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Benjamin A Garcia - One of the best experts on this subject based on the ideXlab platform.
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isoform specific phosphorylation of human linker Histone H1 4 in mitosis by the kinase aurora b
Journal of Cell Science, 2011Co-Authors: Sonja P Hergeth, Benjamin A Garcia, Miroslav Dundr, Philipp Tropberger, Barry M Zee, Sylvain Daujat, Robert SchneiderAbstract:The linker Histone H1 plays an essential role in maintaining and establishing higher-order chromatin structure. As with core Histones, Histone H1 is also extensively covalently modified. We showed previously that phosphorylation of S27 in human Histone H1.4 (H1.4S27-P), prevents binding of heterochromatin protein 1 (HP1) family members (officially known as chromobox protein homologs) to the neighboring dimethylated K26. Here, we present the first functional characterization of H1.4S27-P in vivo and in vitro. We show that H1.4S27 phosphorylation is cell-cycle-regulated and its levels peak on metaphase chromosomes. We identify further Aurora B as the kinase phosphorylating H1.4S27. We demonstrate that Histone H1.4 is the only somatic linker Histone variant targeted by Aurora B and that Aurora B exclusively phosphorylates S27. Adjacent K26 dimethylation can regulate Aurora B activity towards S27, uncovering a crosstalk between these modifications. Finally, our fluorescence recovery after photobleaching (FRAP) analysis on Histone H1.4 mutants suggests a role of S27 phosphorylation in the regulation of Histone H1.4 mobility and chromatin binding in mitosis.
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Histone H1 variant specific lysine methylation by g9a kmt1c and glp1 kmt1d
Epigenetics & Chromatin, 2010Co-Authors: Thomas Weiss, Benjamin A Garcia, Annalisa Izzo, Sonja P Hergeth, Miroslav Dundr, Philipp Tropberger, Barry M Zee, Sylvain Daujat, Ulrike Zeissler, Robert SchneiderAbstract:Background The linker Histone H1 has a key role in establishing and maintaining higher order chromatin structure and in regulating gene expression. Mammals express up to 11 different H1 variants, with H1.2 and H1.4 being the predominant ones in most somatic cells. Like core Histones, H1 has high levels of covalent modifications; however, the full set of modifications and their biological role are largely unknown.
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comprehensive phosphoprotein analysis of linker Histone H1 from tetrahymena thermophila
Molecular & Cellular Proteomics, 2006Co-Authors: Benjamin A Garcia, Swati Joshi, Eric C Thomas, Raghu K Chitta, Robert L Diaz, Scott A Busby, Phillip C Andrews, Rachel Ogorzalek R Loo, Jeffrey Shabanowitz, Neil L KelleherAbstract:Linker Histone H1 is highly phosphorylated in normal growing Tetrahymena thermophila but becomes noticeably dephosphorylated in response to certain conditions such as prolonged starvation. Because phosphorylation of H1 has been associated with the regulation of gene expression, DNA repair, and other critical processes, we sought to use mass spectrometry-based approaches to obtain an in depth phosphorylation "signature" for this linker Histone. Histone H1 from both growing and starved Tetrahymena was analyzed by nanoflow reversed-phase HPLC MS/MS following enzymatic digestions, propionic anhydride derivatization, and phosphopeptide enrichment via IMAC. We confirmed five phosphorylation sites identified previously and detected two novel sites of phosphorylation and two novel minor sites of acetylation. The sequential order of phosphorylation on H1 was deduced by using mass spectrometry to define the modified sites on phosphorylated H1 isoforms separated by cation-exchange chromatography. Relative levels of site-specific phosphorylation on H1 isolated from growing and starved Tetrahymena were obtained using a combination of stable isotopic labeling, IMAC, and tandem mass spectrometry.
