Identification of Transcription Complexes that Contain the Double Bromodomain Protein Brd2 and Chromatin Remodeling Machines

Boston University, Boston, Massachusetts, United States
Journal of Proteome Research (Impact Factor: 4.25). 04/2006; 5(3):502-11. DOI: 10.1021/pr050430u
Source: PubMed


We use affinity purification of the double bromodomain protein Brd2 to isolate a multicomponent nuclear complex from cultured cells, and apply mass spectrometry/proteomics methods to identify the participants. We then confirm by immunoblot several transcription co-activators and co-repressors, proteins of the Swi/Snf chromatin remodeling complex, which regulate transcription control of cyclin A. This multiprotein complex is likely to contribute to cell cycle control and play a role in proliferation and cancer.

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    • "While these studies indicate a definite role of ''writers'' and ''erasers'' of histone modifications in regulating dendrite morphogenesis, the role of ''reader'' scaffolding proteins associated with histone acetylation has not been thoroughly investigated. Double-bromo and extraterminal (BET) domain-containing proteins bind acetylated histone tails (Umehara et al. 2010a,b) and modulate gene expression (Kanno et al. 2004; Sinha et al. 2005; Denis et al. 2006; Chang et al. 2007). In mice, mutations in one BET family member, BRD2, cause neural tube closure defects, behavioral abnormalities, and altered interneuron numbers (Gyuris et al. 2009; Shang et al. 2009; Vel ı sek et al. 2011). "
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    ABSTRACT: A complex array of genetic factors regulates neuronal dendrite morphology. Epigenetic regulation of gene expression represents a plausible mechanism to control pathways responsible for specific dendritic arbor shapes. By studying the Drosophila dendritic arborization (da) neurons, we discovered a role of the double-bromodomain and extraterminal (BET) family proteins in regulating dendrite arbor complexity. A loss-of-function mutation in the single Drosophila BET protein encoded by female sterile 1 homeotic [fs(1)h] causes loss of fine, terminal dendritic branches. Moreover, fs(1)h is necessary for the induction of branching caused by a previously identified transcription factor, Cut (Ct), which regulates subtype-specific dendrite morphology. Finally, disrupting fs(1)h function impairs the mechanosensory response of class III da sensory neurons without compromising the expression of the ion channel NompC, which mediates the mechanosensitive response. Thus, our results identify a novel role for BET family proteins in regulating dendrite morphology and a possible separation of developmental pathways specifying neural cell morphology and ion channel expression. Since the BET proteins are known to bind acetylated histone tails, these results also suggest a role of epigenetic histone modifications and the "histone code," in regulating dendrite morphology.
    Genes & development 09/2015; 28(17):1940-56. DOI:10.1101/gad.239962.114 · 10.80 Impact Factor
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    • "Further, the transcriptional repressors remodeling and spacing factor 1 (rsf1) and mbt domain containing 1 [39] were present in unfertilized and fertilized oocytes, respectively. A maternally supplied co-activator bromodomain containing 2 (brd2) [40, 41] can be important for the early embryo cell cycle control. Fertilized oocytes contained transcripts for a protein involved in DNA methylation (PWWP domain containing 2 isoform 1). "
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    ABSTRACT: Background Regulation of gene expression plays a central role in embryonic development. Early stages are controlled by gametic transcripts, which are subsequently substituted with transcripts from the genome of the zygote. Transcriptomic analyses provide an efficient approach to explore the temporal gene expression profiles in embryos and to search for the developmental regulators. We report a study of early Atlantic cod development that used a genome-wide oligonucleotide microarray to examine the composition and putative roles of polyadenylated transcripts. Results The analyses were carried out in unfertilized oocytes, newly fertilized oocytes and embryos at the stages of mid-blastula transition and segmentation. Numerous genes transcribed in oocytes are involved in multiple aspects of cell maintenance and protection, including metabolism, signal perception and transduction, RNA processing, cell cycle, defense against pathogens and DNA damage. Transcripts found in unfertilized oocytes also encoded a large number of proteins implicated in cell adherence, tight junction and focal adhesion, suggesting high complexity in terms of structure and cellular interactions in embryos prior to midblastula transition (MBT). Prezygotic transcripts included multiple regulators that are most likely involved in developmental processes that take place long after fertilization, such as components of ErbB, hedgehog, notch, retinoid, TGFb, VEGF and Wnt signaling pathways, as well as transcripts involved in the development of nervous system. The major event of MBT was the activation of a large group of histones and other genes that modify chromatin structure preceding massive gene expression changes. A hallmark of events observed during segmentation was the induction of multiple transcription factors, including a large group of homeobox proteins in pace with decay of a large fraction of maternal transcripts. Microarray analyses detected a suite of master developmental regulators that control differentiation and maintenance of diverse cell lineages. Conclusions Transcriptome profiling of the early stages in Atlantic cod revealed the presence of transcripts involved in patterning and development of tissues and organs long before activation of the zygotic genome. The switch from maternal to zygotic developmental programs is associated with large-scale modification of chromosomes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-594) contains supplementary material, which is available to authorized users.
    BMC Genomics 07/2014; 15(1):594. DOI:10.1186/1471-2164-15-594 · 3.99 Impact Factor
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    • "Using GSEA, we found that nearly all of these 53 genes were also suppressed following Brg1 knockdown (Supplemental Fig. 6B), suggesting that Brg1 and Brd4 regulate a highly overlapping set of genes in RN2 cells, which includes Myc. Prior proteomic studies found an association between SWI/SNF subunits and BET proteins (Denis et al. 2006; Dawson et al. 2011; Rahman et al. 2011), which we also have confirmed and found to be mediated by the ET domain of Brd4 (Supplemental Fig. 6C–E). However, using ChIP-qPCR, we found that Brg1 and Brd4 occupy chromatin independently of one another at all of the sites we examined (Supplemental Fig. 6F,G), suggesting that, despite their apparent physical association , Brg1 and Brd4 operate in parallel pathways to maintain a common gene regulatory network in this disease. "
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    ABSTRACT: Cancer cells frequently depend on chromatin regulatory activities to maintain a malignant phenotype. Here, we show that leukemia cells require the mammalian SWI/SNF chromatin remodeling complex for their survival and aberrant self-renewal potential. While Brg1, an ATPase subunit of SWI/SNF, is known to suppress tumor formation in several cell types, we found that leukemia cells instead rely on Brg1 to support their oncogenic transcriptional program, which includes Myc as one of its key targets. To account for this context-specific function, we identify a cluster of lineage-specific enhancers located 1.7 Mb downstream from Myc that are occupied by SWI/SNF as well as the BET protein Brd4. Brg1 is required at these distal elements to maintain transcription factor occupancy and for long-range chromatin looping interactions with the Myc promoter. Notably, these distal Myc enhancers coincide with a region that is focally amplified in ∼3% of acute myeloid leukemias. Together, these findings define a leukemia maintenance function for SWI/SNF that is linked to enhancer-mediated gene regulation, providing general insights into how cancer cells exploit transcriptional coactivators to maintain oncogenic gene expression programs.
    Genes & development 11/2013; 27(24). DOI:10.1101/gad.232710.113 · 10.80 Impact Factor
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