Brr6 Plays a Role in Gene Recruitment and Transcriptional Regulation at the Nuclear envelope
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA453911 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7072980.fastq.gz | Fastqsanger.gz | |||
| SRR7072981.fastq.gz | Fastqsanger.gz | |||
| SRR7072972.fastq.gz | Fastqsanger.gz | |||
| SRR7072982.fastq.gz | Fastqsanger.gz | |||
| SRR7072973.fastq.gz | Fastqsanger.gz |
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Project description:Correlation between transcriptional regulation and positioning of genes at the nuclear envelope is well established in eukaryotes but the mechanisms involved are not well understood. We provide evidence that Brr6 interacts with chromatin, helping to maintain normal chromatin architecture and transcriptional regulation of certain loci at the nuclear envelope. Specifically, our results showed that brr6-1 impairs PAB1 transcript levels and disrupts PAB1 and GAL1-10 locus positioning. In addition, RNAseq analysis revealed misregulation of both coding and non-coding transcription across the FUR4-GAL1,10,7 region as well as changes at numerous other genes. The discovery that brr6-1 is disomic for CHIII raised the possibility that some of these effects stemmed from increased copy number of CHIII genes. However, disomy was not present in wild type cells where the NLS-Brr6N fragment was expressed, therefore we were able to use the Brr6N fragment to link many of the brr6-1 effects at the PAB1 and FUR4-GAL1,10,7 loci to Brr6 function, including: 1) decreased PAB1 expression, 2) defective PAB1 locus positioning, and 3) misregulation across the FUR4-GAL1-10 region. Together with our ChIPseq results showing zinc finger-dependent association of the Brr6N fragment with the FUR4 gene, these results strongly argue for a role for Brr6 in gene recruitment and regulation at the nuclear envelope.
2018-09-01 | GSE113746 | GEO
Project description:Correlation between transcriptional regulation and positioning of genes at the nuclear envelope is well established in eukaryotes, but the mechanisms involved are not well understood. We show that brr6-1, a mutant of the essential yeast envelope transmembrane protein Brr6p, impairs normal positioning and expression of the PAB1 and FUR4- GAL1,10,7 loci. Similarly, expression of a dominant negative nucleoplasmic Brr6 fragment in wild-type cells reproduced many of the brr6-1 effects. Histone chromatin immunoprecipitation (ChIP) experiments showed decreased acetylation at the key histone H4K16 residue in the FUR4-GAL1,10,7 region in brr6-1. Importantly, blocking deacetylation significantly suppressed selected brr6-1 phenotypes. ChIPseq with FLAG-tagged Brr6 fragments showed enrichment at FUR4 and several other genes that showed striking changes in brr6-1 RNAseq data. These associations depended on a Brr6 putative zinc finger domain. Importantly, artificially tethering the GAL1 locus to the envelope suppressed the brr6-1 effects on GAL1 and FUR4 expression and increased H4K16 acetylation between GAL1 and FUR4 in the mutant. Together these results argue that Brr6 interacts with chromatin, helping to maintain normal chromatin architecture and transcriptional regulation of certain loci at the nuclear envelope.
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Project description:Transcriptionally silent chromatin often localizes at the nuclear periphery, but whether post-transcriptional gene repression also occurs at the nuclear envelope (NE) remains unknown. Here we demonstrate that the NE protein Lem2 cooperates with the nuclear exosome in RNA degradation. Loss of Lem2 causes the accumulation of non-coding RNAs and meiotic transcripts. We demonstrate that an engineered exosome RNA substrate preferentially localizes at the nuclear periphery dependent on Lem2. While Lem2 itself does not bind RNA, it physically interacts with the exosome-targeting MTREC complex and promotes the recruitment of RNAs. This Lem2-dependent pathway acts separately from nuclear bodies into which exosome factors assemble, revealing the existence of multiple degradation pathways. We propose that Lem2 recruits exosome co-factors to the nuclear periphery to coordinate RNA surveillance and fine-tunes the transcriptional program during the switch from mitotic to meiotic growth.