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comprehensive phosphoprotein analysis of linker Histone H1 from tetrahymena thermophila
Molecular & Cellular Proteomics, 2006Co-Authors: Benjamin A Garcia, Swati Joshi, Eric C Thomas, Raghu K Chitta, Robert L Diaz, Scott A Busby, Phillip C Andrews, Jeffrey Shabanowitz, Neil L KelleherAbstract:Linker Histone H1 is highly phosphorylated in normal growing Tetrahymena thermophila but becomes noticeably dephosphorylated in response to certain conditions such as prolonged starvation. Because phosphorylation of H1 has been associated with the regulation of gene expression, DNA repair, and other critical processes, we sought to use mass spectrometry-based approaches to obtain an in depth phosphorylation “signature” for this linker Histone. Histone H1 from both growing and starved Tetrahymena was analyzed by nanoflow reversed-phase HPLC MS/MS following enzymatic digestions, propionic anhydride derivatization, and phosphopeptide enrichment via IMAC. We confirmed five phosphorylation sites identified previously and detected two novel sites of phosphorylation and two novel minor sites of acetylation. The sequential order of phosphorylation on H1 was deduced by using mass spectrometry to define the modified sites on phosphorylated H1 isoforms separated by cation-exchange chromatography. Relative levels of site-specific phosphorylation on H1 isolated from growing and starved Tetrahymena were obtained using a combination of stable isotopic labeling, IMAC, and tandem mass spectrometry. Molecular & Cellular Proteomics 5: 1593–1609, 2006.
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characterization of phosphorylation sites on Histone H1 isoforms by tandem mass spectrometry
Journal of Proteome Research, 2004Co-Authors: Benjamin A Garcia, Scott A Busby, Jeffrey Shabanowitz, Cynthia M Barber, And David C Allis, Donald F HuntAbstract:Histone H1 isoforms isolated from asynchronously grown HeLa cells were subjected to enzymatic digestion and analyzed by nano-flow reversed-phase high performance liquid chromatography (RP-HPLC) tandem mass spectrometry (MS/MS) on both quadrupole ion trap and linear quadrupole ion trap-Fourier transform ion cyclotron resonance mass spectrometers. We have observed all five major isoforms of Histone H1 (H1.1, H1.2, H1.3, H1.4, and H1.5) as well as a lesser studied H1, isoform H1.X. MS/MS experiments confirmed N-terminal acetylation on all isoforms plus a single internal acetylation site. Immobilized metal affinity chromatography in combination with tandem mass spectrometry was utilized to identify 19 phosphorylation sites on the five major H1 isoforms plus H1.X. Fourteen of these phosphorylation sites were located on peptides containing the cyclin dependent kinase (CDK) consensus motif (S/T)−P−X−Z (where X is any amino acid and Z is a basic amino acid). Five phosphorylation sites were identified in regions t...
Albert Jordan - One of the best experts on this subject based on the ideXlab platform.
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towards understanding the regulation of Histone H1 somatic subtypes with omics
Journal of Molecular Biology, 2021Co-Authors: Inma Ponte, Albert Jordan, Marta Andres, Alicia RoqueAbstract:Histone H1 is involved in the regulation of chromatin higher-order structure and compaction. In humans, Histone H1 is a multigene family with seven subtypes differentially expressed in somatic cells. Which are the regulatory mechanisms that determine the variability of the H1 complement is a long-standing biological question regarding Histone H1. We have used a new approach based on the integration of OMICs data to address this issue. We have examined the 3D-chromatin structure, the binding of transcription factors (TFs), and the expression of somatic H1 genes in human cell lines, using data from public repositories, such as ENCODE. Analysis of Hi-C, ChIP-seq, and RNA-seq data, have revealed that transcriptional control has a greater impact on H1 regulation than previously thought. Somatic H1 genes located in topologically associated domains (TADs) show higher expression than in boundary regions. H1 genes are targeted by a variable number of transcription factors including cell cycle-related TFs, and tissue-specific TFs, suggesting a fine-tuned, subtype-specific transcriptional control. We describe, for the first time, that all H1 somatic subtypes are under transcriptional co-regulation. The replication-independent subtypes, which are encoded in different chromosomes isolated from other Histone genes, are also co-regulated with the rest of the somatic H1 genes, indicating that transcriptional co-regulation extends beyond the Histone cluster. Transcriptional control and transcriptional co-regulation explain, at least in part, the variability of H1 complement, the fluctuations of H1 subtypes during development, and also the compensatory effects observed, in model systems, after perturbation of one or more H1 subtypes.
