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Dynamic association of IκBα to chromatin during intestinal differentiation is regulated by Acetylation and N-terminal cleavage of histone H4

ABSTRACT: Dynamic association of IκBα to chromatin during intestinal differentiation is regulated by Acetylation and N-terminal cleavage of histone H4

PROVIDER: PRJNA702981 | ENA |

REPOSITORIES: ENA

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Dynamic association of IκBα to chromatin during intestinal differentiation is regulated by Acetylation and N-terminal cleavage of histone H4

Project description:IκBs exert a principal function as cytoplasmic inhibitors of the NF-kB transcription factors. Additional functions for specific IκB homologues have also been described including their association to chromatin to directly regulate gene transcription. Phosphorylated and SUMOylated IκBα (pS-IκBα) specifically binds histones H2A and H4 in the stem and progenitor compartment of skin and intestine, but the mechanisms that control the recruitment of nuclear pS-IκBα to the chromatin are largely unstudied. We here show thatserine 32-36 phosphorylation of IκBα favors its binding with nucleosomes and demonstrated that p-IκBαassociation to H4 is favored by acetylation at specific H4 lysine (K) residues. Acetylated N-terminal tail of H4 is lost during intestinal cell differentiation due to histone cleavage at amino acids 17-19 by the action of trypsin or chymotrypsin, which interferes p-IκBα association to chromatin. Paradoxically, pharmacologic or genetic inhibition of trypsin and chymotrypsin activity in HT29 cells increased p-IκBα chromatin binding, associated to impaired goblet cell differentiation, which was comparable to IκBα deletion. Together our results indicate that dynamic binding of IκBα to chromatin is a requirement for intestinal cell differentiation and provide a molecular base for the restricted nuclear distribution of p-IκBα at specific stem cell compartments.

2021-06-21 | GSE167087 | GEO

Histone H4 N-terminal tail mutants

Project description:A series of yeast carrying K->R mutations in the histone H4 N-terminal tail were profiled by gene expression array in mid-log phase.

2010-06-10 | E-GEOD-2324 | biostudies-arrayexpress

Histone H4 N-terminal tail mutants

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Dynamic competing histone H4 K5K8 acetylation and butyrylation are hallmarks of highly active gene promoters

Project description:Newly discovered histone lysine acylations increase the functional diversity of nucleosomes well beyond acetylation. Here, we focus on histone butyrylation in the context of sperm cell differentiation. Specifically, we investigate the butyrylation of histone H4 lysine 5 and 8 at gene promoters, where acetylation guides the binding of Brdt, a bromodomain-and-extra-terminal protein, thereby mediating stage-specific gene expression programs. Genome-wide mapping data show that highly active Brdt-bound gene promoters systematically harbour competing histone acetylation and butyrylation marks at H4 K5 and K8. Histone butyrylation, despite acting as a direct stimulator of transcription, competes with acetylation, especially at H4 K5, to prevent Brdt binding. The observed in vivo H4 K5K8 acetylation butyrylation state at active promoters is reproduced in vitro where p300 indistinctly acetylates and butyrylates H4 K5 and K8. Altogether, highly active gene promoter regions are characterized by alternating H4 acetylation and butyrylation sustaining direct gene activation and a dynamic bromodomain binding.

2016-07-13 | GSE77277 | GEO

Genome-wide analysis of SAS-I-mediated H4 K16 acetylation

Project description:The MYST HAT Sas2 is part of the SAS-I complex. The target for acetylation by Sas2 is Lys16 of histone H4 (H4 K16Ac). This acetylation site marks euchromatic regions and opposes the spreading of heterochromatin at telomere-proximal regions. Changes of SAS-I-mediated H4 K16Ac on a genome-wide scale comparing wt and sas2M-bM-^HM-^F cells were investigated in this study. We found a pronounced, genome-wide loss of H4 K16 acetylation in the body of transcribed genes in the absence of Sas2. Furthermore, the influence of Sas2 on gene expression was investigated in RNA expression arrays. H4 K16Ac and H4 in wt and sas2M-bM-^HM-^F was ChIPed. ChIP experiments were performed three times with independent chromatin preparations.

2012-01-18 | E-GEOD-19962 | biostudies-arrayexpress

N-terminal acetylation for identification of cleavage sites on immunoprecipitated PrP

Project description:In-gel N-terminal acetylation of immunoprecipitated prion protein for identification of cleavage sites. Mouse expressing either WT or mutant (S3) form of PrP were used in this study. Three replicates from single brains were included in this experiment.

2023-07-27 | MSV000092543 | MassIVE

Expression data from RH30 vector and RH30 IκBα SR cells

Project description:Classical NF-κB activity can be inhibited by overexpression of the IκBα super repressor (SR). To determine the role of NF-κB in rhabdomyosarcoma cells, we overexpressed the IκBα SR in RH30 rhabdomyosarcoma cells. IκBα SR was overexpressed in RH30 cells. RH30 vector cells were used as control group.

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Dynamic chromatin association of I?B? is regulated by acetylation and cleavage of histone H4

Project description: Not available

| S-SCDT-EMBOR-2021-52649V1 | biostudies-other

Genome-wide analysis of SAS-I-mediated H4 K16 acetylation

Project description:The MYST HAT Sas2 is part of the SAS-I complex. The target for acetylation by Sas2 is Lys16 of histone H4 (H4 K16Ac). This acetylation site marks euchromatic regions and opposes the spreading of heterochromatin at telomere-proximal regions. Changes of SAS-I-mediated H4 K16Ac on a genome-wide scale comparing wt and sas2∆ cells were investigated in this study. We found a pronounced, genome-wide loss of H4 K16 acetylation in the body of transcribed genes in the absence of Sas2. Furthermore, the influence of Sas2 on gene expression was investigated in RNA expression arrays.

2012-01-18 | GSE19962 | GEO

Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail

Project description:ISWI-family nucleosome remodeling enzymes need the histone H4 N-terminal tail to mobilize nucleosomes. Here we mapped the H4-tail binding pocket of ISWI. Surprisingly the binding site was adjacent to but not overlapping with the docking site of an auto-regulatory motif, AutoN, in the N-terminal region (NTR) of ISWI, indicating that AutoN does not act as a simple pseudosubstrate as suggested previously. Rather, AutoN cooperated with a hitherto uncharacterized motif, termed AcidicN, to confer H4-tail sensitivity and discriminate between DNA and nucleosomes. A third motif in the NTR, ppHSA, was functionally required in vivo and provided structural stability by clamping the NTR to Lobe 2 of the ATPase domain. This configuration is reminiscent of Chd1 even though Chd1 contains an unrelated NTR. Our results shed light on the intricate structural and functional regulation of ISWI by the NTR and uncover surprising parallels with Chd1. Elife. 2017 Jan 21;6. pii: e21477. doi: 10.7554/eLife.21477. [Epub ahead of print]

2017-02-02 | PXD005831 | Pride

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