/pmic.201300344] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 11/06/2013] [Accepted: 11/21/2013] [Indexed: 12/22/2022]
Affiliation(s)
- A. Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V; Dortmund Germany
| | | | - René P. Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V; Dortmund Germany
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28
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Bhaskara RM, de Brevern AG, Srinivasan N. Understanding the role of domain–domain linkers in the spatial orientation of domains in multi-domain proteins. J Biomol Struct Dyn 2013; 31:1467-80. [DOI: 10.1080/07391102.2012.743438] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Mayne J, Starr AE, Ning Z, Chen R, Chiang CK, Figeys D. Fine Tuning of Proteomic Technologies to Improve Biological Findings: Advancements in 2011–2013. Anal Chem 2013; 86:176-95. [DOI: 10.1021/ac403551f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Zhibin Ning
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Rui Chen
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Daniel Figeys
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
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30
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Harshman SW, Young NL, Parthun MR, Freitas MA. H1 histones: current perspectives and challenges. Nucleic Acids Res 2013; 41:9593-609. [PMID: 23945933 PMCID: PMC3834806 DOI: 10.1093/nar/gkt700] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
H1 and related linker histones are important both for maintenance of higher-order chromatin structure and for the regulation of gene expression. The biology of the linker histones is complex, as they are evolutionarily variable, exist in multiple isoforms and undergo a large variety of posttranslational modifications in their long, unstructured, NH2- and COOH-terminal tails. We review recent progress in understanding the structure, genetics and posttranslational modifications of linker histones, with an emphasis on the dynamic interactions of these proteins with DNA and transcriptional regulators. We also discuss various experimental challenges to the study of H1 and related proteins, including limitations of immunological reagents and practical difficulties in the analysis of posttranslational modifications by mass spectrometry.
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Affiliation(s)
- Sean W Harshman
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA, College of Medicine and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, USA, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA and Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio, USA
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31
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Jia C, Lietz CB, Ye H, Hui L, Yu Q, Yoo S, Li L. A multi-scale strategy for discovery of novel endogenous neuropeptides in the crustacean nervous system. J Proteomics 2013; 91:1-12. [PMID: 23806756 DOI: 10.1016/j.jprot.2013.06.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/26/2013] [Accepted: 06/16/2013] [Indexed: 12/18/2022]
Abstract
UNLABELLED The conventional mass spectrometry (MS)-based strategy is often inadequate for the comprehensive characterization of various size neuropeptides without the assistance of genomic information. This study evaluated sequence coverage of different size neuropeptides in two crustacean species, blue crab Callinectes sapidus and Jonah crab Cancer borealis using conventional MS methodologies and revealed limitations to mid- and large-size peptide analysis. Herein we attempt to establish a multi-scale strategy for simultaneous and confident sequence elucidation of various sizes of peptides in the crustacean nervous system. Nine novel neuropeptides spanning a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ, the sinus gland of the spiny lobster Panulirus interruptus. These novel neuropeptides included seven allatostatin (A- and B-type) peptides, one crustacean hyperglycemic hormone precursor-related peptide, and one crustacean hyperglycemic hormone. Highly accurate multi-scale characterization of a collection of varied size neuropeptides was achieved by integrating traditional data-dependent tandem MS, improved bottom-up sequencing, multiple fragmentation technique-enabled top-down sequencing, chemical derivatization, and in silico homology search. Collectively, the ability to characterize a neuropeptidome with vastly differing molecule sizes from a neural tissue extract could find great utility in unraveling complex signaling peptide mixtures employed by other biological systems. BIOLOGICAL SIGNIFICANCE Mass spectrometry (MS)-based neuropeptidomics aims to completely characterize the neuropeptides in a target organism as an important first step toward a better understanding of the structure and function of these complex signaling molecules. Although liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) with data-dependent acquisition is a powerful tool in peptidomic research, it often lacks the capability for de novo sequencing of mid-size and large peptides due to inefficient fragmentation of peptides larger than 4kDa. This study describes a multi-scale strategy for complete and confident sequence elucidation of various sizes of neuropeptides in the crustacean nervous system. The aim is to fill a technical gap where the conventional strategy is inefficient for comprehensive characterization of a complex neuropeptidome without assistance of genomic information. Nine novel neuropeptides in a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ of the spiny lobster, P. interruptus. The resulting molecular information extracted from such multi-scale peptidomic analysis will greatly accelerate functional studies of these novel neuropeptides.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy, University of Wisconsin-Madison, WI, USA; Department of Chemistry, University of Wisconsin-Madison, WI, USA
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32
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Abstract
Integral membrane proteins reside within the bilayer membranes that surround cells and organelles, playing critical roles in movement of molecules across them and the transduction of energy and signals. While their extreme amphipathicity presents technical challenges, biological mass spectrometry has been applied to all aspects of membrane protein chemistry and biology, including analysis of primary, secondary, tertiary, and quaternary structures as well as the dynamics that accompany functional cycles and catalysis.
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Affiliation(s)
- Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The NPI-Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, California 90095, United States.
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