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Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process (RNA-Seq)

ABSTRACT: The involvement of the histone variant H2A.Z and its isoforms in the regulation of gene expression is an increasing exciting field considering the impact of such regulations in physio-pathology. Indeed, we and other recently showed that H2A.Z.1 and H2A.Z.2 isoforms exert cooperative or antagonistic transcriptional regulations on subsets of genes involved in key processes, such as proliferation, senescence or several organ functions. In this work, we analyze the relative role of both H2A.Z isoforms on parameters of the intestinal epithelial homeostasis. We observed that the amount of H2A.Z.1 and H2A.Z.2 at TSS and gene bodies are highly correlated and that the two H2A.Z isoforms can replace each other when depleted. We highlighted the role of their respective deposition onto chromatin by specific incorporators in some discrete isoform-specific contribution to the differentiation process. We have also uncovered an unexpected link between H2A.Z isoforms occupancy at gene bodies and the propensity of genes to be induced in enterocyte differentiation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE232113 | GEO | 2024/10/15

REPOSITORIES: GEO

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Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process (ChIP-Seq)

Project description:The involvement of the histone variant H2A.Z and its isoforms in the regulation of gene expression is an increasing exciting field considering the impact of such regulations in physio-pathology. Indeed, we and other recently showed that H2A.Z.1 and H2A.Z.2 isoforms exert cooperative or antagonistic transcriptional regulations on subsets of genes involved in key processes, such as proliferation, senescence or several organ functions. In this work, we analyze the relative role of both H2A.Z isoforms on parameters of the intestinal epithelial homeostasis. We observed that the amount of H2A.Z.1 and H2A.Z.2 at TSS and gene bodies are highly correlated and that the two H2A.Z isoforms can replace each other when depleted. We highlighted the role of their respective deposition onto chromatin by specific incorporators in some discrete isoform-specific contribution to the differentiation process. We have also uncovered an unexpected link between H2A.Z isoforms occupancy at gene bodies and the propensity of genes to be induced in enterocyte differentiation.

2024-10-15 | GSE232112 | GEO

Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process

Project description:The histone variant H2A.Z plays important functions in the regulation of gene expression. In mammals, it is encoded by two genes, giving rise to two highly related isoforms named H2A.Z.1 and H2A.Z.2, which can have similar or antagonistic functions depending on the promoter. Knowledge of the physiopathological consequences of such functions emerges, but how the balance between these isoforms regulates tissue homeostasis is not fully understood. Here, we investigated the relative role of H2A.Z isoforms in intestinal epithelial homeostasis. Through genome-wide analysis of H2A.Z genomic localization in differentiating Caco-2 cells, we uncovered an enrichment of H2A.Z isoforms on the bodies of genes which are induced during enterocyte differentiation, stressing the potential importance of H2A.Z isoforms dynamics in this process. Through a combination of in vitro and in vivo experiments, we further demonstrated the two isoforms cooperate for stem and progenitor cells proliferation, as well as for secretory lineage differentiation. However, we found that they antagonistically regulate enterocyte differentiation, with H2A.Z.1 preventing terminal differentiation and H2A.Z.2 favoring it. Altogether, these data indicate that H2A.Z isoforms are critical regulators of intestine homeostasis and may provide a paradigm of how the balance between two isoforms of the same chromatin structural protein can control physiopathological processes.

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Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process

Project description:Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process

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Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process (ChIP-Seq)

Project description:Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process (ChIP-Seq)

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Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process (RNA-Seq)

Project description:Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process (RNA-Seq)

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Integrated analysis of H2A.Z isoforms reveals a complex interplay in gene regulation [ChIP-seq]

Project description:The H2A.Z histone variant plays major roles in the control of gene expression. In human, H2A.Z is encoded by two genes expressing two isoforms, H2A.Z.1 and H2A.Z.2 differing by three amino acids. Here, we undertook an integrated analysis of the independent and interdependent functions of these two isoforms in gene expression using endogenously-tagged isoform. RNA-Seq analysis following depletion of either isoform or both together in untransformed cells showed that they can regulate both distinct and overlapping sets of genes positively or negatively in a context-dependent manner. Our data revealed that the two isoforms have similar or antagonistic function depending on the gene. H2A.Z.1 and H2A.Z.2 can replace each other at Transcription Start Sites, providing a molecular explanation for this interplay. Mass spectrometry analysis showed that H2A.Z.1 and H2A.Z.2 have specific interactors, PHF14 and associated proteins for H2A.Z.1 and the histone deacetylase SIRT1 for H2A.Z.2. Moreover, we show that PHF14 and SIRT1 mediate the functional antagonism between H2A.Z.1 and H2A.Z.2. In conclusion, we propose a model in which the balance between H2A.Z.1 and H2A.Z.2 at promoters is critically important to regulate specific gene expression and depends on the recruitment of specific proteins. Our work thus provides an additional layer of complexity to the control of gene expression by histone variants.

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Integrated analysis of H2A.Z isoforms reveals a complex interplay in gene regulation [WI38_siPHF14-siSIRT1 RNA-seq]

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Genetic complementation analysis revealed distinct contributions of the N-terminal tail of H2A.Z to epigenetic regulations

Project description:The histone variant H2A.Z is one of the most evolutionally conserved histone variants. In vertebrates, two isoforms, H2A.Z.1 and H2A.Z.2, are identified and are involved in multiple epigenetic regulations. However, the role of H2A.Z in epigenetic regulations largely remains unknown especially in vertebrate. Previously, we derived tetracycline-inducible H2A.Z isofmrs double knockout (DKO) cells by using DT40 cells. With this cell, we showed that H2A.Z DKO leads to defects in mitotic progression and gene expression. To elucidate the function of H2A.Z further, we established genetic complementation system and confirmed that introducing exogenous H2A.Z complemented phenotypes of H2A.Z DKO cells. Given that acetylation of the N-terminal tail of H2A.Z reportedly contributes to significant roles in H2A.Z functions, we introduced two types of H2A.Z mutants, non-acetylable H2A.Z (5KR-H2A.Z) and chimeric H2A.Z in which its N-terminal tail is replaced with that of canonical H2A (H2A-H2A.Z), into H2A.Z DKO cells. These H2A.Z mutants complemented defects in mitotic progression. However, significant transcriptional dysregulation was observed in H2A.Z DKO cells stably expressing 5KR-H2A.Z and H2A-H2A.Z. These results suggest that the core domain and the N-terminal tail of the vertebrate H2A.Z contribute individually to mitotic progression and transcription regulation, respectively.

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