| 1. |
- Eberle, Andrea B., et al.
(författare)
-
An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster
- 2015
-
Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 11:9
-
Tidskriftsartikel (refereegranskat)abstract
- RNA surveillance factors are involved in heterochromatin regulation in yeast and plants, but less is known about the possible roles of ribonucleases in the heterochromatin of animal cells. Here we show that RRP6, one of the catalytic subunits of the exosome, is necessary for silencing heterochromatic repeats in the genome of Drosophila melanogaster. We show that a fraction of RRP6 is associated with heterochromatin, and the analysis of the RRP6 interaction network revealed physical links between RRP6 and the heterochromatin factors HP1a, SU(VAR)3-9 and RPD3. Moreover, genome-wide studies of RRP6 occupancy in cells depleted of SU(VAR)3-9 demonstrated that SU(VAR)3-9 contributes to the tethering of RRP6 to a subset of heterochromatic loci. Depletion of the exosome ribonucleases RRP6 and DIS3 stabilizes heterochromatic transcripts derived from transposons and repetitive sequences, and renders the heterochromatin less compact, as shown by micrococcal nuclease and proximity-ligation assays. Such depletion also increases the amount of HP1a bound to heterochromatic transcripts. Taken together, our results suggest that SU(VAR)3-9 targets RRP6 to a subset of heterochromatic loci where RRP6 degrades chromatin-associated non-coding RNAs in a process that is necessary to maintain the packaging of the heterochromatin.
|
|
| 2. |
- Gañez Zapater, Antoni, 1986-
(författare)
-
Gene regulation by chromatin remodelling complexes : SWI/SNF complex in mRNA processing and B-WICH complex in ribosomal gene expression
- 2018
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this project is to investigate the roles of chromatin remodelling complexes in gene regulation. It is focused on two groups of chromatin complexes: the mammalian BRG1 and BRM SWI/SNF complexes and the ISWI-containing B-WICH complex.Study 1 investigates the role of SWI/SNF complexes in alternative splicing. We show that the presence of the ATPase core subunits Brg1 and Brm influence the alternative splicing outcome of a subset of genes. We show that Brg1 and Brm interact with several splicing related factors in the nascent RNA, and that the recruitment of some of these factors to their target sites is regulated by the presence of Brg1 and Brm. We propose that SWI/SNF ATPases can modulate the interactions of RNA binding factors to the nascent RNA and in that way alter alternative splicing outcome.Study 2 focuses on SWI/SNF complexes and their influence on cleavage and polyadenylation of mRNA. We show that Brg1 and Brm interact with subunits of the cleavage and polyadenylation complexes in the nascent mRNA. SWI/SNF complexes facilitate the recruitment of the cleavage and polyadenylation complex to the polyadenylation site in a subset of genes, and this results in a more efficient cleavage and polyadenylation.Study 3 shows that B-WICH is required for ribosome gene transcriptional activation upon glucose stimulation. WSTF and SNF2h, two of the B-WICH subunits, are needed to establish an active chromatin state in the RNA pol I gene promoter when the glucose concentration is raised after a period of deprivation. We propose that it counteracts the silent, poised chromatin state imposed by the silencing chromatin remodelling complex NuRD to allow for the RNA pol I machinery to bind to the promoter.These studies show that the influence of chromatin remodelling complexes upon gene expression is important for remodelling nucleosomes at the promoter, for alternative splicing, cleavage and polyadenylation and transcriptional initiation. These complexes work together with other chromatin remodelling factors, interact with other complexes and regulate their activity by affecting their recruitment dynamics.
|
|
| 3. |
|
|
| 4. |
- Gañez-Zapater, Antoni, 1986-, et al.
