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Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos
The Wenner-Gren Institute, Developmental Biology, Stockholm University, Stockholm.
The Wenner-Gren Institute, Developmental Biology, Stockholm University, Stockholm.
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). (Per Stenberg, Computational Life Science Cluster (CLiC))ORCID iD: 0000-0001-8752-0794
The Wenner-Gren Institute, Developmental Biology, Stockholm University, Stockholm.
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2012 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 8, no 6, e1002769- p.Article in journal (Refereed) Published
Abstract [en]

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-ß/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 dorso-ventral patterning and that CBP binds silent genes without causing histone hyperacetylation.

Place, publisher, year, edition, pages
San Francisco: Public Library of Science , 2012. Vol. 8, no 6, e1002769- p.
National Category
Genetics
Research subject
Genetics
Identifiers
URN: urn:nbn:se:umu:diva-56930DOI: 10.1371/journal.pgen.1002769ISI: 000305961000033PubMedID: 22737084OAI: oai:DiVA.org:umu-56930DiVA: diva2:538458
Available from: 2012-06-29 Created: 2012-06-29 Last updated: 2017-12-07Bibliographically approved
In thesis
1. Mining DNA elements involved in targeting of chromatin modifiers
Open this publication in new window or tab >>Mining DNA elements involved in targeting of chromatin modifiers
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Background: In all higher organisms, the nuclear DNA is condensed into nucleosomes that consist of DNA wrapped around a core of highly conserved histone proteins. DNA bound to histones and other structural proteins form the chromatin. Generally, only few regions of DNA are accessible and most of the time RNA polymerase and other DNA binding proteins have to overcome this compaction to initiate transcription. Several proteins are involved in making the chromatin more compact or open. Such chromatin-modifying proteins make distinct post-translational modifications of histones – especially in the histone tails – to alter their affinity to DNA. Aim: The main aim of my thesis work is to study the targeting of chromatin modifiers important for correct gene expression in Drosophila melanogaster (fruit flies). Primary DNA sequences, chromatin associated proteins, transcription, and non-coding RNAs are all likely to be involved in targeting mechanisms. This thesis work involves the development of new computational methods for identification of DNA motifs and protein factors involved in the targeting of chromatin modifiers. Targeting and functional analysis of two chromatin modifiers, namely male-specific lethal (MSL) complex and CREB-binding protein (CBP) are specifically studied. The MSL complex is a protein complex that mediates dosage compensation in flies. CBP protein is known as a transcriptional co-regulator in metazoans and it has histone acetyl transferase activity and CBP has been used to predict novel enhancers. Results: My studies of the binding sites of MSL complex shows that promoters and coding sequences of MSL-bound genes on the X-chromosome of Drosophila melanogaster can influence the spreading of the complex along the X-chromosome. Analysis of MSL binding sites when two non-coding roX RNAs are mutated shows that MSL-complex recruitment to high-affinity sites on the Xchromosome is independent of roX, and the role of roX RNAs is to prevent binding to repeats in autosomal sites. Functional analysis of MSL-bound genes using their dosage compensation status shows that the function of the MSL complex is to enhance the expression of short housekeeping genes, but MSL-independent mechanisms exist to achieve complete dosage compensation. Studies of the binding sites of the CBP protein show that, in early embryos, Dorsal in cooperation with GAGA factor (GAF) and factors like Medea and Dichaete target CBP to its binding sites. In the S2 cell line, GAF is identified as the targeting factor of CBP at promoters and enhancers, and GAF and CBP together are found to induce high levels of polymerase II pausing at promoters. In another study using integrated data analysis, CBP binding sites could be classified into polycomb protein binding sites, repressed enhancers, insulator protein-bound regions, active promoters, and active enhancers, and this suggested different potential roles for CBP. A new approach was also developed to eliminate technical bias in skewed experiments. Our study shows that in the case of skewed datasets it is always better to identify non-altered variables and to normalize the data using only such variables.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2014. 76 p.
Keyword
nucleosome, histone, chromatin, chromatin modifiers, targeting, DNA motifs, protein factors, MSL
National Category
Bioinformatics and Systems Biology Biochemistry and Molecular Biology Genetics
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-92979 (URN)978-91-7601-118-8 (ISBN)
Public defence
2014-10-03, E 04 Unod R1, Norrland University Hospital, Umeå, 09:00 (English)
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Supervisors
Available from: 2014-09-12 Created: 2014-09-09 Last updated: 2014-09-23Bibliographically approved

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