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Antisense-mediated repression of SAGA-dependent genes involves the HIR histone chaperone

ABSTRACT: Antisense-mediated repression of SAGA-dependent genes involves the HIR histone chaperone

PROVIDER: PRJNA734519 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14711035.fastq.gz	Fastqsanger.gz
	SRR14711036.fastq.gz	Fastqsanger.gz
	SRR14711037.fastq.gz	Fastqsanger.gz
	SRR14711038.fastq.gz	Fastqsanger.gz
	SRR14711039.fastq.gz	Fastqsanger.gz

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Antisense-mediated repression of SAGA-dependent genes involves the HIR histone chaperone

Project description:Eukaryotic genomes are pervasively transcribed by RNA polymerase II (RNAPII), and transcription of long non-coding RNAs often overlaps with coding gene promoters. This might lead to coding gene repression in a process named Transcription Interference (TI). In Saccharomyces cerevisiae (S. cerevisiae), TI is mainly driven by antisense non-coding transcription and occurs through re-shaping of promoter Nucleosome-Depleted Regions (NDRs). In this study, we developed a genetic screen to identify new players involved in Antisense-Mediated Transcription Interference (AMTI). Among the candidates, we found the HIR histone chaperone complex known to be involved in de novo histone deposition. Using genome-wide approaches, we reveal that HIR-dependent histone deposition represses the promoters of SAGA-dependent genes via antisense non-coding transcription. However, while antisense transcription is enriched at promoters of SAGA-dependent genes, this feature is not sufficient to define the mode of gene regulation. We further show that the balance between HIR-dependent nucleosome incorporation and transcription factor binding at promoters directs transcription into a SAGA- or TFIID-dependent regulation. This study sheds light on a new connection between antisense non-coding transcription and the nature of coding transcription initiation.

2021-06-03 | GSE175991 | GEO

Structure of the Hir histone chaperone complex

Project description:The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1/Asf1 co-chaperone cooperate for replication-independent chromatin assembly. Here we report the molecular architecture of the Hir complex with Asf1/H3/H4 via single-particle cryo-EM and crosslinking mass spectrometry.

2024-08-22 | PXD040705 | Pride

Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes

Project description:Transcription initiation involves the coordinated activities of large multimeric complexes that are organized into functional modules. Little is known about the mechanisms and pathways that govern their assembly from individual components. We report here several principles governing the assembly of the highly conserved SAGA and NuA4 co-activator complexes. Using fission yeast, which contain two functionally non-redundant paralogs of the shared Tra1 subunit, we demonstrate that Tra1 contributes to scaffolding the entire NuA4 complex. In contrast, within SAGA, Tra1 specifically promotes the incorporation of the de-ubiquitination module (DUB), defining an ordered assembly pathway. Biochemical and functional analyses elucidated the mechanism by which Tra1 assemble differentially into SAGA or NuA4 and identified a small, conserved region of Spt20 that is both necessary and sufficient to anchor Tra1 within SAGA. Finally, we establish that Hsp90 and its cochaperone TTT are required for Tra1 de novo incorporation into both SAGA and NuA4, indicating that Tra1, a pseudokinase of the PIKK family, shares a dedicated chaperone machinery with its cognate kinases. Overall, our work brings mechanistic insights into the de novo assembly of transcriptional complexes through ordered pathways and reveals the contribution of dedicated chaperones to this process.

2019-09-30 | GSE128448 | GEO

Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes

2019-10-02 | PXD013256 | Pride

The histone chaperone HIR establishes chromatin states controling nitrogen assimilation and virulence in Candida albicans

Project description:The histone chaperone HIR establishes chromatin states controling nitrogen assimilation and virulence in Candida albicans

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Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes

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The histone chaperone HIR establishes chromatin states controling nitrogen assimilation and virulence in Candida albicans [ATAC-seq]

Project description:The histone chaperone HIR establishes chromatin states controling nitrogen assimilation and virulence in Candida albicans [ATAC-seq]

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The histone chaperone HIR establishes chromatin states controling nitrogen assimilation and virulence in Candida albicans [RNA-seq]

Project description:The histone chaperone HIR establishes chromatin states controling nitrogen assimilation and virulence in Candida albicans [RNA-seq]

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SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes

Project description:Genome-wide binding of the histone chaperone Rtt106 was analysed by ChIP-seq. Rtt106 binding was analysed in WT and the mutant backgrounds lacking transcription factors Pdr1 and Pdr3, the HIR histone chaperone subunit Hir1, or the boundary protein Yta7. Two biological replicates had been submitted. mRNA profiles in WT and the mutants lacking Rtt106, Pdr1, Pdr3 or the SWI/SNF subunit Snf2 were analysed by RNA-seq. mRNA profiles in those yeast cells grown in rich media (YPD) and in the glucose-starved condition (YEP) and in response to ketoconazole (YEP+ket) were analysed. Three biological samples for each condition had been submitted.

2022-02-21 | E-MTAB-9787 | biostudies-arrayexpress

BS3 intermolecular crosslinking map of SAGA and SLIK (SAGA-like) transcription coactivators

Project description:The SAGA-like complex SLIK is a modified version of the Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex. SLIK is formed through C-terminal truncation of the Spt7 SAGA subunit, causing loss of Spt8 that interacts with the TATA-binding protein. SLIK and SAGA are both coactivators of RNA polymerase II transcription in yeast. In addition, both SAGA and SLIK perform chromatin modifications and the two complexes have been speculated to uniquely contribute to transcription regulation. To test the respective contribution of SAGA vs. SLIK in transcription regulation, we assayed the chromatin modifying functions of SAGA vs. SLIK, revealing identical kinetics on minimal substrates in vitro. Furthermore, we determined a low-resolution cryo-EM structure of SLIK, revealing a modular architecture identical to SAGA. Finally, we performed a comprehensive study of DNA-binding properties of both coactivators. Purified SAGA and SLIK both associate with ssDNA and dsDNA with high affinity (KD = 10-17 nM) and the binding is sequence-independent. In conclusion, our study shows that the cleavage of Spt7 and the absence of Spt8 subunit in SLIK neither drive any major conformational differences in its structure compared to SAGA, nor significantly affect HAT, DUB or DNA binding activities in vitro.

2021-04-19 | PXD024640 | Pride

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