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towards understanding the regulation of Histone H1 somatic subtypes with omics
bioRxiv, 2020Co-Authors: Inma Ponte, Albert Jordan, Marta Andres, Alicia RoqueAbstract:Abstract Background Histone H1 is involved in the regulation of chromatin higher-order structure and compaction. In humans, Histone H1 is a multigene family with seven subtypes differentially expressed in somatic cells. Which are the regulatory mechanisms that determine the variability of the H1 complement is a long-standing biological question regarding Histone H1. We have used a new approach based on the integration of OMICs data to address this question. Results We have examined the 3D-chromatin structure, the binding of transcription factors (TFs), and the expression of somatic H1 genes in human cell lines, using data from public repositories, such as ENCODE. Analysis of Hi-C, ChIP-seq, and RNA-seq data, have shown that transcriptional control has a greater impact on H1 regulation than previously thought. Somatic H1 genes located in TADs show higher expression than in boundaries. H1 genes are targeted by a variable number of transcription factors including cell cycle-related TFs, and tissue-specific TFs, suggesting a finetuned, subtype-specific transcriptional control. We describe, for the first time, that all H1 somatic subtypes are under transcriptional co-regulation. The replication-independent subtypes, which are encoded in different chromosomes, isolated from other Histone genes are also co-regulated with the rest of the somatic H1 genes, indicating that transcriptional co-regulation extends beyond the Histone cluster. Conclusions Transcriptional control and transcriptional co-regulation explain, at least in part, the variability of H1 complement, the fluctuations of H1 subtypes during development, and also the compensatory effects observed, in model systems, after perturbation of one or more H1 subtypes.
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specificities and genomic distribution of somatic mammalian Histone H1 subtypes
Biochimica et Biophysica Acta, 2016Co-Authors: Lluis Millanarino, Andrea Izquierdobouldstridge, Albert JordanAbstract:Histone H1 is a structural component of chromatin that may have a role in the regulation of chromatin dynamics. Unlike core Histones, the linker Histone H1 family is evolutionarily diverse and many organisms have multiple H1 variants or subtypes, distinguishable between germ-line and somatic cells. In mammals, the H1 family includes seven somatic H1 variants with a prevalence that varies between cell types and over the course of differentiation, H1.1 to H1.5 being expressed in a replication-dependent manner, whereas H1.0 and H1X are replication-independent. Until recently, it has not been known whether the different variants had specific roles in the regulation of nuclear processes or were differentially distributed across the genome. To address this, an increasing effort has been made to investigate divergent features among H1 variants, regarding their structure, expression patterns, chromatin dynamics, post-translational modifications and genome-wide distribution. Although H1 subtypes seem to have redundant functions, several reports point to the idea that they are also differently involved in specific cellular processes. Initial studies investigating the genomic distribution of H1 variants have started to suggest that despite a wide overlap, different variants may be enriched or preferentially located at different chromatin types, but this may depend on the cell type, the relative abundance of the variants, the differentiation state of the cell, or whether cells are derived from a neoplastic process. Understanding the heterogeneity of the Histone H1 family is crucial to elucidate their role in chromatin organization, gene expression regulation and other cellular processes.
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depletion of human Histone H1 variants uncovers specific roles in gene expression and cell growth
PLOS Genetics, 2008Co-Authors: Monica Sancho, Miguel Beato, Erika Diani, Albert JordanAbstract:At least six Histone H1 variants exist in somatic mammalian cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be actively involved in the regulation of gene expression. However, it is not well known whether the different variants have distinct roles or if they regulate specific promoters. We have explored this by inducible shRNA-mediated knock-down of each of the H1 variants in a human breast cancer cell line. Rapid inhibition of each H1 variant was not compensated for by changes of expression of other variants. Microarray experiments have shown a different subset of genes to be altered in each H1 knock-down. Interestingly, H1.2 depletion caused specific effects such as a cell cycle G1-phase arrest, the repressed expression of a number of cell cycle genes, and decreased global nucleosome spacing. On its side, H1.4 depletion caused cell death in T47D cells, providing the first evidence of the essential role of an H1 variant for survival in a human cell type. Thus, specific phenotypes are observed in breast cancer cells depleted of individual Histone H1 variants, supporting the theory that distinct roles exist for the linker Histone variants.
Haiyi Li - One of the best experts on this subject based on the ideXlab platform.
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Histone H1 defect in escort cells triggers germline tumor in drosophila ovary
Developmental Biology, 2017Co-Authors: Zhihao Yang, Yuzhao Hu, Huanhuan Qiao, Ronggang Xu, Bowen Xu, Jiang Xu, Fang Wang, Yifan Zhang, Xia Wang, Haiyi LiAbstract:Drosophila ovary is recognized as one of the best model systems to study stem cell biology in vivo. We had previously identified an autonomous role of the Histone H1 in germline stem cell (GSC) maintenance. Here, we found that Histone H1 depletion in escort cells (ECs) resulted in an increase of spectrosome-containing cells (SCCs), an ovary tumor-like phenotype. Further analysis showed that the Dpp pathway is excessively activated in these SCC cells, while the expression of bam is attenuated. In the H1-depleted ECs, both transposon activity and DNA damage had increased dramatically, followed by EC apoptosis, which is consistent with the role of H1 in other somatic cells. Surprisingly, H1-depleted ECs acquired cap cell characteristics including dpp expression, and the resulting abnormal Dpp level inhibits SCC further differentiation. Most interestingly, double knockdown of H1 and dpp in ECs can reduce the number of SCCs to the normal level, indicating that the additional Dpp secreted by ECs contributes to the germline tumor. Taken together, our findings indicate that Histone H1 is an important epigenetic factor in controlling EC characteristics and a key suppressor of germline tumor.