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Project description:Lamins and transmembrane proteins within the nuclear envelope regulate nuclear structure and chromatin organization. Nuclear Envelope Transmembrane Protein 39 (Net39) is muscle nuclear envelope protein whose functions in vivo have not been explored. We show that mice lacking Net39 succumb to severe myopathy and juvenile lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression and metabolism. These abnormalities resemble those of Emery-Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type Lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings highlight the role of Net39 at the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and its potential contribution to the molecular etiology of EDMD.
2020-11-23 | GSE154850 | GEO
Project description:Lamins and transmembrane proteins within the nuclear envelope are regulators of nuclear structure and chromatin organization. Nuclear Envelope Transmembrane Protein 39 (Net39) is a muscle-restricted nuclear envelope protein. We show that mice lacking Net39 succumb to severe myopathy and neonatal lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression and metabolism. These abnormalities resemble those of Emery-Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type Lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings reveal an intimate role for the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and highlight the importance of Net39 in these processes and in the molecular etiology of EDMD.
2020-11-24 | GSE154848 | GEO
Project description:Lamins and transmembrane proteins within the nuclear envelope are regulators of nuclear structure and chromatin organization. Nuclear Envelope Transmembrane Protein 39 (Net39) is a muscle-restricted nuclear envelope protein. We show that mice lacking Net39 succumb to severe myopathy and neonatal lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression and metabolism. These abnormalities resemble those of Emery-Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type Lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings reveal an intimate role for the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and highlight the importance of Net39 in these processes and in the molecular etiology of EDMD.
2020-11-24 | GSE154847 | GEO
Project description:Lamins and transmembrane proteins within the nuclear envelope are regulators of nuclear structure and chromatin organization. Nuclear Envelope Transmembrane Protein 39 (Net39) is a muscle-restricted nuclear envelope protein. We show that mice lacking Net39 succumb to severe myopathy and neonatal lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression and metabolism. These abnormalities resemble those of Emery-Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type Lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings reveal an intimate role for the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and highlight the importance of Net39 in these processes and in the molecular etiology of EDMD.
2020-11-24 | GSE154849 | GEO
Project description:Guanylate Binding Proteins (GBPs) are prominent regulators of immunity unknown to be required for nuclear envelope formation and function. The Arabidopsis GBP orthologue AtGBPL3 was identified as a novel component of the plant lamina, with essential functions in mitotic nuclear envelope reformation. AtGBPL3 is preferentially expressed in mitotically active root tips, accumulates at the nuclear envelope and interacts with further components of the nuclear lamina. To investigate effects of defective lamina components on gene expression, we analysed the transcriptomes of 4 day old wild-type, gbpl3-5, crwn4-1, crwn1-1crwn4-1, as well as gbpl3-5 mutants expressing GBPL3-GFP or the GTPase-dead GBPL3(K83A)-GFP under control of the AtGBPL3-promoter.
2022-12-23 | GSE221661 | GEO
Project description:Guanylate Binding Proteins (GBPs) are prominent regulators of immunity unknown to be required for nuclear envelope formation and function. The Arabidopsis GBP orthologue AtGBPL3 was identified as a novel component of the plant lamina, with essential functions in mitotic nuclear envelope reformation. AtGBPL3 is preferentially expressed in mitotically active root tips and accumulates at the nuclear envelope. Furthermore, fluorescent lifetime imaging experiments in the presence or absence of the chromatin-labelling dye Sytox-Orange suggested that GBPL3 might be able to interact with chromatin. Chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) revealed only few GBPL3-associated chromatin domains, which were concentrated particularly within or near centromeric regions.
2022-12-23 | GSE221668 | GEO
Project description:RNA surveillance and the periphery: a novel role for nuclear envelope protein Lem2
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