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| 2. |
- Boija, Ann, et al.
(författare)
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CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II
- 2017
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Ingår i: Molecular Cell. - : Elsevier BV. - 1097-2765 .- 1097-4164. ; 68:3, s. 491-503.e5
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Tidskriftsartikel (refereegranskat)abstract
- Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide. Promoters strongly occupied by CBP and GAGA factor have high levels of paused Pol II, a unique chromatin signature, and are highly expressed regardless of cell type. Interestingly, CBP activity is rate limiting for Pol II recruitment to these highly paused promoters through an interaction with TFIIB but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes.
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| 3. |
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| 4. |
- Holmqvist, Per-Henrik, et al.
(författare)
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Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos
- 2012
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Ingår i: PLOS Genetics. - San Francisco : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 8:6
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Tidskriftsartikel (refereegranskat)abstract
- CBP and the related p300 protein are widely used transcriptional co-activators in metazoans that interact with multiple transcription factors. Whether CBP/p300 occupies the genome equally with all factors or preferentially binds together with some factors is not known. We therefore compared Drosophila melanogaster CBP (nejire) ChIP-seq peaks with regions bound by 40 different transcription factors in early embryos, and we found high co-occupancy with the Rel-family protein Dorsal. Dorsal is required for CBP occupancy in the embryo, but only at regions where few other factors are present. CBP peaks in mutant embryos lacking nuclear Dorsal are best correlated with TGF-beta/Dpp-signaling and Smad-protein binding. Differences in CBP occupancy in mutant embryos reflect gene expression changes genome-wide, but CBP also occupies some non-expressed genes. The presence of CBP at silent genes does not result in histone acetylation. We find that Polycomb-repressed H3K27me3 chromatin does not preclude CBP binding, but restricts histone acetylation at CBP-bound genomic sites. We conclude that CBP occupancy in Drosophila embryos preferentially overlaps factors controlling dorsoventral patterning and that CBP binds silent genes without causing histone hyperacetylation.
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| 5. |
- Yeung, Kelvin, et al.
(författare)
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Atrophin controls developmental signaling pathways via interactions with Trithorax-like
- 2017
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Ingår i: eLIFE. - 2050-084X. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atros critical role in development and disease, relatively little is known about Atros binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. ChIP-seq identified 1300 potential direct targets of Atro including engrailed, and components of the Dpp and Notch signaling pathways. We show that Atro regulates Dpp and Notch signaling in larval imaginal discs, at least partially via regulation of thickveins and fringe. In addition, bioinformatics analyses, sequential ChIP and coimmunoprecipitation experiments reveal that Atro interacts with the Drosophila GAGA Factor, Trithorax-like (Trl), and they bind to the same loci simultaneously. Phenotypic analyses of Trl and Atro clones suggest that Atro is required to modulate the transcription activation by Trl in larval imaginal discs. Taken together, these data indicate that Atro is a major Trl cofactor that functions to moderate developmental gene transcription.
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| 6. |
- Crona, Filip, 1977-, et al.
(författare)
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Brakeless can directly activate and repress trancription in early Drosophila embryos
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The Brakeless protein performs many important functions during development in Drosophila, but how it controls gene expression is not understood. We previously showed that Brakeless can function as a transcriptional co-repressor. In this work, we perform transcriptional profiling of brakeless mutant embryos. Unexpectedly, the majority of target genes are down-regulated in brakeless mutants. We demonstrate that genomic regions in close proximity to some of the affected genes are occupied by Brakeless, that over-expression of Brakeless causes a reciprocal effect on expression of these genes, and that the activator function of Brakeless is intact when an activation domain is fused to Brakeless. By contrast, Brakeless repressor function is neutralized by the activation domain. Together, this shows that Brakeless can both repress and activate gene expression. To identify protein interactions that result in gene repression or activation, a yeast two-hybrid screen was performed. We find that the Mediator complex subunit Med19 interacts with an evolutionarily conserved part of Brakeless. Interestingly, down-regulated but not up-regulated Brakeless target genes are also affected in Med19-depleted embryos. Our data provide support for a Brakeless activator function that regulates transcription by interacting with Med19.
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| 7. |
- Crona, Filip, et al.
(författare)
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The Brakeless co-regulator can directly activate and repress transcription in early Drosophila embryos
- 2015
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Ingår i: Developmental Biology. - : Elsevier BV. - 0012-1606 .- 1095-564X. ; 407:1, s. 173-181
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Tidskriftsartikel (refereegranskat)abstract
- The Brakeless protein performs many important functions during Drosophila development, but how it controls gene expression is poorly understood. We previously showed that Brakeless can function as a transcriptional co-repressor. In this work, we perform transcriptional profiling of brakeless mutant embryos. Unexpectedly, the majority of affected genes are down-regulated in brakeless mutants. We demonstrate that genomic regions in close proximity to some of these genes are occupied by Brakeless, that over-expression of Brakeless causes a reciprocal effect on expression of these genes, and that Brakeless remains an activator of the genes upon fusion to an activation domain. Together, our results show that Brakeless can both repress and activate gene expression. A yeast two-hybrid screen identified the Mediator complex subunit Med19 as interacting with an evolutionarily conserved part of Brakeless. Both down- and up-regulated Brakeless target genes are also affected in Med19-depleted embryos, but only down-regulated targets are influenced in embryos depleted of both Brakeless and Med19. Our data provide support for a Brakeless activator function that regulates transcription by interacting with Med19. We conclude that the transcriptional co-regulator Brakeless can either activate or repress transcription depending on context.
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| 8. |
- Dahlberg, Olle, et al.
