SUMOylation of linker histone H1 drives chromatin condensation and restriction of embryonic cell fate identity

Cellular senescence is a tumor-suppressing mechanism that is accompanied by characteristic chromatin condensation called senescence-associated heterochromatic foci (SAHFs). We found that individual SAHFs originate from individual chromosomes. SAHFs do not show alterations of posttranslational modifications of core histones that mark condensed chromatin in mitotic chromosomes, apoptotic chromatin, or transcriptionally inactive heterochromatin. Remarkably, SAHF-positive senescent cells lose linker histone H1 and exhibit increased levels of chromatin-bound high mobility group A2 (HMGA2). The expression of N-terminally enhanced green fluorescent protein (EGFP)–tagged histone H1 induces premature senescence phenotypes, including increased levels of phosphorylated p53, p21, and hypophosphorylated Rb, and a decrease in the chromatin-bound endogenous histone H1 level but not in p16 level accumulation or SAHF formation. However, the simultaneous ectopic expression of hemagglutinin-tagged HMGA2 and N-terminally EGFP-tagged histone H1 leads to significant SAHF formation (P < 0.001). It is known that histone H1 and HMG proteins compete for a common binding site, the linker DNA. These results suggest that SAHFs are a novel type of chromatin condensation involving alterations in linker DNA–binding proteins.

Download Full-text

Faculty Opinions recommendation of Phosphorylation of the linker histone H1 by CDK regulates its binding to HP1alpha.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1033234.375772 ◽

2006 ◽

Author(s):

William Earnshaw

Keyword(s):

Histone H1 ◽

Linker Histone ◽

Linker Histone H1

Download Full-text

Site-specific ubiquitylation acts as a regulator of linker histone H1

Nature Communications ◽

10.1038/s41467-021-23636-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Eva Höllmüller ◽

Simon Geigges ◽

Marie L. Niedermeier ◽

Kai-Michael Kammer ◽

Simon M. Kienle ◽

...

Keyword(s):

Posttranslational Modifications ◽

Histone H1 ◽

Linker Histone ◽

Active Chromatin ◽

Site Specific ◽

Linker Histone H1 ◽

Fundamental Process ◽

Core Histones ◽

Wide Scale

AbstractDecoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. This is well studied for PTMs of core histones but not for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the chemical synthesis of site-specifically mono-ubiquitylated H1.2 and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that site-specific ubiquitylation of H1 at position K64 modulates interactions with deubiquitylating enzymes and the deacetylase SIRT1. Moreover, it affects H1-dependent chromatosome assembly and phase separation resulting in a more open chromatosome conformation generally associated with a transcriptionally active chromatin state. In summary, we propose that site-specific ubiquitylation plays a general regulatory role for linker histone H1.

Download Full-text

The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation

Nature Communications ◽

10.1038/s41467-021-22993-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Pierre Bourguet ◽

Colette L. Picard ◽

Ramesh Yelagandula ◽

Thierry Pélissier ◽

Zdravko J. Lorković ◽

...

Keyword(s):

Dna Methylation ◽

Histone H1 ◽

Epigenetic Modifications ◽

Flowering Plants ◽

Linker Histone ◽

Histone Variant ◽

Null Mutant ◽

Chromatin Compaction ◽

Linker Histone H1

AbstractIn flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of the linker histone H1, and specific epigenetic modifications, such as high levels of DNA methylation at both CG and non-CG sites. How H2A.W regulates heterochromatin organization and interacts with other heterochromatic features is unclear. Here, we create a h2a.w null mutant via CRISPR-Cas9, h2a.w-2, to analyze the in vivo function of H2A.W. We find that H2A.W antagonizes deposition of H1 at heterochromatin and that non-CG methylation and accessibility are moderately decreased in h2a.w-2 heterochromatin. Compared to H1 loss alone, combined loss of H1 and H2A.W greatly increases accessibility and facilitates non-CG DNA methylation in heterochromatin, suggesting co-regulation of heterochromatic features by H2A.W and H1. Our results suggest that H2A.W helps maintain optimal heterochromatin accessibility and DNA methylation by promoting chromatin compaction together with H1, while also inhibiting excessive H1 incorporation.

Download Full-text

Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples

International Journal of Molecular Sciences ◽

10.3390/ijms21197330 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7330

Author(s):

Roberta Noberini ◽

Cristina Morales Torres ◽

Evelyn Oliva Savoia ◽

Stefania Brandini ◽

Maria Giovanna Jodice ◽

...