(författare)
-
The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA
- 2022
-
Ingår i: Molecular Genetics and Genomics. - : Springer Science and Business Media LLC. - 1617-4615 .- 1617-4623. ; 297:2, s. 463-484
-
Tidskriftsartikel (refereegranskat)abstract
- BRG1 and BRM are ATPase core subunits of the human SWI/SNF chromatin remodelling complexes mainly associated with transcriptional initiation. They also have a role in alternative splicing, which has been shown for BRM-containing SWI/SNF complexes at a few genes. Here, we have identified a subset of genes which harbour alternative exons that are affected by SWI/SNF ATPases by expressing the ATPases BRG1 and BRM in C33A cells, a BRG1- and BRM-deficient cell line, and analysed the effect on splicing by RNA sequencing. BRG1- and BRM-affected sub-sets of genes favouring both exon inclusion and exon skipping, with only a minor overlap between the ATPase. Some of the changes in alternative splicing induced by BRG1 and BRM expression did not require the ATPase activity. The BRG1-ATPase independent included exons displayed an exon signature of a high GC content. By investigating three genes with exons affected by the BRG-ATPase-deficient variant, we show that these exons accumulated phosphorylated RNA pol II CTD, both serine 2 and serine 5 phosphorylation, without an enrichment of the RNA polymerase II. The ATPases were recruited to the alternative exons, together with both core and signature subunits of SWI/SNF complexes, and promoted the binding of RNA binding factors to chromatin and RNA at the alternative exons. The interaction with the nascent RNP, however, did not reflect the association to chromatin. The hnRNPL, hnRNPU and SAM68 proteins associated with chromatin in cells expressing BRG1 and BRM wild type, but the binding of hnRNPU to the nascent RNP was excluded. This suggests that SWI/SNF can regulate alternative splicing by interacting with splicing-RNA binding factor and influence their binding to the nascent pre-mRNA particle.
|
|
| 5. |
|
|
| 6. |
- Rolicka, Anna, et al.
(författare)
-
The chromatin‐remodeling complexes B‐WICH and NuRD regulate ribosomal transcription in response to glucose
- 2020
-
Ingår i: The FASEB Journal. - 0892-6638 .- 1530-6860. ; 34:8, s. 10818-10834
-
Tidskriftsartikel (refereegranskat)abstract
- Regulation of ribosomal transcription is under tight control from environmental stimuli, and this control involves changes in the chromatin structure. The underlying mechanism of how chromatin changes in response to nutrient and energy supply in the cell is still unclear. The chromatin‐remodeling complex B‐WICH is involved in activating the ribosomal transcription, and we show here that knock down of the B‐WICH component WSTF results in cells that do not respond to glucose. The promoter is less accessible, and RNA pol I and its transcription factors SL1/TIF‐1B and RRN3/TIF‐1A, as well as the proto‐oncogene c‐MYC and the activating deacetylase SIRT7 do not bind upon glucose stimulation. In contrast, the repressive chromatin state that forms after glucose deprivation is reversible, and RNA pol I factors are recruited. WSTF knock down results in an accumulation of the ATPase CHD4, a component of the NuRD chromatin remodeling complex, which is responsible for establishing a repressive poised state at the promoter. The TTF‐1, which binds and affect the binding of the chromatin complexes, is important to control the association of activating chromatin component UBF. We suggest that B‐WICH is required to allow for a shift to an active chromatin state upon environmental stimulation, by counteracting the repressive state induced by the NuRD complex.
|
|
| 7. |
|
|
| 8. |
- Yu, Simei, et al.
(författare)
-
SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing
- 2018
-
Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 46:16, s. 8557-8573
-
Tidskriftsartikel (refereegranskat)abstract
- SWI/SNF complexes associate with genes and regulate transcription by altering the chromatin at the promoter. It has recently been shown that these complexes play a role in pre-mRNA processing by associating at alternative splice sites. Here, we show that SWI/SNF complexes are involved also in pre-mRNA 3′ end maturation by facilitating 3′ end cleavage of specific pre-mRNAs. Comparative proteomics show that SWI/SNF ATPases interact physically with subunits of the cleavage and polyadenylation complexes in fly and human cells. In Drosophila melanogaster, the SWI/SNF ATPase Brahma (dBRM) interacts with the CPSF6 subunit of cleavage factor I. We have investigated the function of dBRM in 3′ end formation in S2 cells by RNA interference, single-gene analysis and RNA sequencing. Our data show that dBRM facilitates pre-mRNA cleavage in two different ways: by promoting the association of CPSF6 to the cleavage region and by stabilizing positioned nucleosomes downstream of the cleavage site. These findings show that SWI/SNF complexes play a role also in the cleavage of specific pre-mRNAs in animal cells.
|
|