(författare)
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P-TEFb, the Super Elongation Complex and Mediator Regulate a Subset of Non-paused Genes during Early Drosophila Embryo Development
- 2015
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Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- Positive Transcription Elongation Factor b (P-TEFb) is a kinase consisting of Cdk9 and Cyclin T that releases RNA Polymerase II (Pol II) into active elongation. It can assemble into a larger Super Elongation Complex (SEC) consisting of additional elongation factors. Here, we use a miRNA-based approach to knock down the maternal contribution of P-TEFb and SEC components in early Drosophila embryos. P-TEFb or SEC depletion results in loss of cells from the embryo posterior and in cellularization defects. Interestingly, the expression of many patterning genes containing promoter-proximal paused Pol II is relatively normal in P-TEFb embryos. Instead, P-TEFb and SEC are required for expression of some non-paused, rapidly transcribed genes in pre-cellular embryos, including the cellularization gene Serendipity-a. We also demonstrate that another P-TEFb regulated gene, terminus, has an essential function in embryo development. Similar morphological and gene expression phenotypes were observed upon knock down of Mediator subunits, providing in vivo evidence that P-TEFb, the SEC and Mediator collaborate in transcription control. Surprisingly, P-TEFb depletion does not affect the ratio of Pol II at the promoter versus the 3' end, despite affecting global Pol II Ser2 phosphorylation levels. Instead, Pol II occupancy is reduced at P-TEFb down-regulated genes. We conclude that a subset of non-paused, pre-cellular genes are among the most susceptible to reduced P-TEFb, SEC and Mediator levels in Drosophila embryos.
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| 9. |
- Holmqvist, Per-Henrik, et al.
(författare)
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Genomic occupancy of the transcriptional co-activators p300 and CBP.
- 2012
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Ingår i: Transcription. - : Informa UK Limited. - 2154-1272 .- 2154-1264. ; 4:1, s. 18-23
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Tidskriftsartikel (refereegranskat)abstract
- The p300 and CBP co-activators are histone acetylases and central regulators of transcription in metazoans. The genomic occupancy of p300/CBP detected by ChIP-seq experiments can be used to identify transcriptional enhancers. However, studies in Drosophila embryos suggest that there is a preference for some transcription factors in directing p300/CBP to the genome. Although p300/CBP occupancy in general correlates with gene activation, they can also be found at silent genomic regions, which does not result in histone acetylation. Polycomb-mediated H3K27me3 is associated with repression, but does not preclude p300/CBP binding. An antagonism between H3K27ac and H3K27me3 indicates that p300/CBP may be involved in switching between repressed and active chromatin states.
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| 10. |
- Holmqvist, Per-Henrik
(författare)
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Transcription factor effects on chromatin organisation and gene regulation
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The intranuclear DNA of all eukaryotic cells is packed into chromatin, generating a repressive environment for the genome. Remodelling of the local chromatin structure is a vital process that allows access to the obscured DNA sequence and may induce the expression of specific genes. To be able to find the appropriate gene in the vast amount of DNA the cell relies on sequence specific transcription factors, which then trigger gene induction. Correct control of gene expression is of fundamental importance for cell function. In this thesis the effect of transcription factor DNA binding on chromatin organisation and transcription was examined in vivo. The MMTV LTR (mouse mammary tumour virus long terminal repeat) was used as a model promoter, and oocytes from Xenopus laevis as cellular system. The ubiquitous transcription factors NF1 (Nuclear Factor 1) and Oct1 (octamer binding factor 1) were found to cooperate in binding and enhanced basal transcription at the non-hormone induced MMTV LTR, which thus is accessible to these factors. Oct1, but not NF1, was found to increase both the basal and the hormone induced transcription. Together NF1 and Oct1 greatly enhanced the MMTV transcription in a synergistic manner. The basis for this cooperativity was an NF1 and Oct1 presetting of the MMTV LTR specific nucleosomal array. This preset state was functionally relevant, as it enabled a more rapid and stronger hormone response. This indicates a fundamental role of the ubiquitous factors NF1 and Oct1 in setting up a chromatin structure poised for transcription. Cooperative binding of GR (glucocorticoid receptor), NF1 and Oct1 upon hormone activation was also revealed. This was explained by a common binding platform at the enhanceosome. A direct effect of NF1 binding on enhanceosome stability was detected. Novel transcription factor sites for FoxA (Forkhead box A) was found in the MMTV LTR. An upstream FoxA site was found to inhibit hormone dependent MMTV transcription. This was likely due to a structural/sterical effect mediated through FoxA1 DNA bending. In the promoter proximal area, a double FoxA site was found to activate basal transcription through FoxA1 activation domains. Binding of FoxA1 occurred independently at each site, and in the absence of hormone activated GR. At the chromatin level, FoxA1 binding resulted in a perturbed chromatin organisation, containing an accessible C-nucleosome. Thus, FoxA1 was able to bind the chromatinised MMTV LTR and create an open structure, i.e. act as a pioneer transcription factor. In addition, the FoxA1 activation domains stabilised an altered organisation of the MMTV enhanceosome. Co-expression of NF1, Oct1 and GR with FoxA1 resulted in a displacement of FoxA1 from the upstream inhibitory site. In concordance the FoxA1 mediated transcriptional inhibition on the hormone activated MMTV LTR was nullified. This could possibly be explained by secondary effects stemming from NF1 and Oct1 influence on the MMTV LTR nucleosomal array. NF1 and Oct1 increased stability for the active MMTV nucleosomal array might be incompatible with FoxA1 binding at the upstream site. Similarly, in a recent report FoxA1 was found to be displaced from several promoters upon ER (estrogen receptor) induction in MCF7 cells. Together this indicates an important role of FoxA1 in nuclear receptor induced transcription. We have been able to study both the cooperative and competitive nature of interactions within an enhanceosome. The differences revealed here emphasise the importance of context effects on transcription factors.
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