Keyword(s):

Mass Spectrometry ◽

Histone H1 ◽

Histone Variants ◽

Linker Histone ◽

Clinical Samples ◽

Label Free ◽

Complex Samples ◽

Linker Histone H1 ◽

Ideal Tool ◽

Free Quantification

Epigenetic aberrations have been recognized as important contributors to cancer onset and development, and increasing evidence suggests that linker histone H1 variants may serve as biomarkers useful for patient stratification, as well as play an important role as drivers in cancer. Although traditionally histone H1 levels have been studied using antibody-based methods and RNA expression, these approaches suffer from limitations. Mass spectrometry (MS)-based proteomics represents the ideal tool to accurately quantify relative changes in protein abundance within complex samples. In this study, we used a label-free quantification approach to simultaneously analyze all somatic histone H1 variants in clinical samples and verified its applicability to laser micro-dissected tissue areas containing as low as 1000 cells. We then applied it to breast cancer patient samples, identifying differences in linker histone variants patters in primary triple-negative breast tumors with and without relapse after chemotherapy. This study highlights how label-free quantitation by MS is a valuable option to accurately quantitate histone H1 levels in different types of clinical samples, including very low-abundance patient tissues.

Download Full-text

Quantitative Assessment of Transition Proteins 1, 2 Spermatid-Specific Linker Histone H1-Like Protein Transcripts in Spermatozoa from Normozoospermic and Asthenozoospermic Men

Archives of Andrology ◽

10.1080/01485010701426430 ◽

2007 ◽

Vol 53 (4) ◽

pp. 199-205 ◽

Cited By ~ 24

Author(s):

Piotr Jedrzejczak ◽

Bartosz Kempisty ◽

Artur Bryja ◽

M. Mostowska ◽

Magdalena Depa-Martynow ◽

...

Keyword(s):

Quantitative Assessment ◽

Histone H1 ◽

Linker Histone ◽

Linker Histone H1

Download Full-text

Phosphorylation and an ATP-dependent process increase the dynamic exchange of H1 in chromatin

The Journal of Cell Biology ◽

10.1083/jcb.200202131 ◽

2002 ◽

Vol 158 (7) ◽

pp. 1161-1170 ◽

Cited By ~ 65

Author(s):

Yali Dou ◽

Josephine Bowen ◽

Yifan Liu ◽

Martin A. Gorovsky

Keyword(s):

Negative Charge ◽

Histone H1 ◽

Linker Histone ◽

Global Effect ◽

Dynamic Binding ◽

Linker Histone H1 ◽

Dependent Process ◽

Dynamic Exchange

In Tetrahymena cells, phosphorylation of linker histone H1 regulates transcription of specific genes. Phosphorylation acts by creating a localized negative charge patch and phenocopies the loss of H1 from chromatin, suggesting that it affects transcription by regulating the dissociation of H1 from chromatin. To test this hypothesis, we used FRAP of GFP-tagged H1 to analyze the effects of mutations that either eliminate or mimic phosphorylation on the binding of H1 to chromatin both in vivo and in vitro. We demonstrate that phosphorylation can increase the rate of dissociation of H1 from chromatin, providing a mechanism by which it can affect H1 function in vivo. We also demonstrate a previously undescribed ATP-dependent process that has a global effect on the dynamic binding of linker histone to chromatin.

Download Full-text

Mechanisms of Nucleosome Reorganization by PARP1

International Journal of Molecular Sciences ◽

10.3390/ijms222212127 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12127

Author(s):

Natalya V. Maluchenko ◽

Dmitry K. Nilov ◽

Sergey V. Pushkarev ◽

Elena Y. Kotova ◽

Nadezhda S. Gerasimova ◽

...

Keyword(s):

Molecular Dynamics ◽

Dna Repair ◽

Gene Regulation ◽

Transcription Initiation ◽

Histone H1 ◽

Linker Histone ◽

Gene Promoters ◽

Linker Histone H1 ◽

Nucleosomal Dna ◽

Dna Ends

Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in DNA repair, chromatin organization and transcription. During transcription initiation, PARP1 interacts with gene promoters where it binds to nucleosomes, replaces linker histone H1 and participates in gene regulation. However, the mechanisms of PARP1-nucleosome interaction remain unknown. Here, using spFRET microscopy, molecular dynamics and biochemical approaches we identified several different PARP1-nucleosome complexes and two types of PARP1 binding to mononucleosomes: at DNA ends and end-independent. Two or three molecules of PARP1 can bind to a nucleosome depending on the presence of linker DNA and can induce reorganization of the entire nucleosome that is independent of catalytic activity of PARP1. Nucleosome reorganization depends upon binding of PARP1 to nucleosomal DNA, likely near the binding site of linker histone H1. The data suggest that PARP1 can induce the formation of an alternative nucleosome state that is likely involved in gene regulation and DNA repair.

Download Full-text