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Histone H1 defect in escort cells triggers germline tumor in drosophila ovary
Developmental Biology, 2017Co-Authors: Zhihao Yang, Yuzhao Hu, Huanhuan Qiao, Ronggang Xu, Bowen Xu, Jiang Xu, Fang Wang, Yifan Zhang, Xia Wang, Haiyi LiAbstract:Drosophila ovary is recognized as one of the best model systems to study stem cell biology in vivo. We had previously identified an autonomous role of the Histone H1 in germline stem cell (GSC) maintenance. Here, we found that Histone H1 depletion in escort cells (ECs) resulted in an increase of spectrosome-containing cells (SCCs), an ovary tumor-like phenotype. Further analysis showed that the Dpp pathway is excessively activated in these SCC cells, while the expression of bam is attenuated. In the H1-depleted ECs, both transposon activity and DNA damage had increased dramatically, followed by EC apoptosis, which is consistent with the role of H1 in other somatic cells. Surprisingly, H1-depleted ECs acquired cap cell characteristics including dpp expression, and the resulting abnormal Dpp level inhibits SCC further differentiation. Most interestingly, double knockdown of H1 and dpp in ECs can reduce the number of SCCs to the normal level, indicating that the additional Dpp secreted by ECs contributes to the germline tumor. Taken together, our findings indicate that Histone H1 is an important epigenetic factor in controlling EC characteristics and a key suppressor of germline tumor.
Neil L Kelleher - One of the best experts on this subject based on the ideXlab platform.
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comprehensive phosphoprotein analysis of linker Histone H1 from tetrahymena thermophila
Molecular & Cellular Proteomics, 2006Co-Authors: Benjamin A Garcia, Swati Joshi, Eric C Thomas, Raghu K Chitta, Robert L Diaz, Scott A Busby, Phillip C Andrews, Rachel Ogorzalek R Loo, Jeffrey Shabanowitz, Neil L KelleherAbstract:Linker Histone H1 is highly phosphorylated in normal growing Tetrahymena thermophila but becomes noticeably dephosphorylated in response to certain conditions such as prolonged starvation. Because phosphorylation of H1 has been associated with the regulation of gene expression, DNA repair, and other critical processes, we sought to use mass spectrometry-based approaches to obtain an in depth phosphorylation "signature" for this linker Histone. Histone H1 from both growing and starved Tetrahymena was analyzed by nanoflow reversed-phase HPLC MS/MS following enzymatic digestions, propionic anhydride derivatization, and phosphopeptide enrichment via IMAC. We confirmed five phosphorylation sites identified previously and detected two novel sites of phosphorylation and two novel minor sites of acetylation. The sequential order of phosphorylation on H1 was deduced by using mass spectrometry to define the modified sites on phosphorylated H1 isoforms separated by cation-exchange chromatography. Relative levels of site-specific phosphorylation on H1 isolated from growing and starved Tetrahymena were obtained using a combination of stable isotopic labeling, IMAC, and tandem mass spectrometry.
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comprehensive phosphoprotein analysis of linker Histone H1 from tetrahymena thermophila
Molecular & Cellular Proteomics, 2006Co-Authors: Benjamin A Garcia, Swati Joshi, Eric C Thomas, Raghu K Chitta, Robert L Diaz, Scott A Busby, Phillip C Andrews, Jeffrey Shabanowitz, Neil L KelleherAbstract:Linker Histone H1 is highly phosphorylated in normal growing Tetrahymena thermophila but becomes noticeably dephosphorylated in response to certain conditions such as prolonged starvation. Because phosphorylation of H1 has been associated with the regulation of gene expression, DNA repair, and other critical processes, we sought to use mass spectrometry-based approaches to obtain an in depth phosphorylation “signature” for this linker Histone. Histone H1 from both growing and starved Tetrahymena was analyzed by nanoflow reversed-phase HPLC MS/MS following enzymatic digestions, propionic anhydride derivatization, and phosphopeptide enrichment via IMAC. We confirmed five phosphorylation sites identified previously and detected two novel sites of phosphorylation and two novel minor sites of acetylation. The sequential order of phosphorylation on H1 was deduced by using mass spectrometry to define the modified sites on phosphorylated H1 isoforms separated by cation-exchange chromatography. Relative levels of site-specific phosphorylation on H1 isolated from growing and starved Tetrahymena were obtained using a combination of stable isotopic labeling, IMAC, and tandem mass spectrometry. Molecular & Cellular Proteomics 5: 1593–1609, 2006.
