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Rolicka A, Guo Y, Gañez Zapater A, Tariq K, Quin J, Vintermist A, Sadeghifar F, Arsenian-Henriksson M, Östlund Farrants AK. The chromatin-remodeling complexes B-WICH and NuRD regulate ribosomal transcription in response to glucose. FASEB J 2020; 34:10818-10834. [PMID: 32598531 DOI: 10.1096/fj.202000411r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/26/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022]
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.
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Affiliation(s)
- Anna Rolicka
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Antoni Gañez Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Kanwal Tariq
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Jaclyn Quin
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Anna Vintermist
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Fatemeh Sadeghifar
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum B7, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
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Yu S, Jordán-Pla A, Gañez-Zapater A, Jain S, Rolicka A, Östlund Farrants AK, Visa N. SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing. Nucleic Acids Res 2019; 46:8557-8573. [PMID: 29860334 PMCID: PMC6144808 DOI: 10.1093/nar/gky438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/08/2018] [Indexed: 12/12/2022] Open
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.
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Affiliation(s)
- Simei Yu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Antoni Gañez-Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Shruti Jain
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Anna Rolicka
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
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Quin JE, Bujila I, Chérif M, Sanou GS, Qu Y, Vafa Homann M, Rolicka A, Sirima SB, O'Connell MA, Lennartsson A, Troye-Blomberg M, Nebie I, Östlund Farrants AK. Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria. eLife 2017; 6:29156. [PMID: 28923166 PMCID: PMC5629023 DOI: 10.7554/elife.29156] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022] Open
Abstract
The Fulani ethnic group has relatively better protection from Plasmodium falciparum malaria, as reflected by fewer symptomatic cases of malaria, lower infection rates, and lower parasite densities compared to sympatric ethnic groups. However, the basis for this lower susceptibility to malaria by the Fulani is unknown. The incidence of classic malaria resistance genes are lower in the Fulani than in other sympatric ethnic populations, and targeted SNP analyses of other candidate genes involved in the immune response to malaria have not been able to account for the observed difference in the Fulani susceptibility to P.falciparum. Therefore, we have performed a pilot study to examine global transcription and DNA methylation patterns in specific immune cell populations in the Fulani to elucidate the mechanisms that confer the lower susceptibility to P.falciparum malaria. When we compared uninfected and infected Fulani individuals, in contrast to uninfected and infected individuals from the sympatric ethnic group Mossi, we observed a key difference: a strong transcriptional response was only detected in the monocyte fraction of the Fulani, where over 1000 genes were significantly differentially expressed upon P.falciparum infection.
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Affiliation(s)
- Jaclyn E Quin
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana Bujila
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Mariama Chérif
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso.,Université Polytechnique de Bobo-Dioulasso, Bobo-Dioulasso, Burkina Faso
| | - Guillaume S Sanou
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Ying Qu
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Manijeh Vafa Homann
- Unit of Infectious Diseases, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Anna Rolicka
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | | | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Marita Troye-Blomberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Issa Nebie
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
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