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Sumoylation regulates general transcription factors at promoters of highly transcribed genes

ABSTRACT: Sumoylation regulates general transcription factors at promoters of highly transcribed genes

PROVIDER: PRJNA704633 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13777456_1.fastq.gz	Fastqsanger.gz
	SRR13777456_2.fastq.gz	Fastqsanger.gz
	SRR13777457_1.fastq.gz	Fastqsanger.gz
	SRR13777457_2.fastq.gz	Fastqsanger.gz
	SRR13777458_1.fastq.gz	Fastqsanger.gz

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Sumoylation regulates general transcription factors at promoters of highly transcribed genes

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-09-21 | GSE167428 | GEO

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Effects of sumoylation-impairing mutation of TFIIF subunit Tfg1 on genome-wide RNA polymerase II (RNAPII) levels in budding yeast

Project description:Many transcription-related proteins, including components of the RNA polymerase II (RNAPII) general transcription factors (GTFs), have been shown through proteomics studies to be modifiable by SUMO conjugation. However, we determined that the large subunit of TFIIF, Tfg1, is likely the major target of sumoylation among GTFs in budding yeast. The primary site of sumoylation on Tfg1 is Lys residues 60 or 61, which lies in a region of the protein that is proximal to the Rpb2 subunit of RNAPII when the GTF-RNAPII preinitiation complex (PIC) assembles at promoters. As TFIIF and RNAPII are highly functionally and physically linked, we examined whether blocking Tfg1 sumoylation through Lys-to-Arg mutations could affect the recruitment or association of RNAPII with chromatin. RNAPII ChIP-seq was performed in strains expressing wild-type (Tfg1-HA) or sumoylation-deficient (Tfg1-K60,61R-HA) forms of Tfg1. Indeed, nearly half of all protein-coding genes showed significantly reduced RNAPII levels in the mutant strain. These data suggest that sumoylation of TFIIF plays an important role in regulating the dynamics of RNAPII association with genes.

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DNA G-quadruplexes modulate highly transcribed genes in human chromatin [ChIPseq]

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Role of Sko1 sumoylation in regulating target site binding

Project description:We examine how SUMO post-translational modification of the yeast transcription factor Sko1 affects its binding site selection and affinity. Chromatin immunoprecipitation followed by next-generation sequencing was performed in strains expressing wild-type Sko1 (Sko1-WT) or Sko1 that harbors an Arg-to-Lys mutation at Lys 567 (Sko1-MT), that impairs its sumoylation. We find that, compared with Sko1-WT, SUMO-deficient Sko1 binds numerous additional sites that are near promoters of non-Sko1 target genes. Furthermore, Sko1-MT shows higher occupancy levels than Sko1-WT on most genes that are occupied by both forms. Osmotic stress causes a general rearrangement of Sko1 positions across the genome, but increased numbers of binding sites and occupancy levels are still observed for Sko1-MT after treatment with NaCl. This study indicates that sumoylation attenuates Sko1 association with chromatin and increases its binding specificity.

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DNA G-quadruplexes modulate highly transcribed genes in human chromatin [ATAC-seq]

Project description:DNA G-quadruplexes modulate highly transcribed genes in human chromatin [ATAC-seq]

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DNA G-quadruplexes modulate highly transcribed genes in human chromatin [RNA-seq]

Project description:DNA G-quadruplexes modulate highly transcribed genes in human chromatin [RNA-seq]

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Transcriptome analysis in sumoylation deficient (ubc9-6) budding yeast and in a strain with a sumoylation-impairing mutation in the TFIIF subunit, Tfg1

Project description:Transcription related proteins are among the most frequently identified targets of SUMO post-translational modification, but the gene-specific and genome-wide effects of transcription machinery sumoylation are not well-understood. To explore this, we examined whether dramatically reducing cellular sumoylation levels affects the levels of mRNAs in budding yeast. RNA-seq was performed using polyadenylate (polyA)-enriched RNAs from the sumoylation-deficient ubc9-6 strain and its wild-type parent. Indeed, the abundance of hundreds of mRNAs were upregulated or downregulated in the mutant strain, implying that sumoylation has a widespread influence on RNA polymerase II (RNAPII) transcription or mRNA stability. Interestingly, about one third of mRNAs that were significantly upregulated in the ubc9-6 strain encode proteins that are involved in small molecule metabolic processes, suggesting that sumoylation is normally involved in restricting these pathways. As part of our analysis of transcription-related sumoylation, we determined that the large subunit of TFIIF, Tfg1, is a major target of sumoylation among the general transcription factors (GTFs) of RNAPII. To determine whether sumoylation of Tfg1 specifically is involved in regulating mRNA levels, we performed RNA-seq on polyA-enriched RNAs derived from strains expressing wild-type (Tfg1-HA) or sumoylation-deficient (Tfg1-K60,61R-HA) forms of Tfg1. However, with few exceptions, impairing Tfg1 sumoylation had no effect on the mRNA transcriptome. Together, our data demonstrate that gene expression is extensively regulated by sumoylation, but this likely involves the coordinated modification of multiple proteins at multiple levels.

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Condensin mediates the chromosomal clustering of highly transcribed genes in bacteria

Project description:Purpose: Study MukB, RNAP, TopA, and ParC binding profiles on E.coli chromosome. Methods: We constructed affinity tagged MukB, ParC, and TopA strains, and immunoprecipitated using anti-FLAG antibodies as well as an RNAP primary antibody. Results: MukB, RNAP, TopA, and ParC were all bound to rDNAs on the coding sequences, as well as the coding regions of 244 highly transcribed genes, including tRNAs, genes coding for ribosomal proteins, housekeeping genes (for example, atpA and rpoB), as well as OriC. Conclusions: We found that the bacterial condensin, MukB, is recruited to actively transcribed genes such as rDNA through transcription induced supercoiling.

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Panoramix SUMOylation at chromatin recruits the heterochromatin machinery to piRNA target loci [GRO-seq]

Project description:Nuclear Argonaute proteins, guided by small RNAs, mediate sequence-specific heterochromatin formation. The molecular principles that link Argonaute–small RNA complexes, once bound to a nascent target RNA, to general heterochromatin effectors are poorly understood. Here, we uncover the mechanistic basis of how the PIWI interacting RNA (piRNA) pathway engages the heterochromatin machinery in Drosophila. Piwi-mediated recruitment of the corepressor complex SFiNX to chromatin leads to SUMOylation of its Panoramix subunit. SUMOylation, together with a hydrophobic LxxLL motif in the intrinsically disordered repressor domain of Panoramix, are necessary and sufficient to recruit Small ovary (Sov), a multi-zinc finger protein essential for general heterochromatin formation and viability. Structure-guided mutations that abrogate the Panoramix-Sov interaction or that prevent Panoramix SUMOylation uncouple Sov from the piRNA pathway, resulting in viable but sterile flies that exhibit de-repression of Piwi-targeted transposons. Thus, coupling the piRNA-guided recruitment of a corepressor to chromatin with its SUMOylation underlies sequence-specific heterochromatin formation.

2021-08-22 | GSE173236 | GEO

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