Robert Schneider - One of the best experts on this subject based on the ideXlab platform.
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the role of linker Histone H1 modifications in the regulation of gene expression and chromatin dynamics
Biochimica et Biophysica Acta, 2016Co-Authors: Annalisa Izzo, Robert SchneiderAbstract: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. This article is part of a Special Issue entitled: Histone H1, edited by Dr. Albert Jordan.
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isoform specific phosphorylation of human linker Histone H1 4 in mitosis by the kinase aurora b
Journal of Cell Science, 2011Co-Authors: Sonja P Hergeth, Benjamin A Garcia, Miroslav Dundr, Philipp Tropberger, Barry M Zee, Sylvain Daujat, Robert SchneiderAbstract:The linker Histone H1 plays an essential role in maintaining and establishing higher-order chromatin structure. As with core Histones, Histone H1 is also extensively covalently modified. We showed previously that phosphorylation of S27 in human Histone H1.4 (H1.4S27-P), prevents binding of heterochromatin protein 1 (HP1) family members (officially known as chromobox protein homologs) to the neighboring dimethylated K26. Here, we present the first functional characterization of H1.4S27-P in vivo and in vitro. We show that H1.4S27 phosphorylation is cell-cycle-regulated and its levels peak on metaphase chromosomes. We identify further Aurora B as the kinase phosphorylating H1.4S27. We demonstrate that Histone H1.4 is the only somatic linker Histone variant targeted by Aurora B and that Aurora B exclusively phosphorylates S27. Adjacent K26 dimethylation can regulate Aurora B activity towards S27, uncovering a crosstalk between these modifications. Finally, our fluorescence recovery after photobleaching (FRAP) analysis on Histone H1.4 mutants suggests a role of S27 phosphorylation in the regulation of Histone H1.4 mobility and chromatin binding in mitosis.
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Histone H1 variant specific lysine methylation by g9a kmt1c and glp1 kmt1d
Epigenetics & Chromatin, 2010Co-Authors: Thomas Weiss, Benjamin A Garcia, Annalisa Izzo, Sonja P Hergeth, Miroslav Dundr, Philipp Tropberger, Barry M Zee, Sylvain Daujat, Ulrike Zeissler, Robert SchneiderAbstract:Background The linker Histone H1 has a key role in establishing and maintaining higher order chromatin structure and in regulating gene expression. Mammals express up to 11 different H1 variants, with H1.2 and H1.4 being the predominant ones in most somatic cells. Like core Histones, H1 has high levels of covalent modifications; however, the full set of modifications and their biological role are largely unknown.
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the Histone H1 family specific members specific functions
Biological Chemistry, 2008Co-Authors: Annalisa Izzo, Kinga Kamieniarz, Robert SchneiderAbstract:The linker Histone H1 binds to the DNA entering and exiting the nucleosomal core particle and has an important role in establishing and maintaining higher order chromatin structures. H1 forms a complex family of related proteins with distinct species, tissue and developmental specificity. In higher eukaryotes all H1 variants have the same general structure, consisting of a central conserved globular domain and less conserved N-terminal and C-terminal tails. These tails are moderately conserved among species, but differ among variants, suggesting a specific function for each H1 variant. Due to compensatory mechanisms and to the lack of proper tools, it has been very difficult to study the biological role of individual variants in chromatin-mediated processes. Our knowledge about H1 variants is indeed limited, and in vitro and in vivo observations have often been contradictory. Therefore, H1 variants were considered to be functionally redundant. However, recent knockout studies and biochemical analyses in different organisms have revealed exciting new insights into the specificity and mechanisms of actions of the H1 family members. Here, we collect and compare the available literature about H1 variants and discuss possible specific roles that challenge the concept of H1 being a mere structural component of chromatin and a general repressor of transcription.