Boundary Element-Associated Factor 32B Connects Chromatin Domains to the Nuclear Matrix

Pathak, Rashmi U.; Rangaraj, Nandini; Kallappagoudar, Satish; Mishra, Krishnaveni; Mishra, Rakesh

doi:10.1128/mcb.00305-07

Cited by 37 publications

(53 citation statements)

References 43 publications

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“…There are a variety of possible mechanisms that could be involved by which BEAF might affect promoter accessibility by positively or negatively influencing nucleosome modifications, structure, or positioning. Another interesting possibility is related to the report that nuclear matrix preparations retain 25% of BEAF (48). Both Su(Hw) and CTCF have also been reported to be retained in nuclear matrix preparations, leading to the proposal that they function in part by organizing chromatin into loop domains (10,17,66).…”

Section: Discussionmentioning

confidence: 98%

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Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

Jiang

Emberly

Cuvier

et al. 2009

Molecular and Cellular Biology

140

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Insulator elements play a role in gene regulation that is potentially linked to nuclear organization. Boundary element-associated factors (BEAFs) 32A and 32B associate with hundreds of sites on Drosophila polytene chromosomes. We hybridized DNA isolated by chromatin immunoprecipitation to genome tiling microarrays to construct a genome-wide map of BEAF binding locations. A distinct difference in the association of 32A and 32B with chromatin was noted. We identified 1,820 BEAF peaks and found that more than 85% were less than 300 bp from transcription start sites. Half are between head-to-head gene pairs. BEAF-associated genes are transcriptionally active as judged by the presence of RNA polymerase II, dimethylated histone H3 K4, and the alternative histone H3.3. Forty percent of these genes are also associated with the polymerase negative elongation factor NELF. Like NELF-associated genes, most BEAF-associated genes are highly expressed. Using quantitative reverse transcription-PCR, we found that the expression levels of most BEAF-associated genes decrease in embryos and cultured cells lacking BEAF. These results provide an unexpected link between BEAF and transcription, suggesting that BEAF plays a role in maintaining most associated promoter regions in an environment that facilitates high transcription levels.Insulator elements participate in gene regulation by limiting potential interactions between promoters and regulatory elements. In transgene assays, an insulator can block enhancer-promoter interactions, but only when located between the enhancer and the promoter (21, 35). Similarly, insulators can block repression mediated by Polycomb group proteins (41). They can also protect bracketed transgenes from chromosomal position effects (36, 52). Because of these properties, insulators are thought to participate in genome organization and gene regulation by defining the boundaries of discrete regulatory domains (9,38,61,63). The mode of action of insulators is unclear but might involve acting as promoter decoys (20) or the formation of chromatin loops through interactions between insulators and perhaps also other nuclear substructures that remain to be biochemically defined (7,10,17,67).The scs and scsЈ elements from the 87A hsp70 heat shock locus were two of the first DNA sequences shown to have insulator activity (35,36,60). Two boundary element-associated factors (BEAFs), 32A and 32B, were identified based on their interaction with the scsЈ insulator element (but not the scs element) (29, 69). 32A and 32B are derived from the same gene and differ only by about 80 amino acids located at their amino termini. These unique regions harbor different atypical C 2 H 2 zinc finger DNA binding domains, termed BED fingers (3). BEAF binding sites are essential for scsЈ insulator activity (16), as is functional BEAF protein (22, 53). BEAF immunolocalizes to hundreds of sites on polytene chromosomes (69). Several of these genomic binding sites have been shown to have insulator activity (16), indicating that BEAF-dependen...

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Section: Discussionmentioning

confidence: 98%

“…Perhaps binding would have been detected if we had used different sequences from the peak regions. Another possibility is that BEAF binds better in vivo, perhaps due to phosphorylation (29,48) or interactions with other, unknown, proteins. Identification of potential BEAF binding sites in BEAF binding regions.…”

mentioning

confidence: 99%

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

Jiang

Emberly

Cuvier

et al. 2009

Molecular and Cellular Biology

140

View full text Add to dashboard Cite

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“…44,45 Another TE, the Hat element, derived an insulated protein (BEAF-32 of Drosophila) that connects the specialized chromatin structure to the adjacent chromatin elements and the nuclear matrix. 46 Other degenerate TE sequences, such as miniature inverted-repeat transposable elements (MITEs), are often transcribed and contain terminal inverted repeats. These MITEs can produce handle RNA, which could theoretically be processed into siRNA.…”

Section: Discussionmentioning

confidence: 99%

Construction and Characterization of a Repetitive DNA Library in Parodontidae (Actinopterygii: Characiformes): A Genomic and Evolutionary Approach to the Degeneration of the W Sex Chromosome

et al. 2014

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Repetitive DNA sequences, including tandem and dispersed repeats, comprise a large portion of eukaryotic genomes and are important for gene regulation, sex chromosome differentiation, and karyotype evolution. In Parodontidae, only the repetitive DNAs WAp and pPh2004 and rDNAs were previously studied using fluorescence in situ hybridization. This study aimed to build a library of repetitive DNA in Parodontidae. We isolated 40 clones using C o t-1; 17 of these clones exhibited similarity to repetitive DNA sequences, including satellites, minisatellites, microsatellites, and class I and class II transposable elements (TEs), from Danio rerio and other organisms. The physical mapping of the clones to chromosomes revealed the presence of a satellite DNA, a Helitron element, and degenerate short interspersed element (SINE), long interspersed element (LINE), and tc1-mariner elements on the sex chromosomes. Some clones exhibited dispersed signals; other sequences were not detected. The 5S rDNA was detected on an autosomal pair. These elements likely function in the molecular degeneration of the W chromosome in Parodontidae. Thus, the location of these elements on the chromosomes is important for understanding the function of these repetitive DNAs and for integrative studies with genome sequencing. The presented data demonstrate that an intensive invasion of TEs occurred during W sex chromosome differentiation in the Parodontidae.

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“…1C) analysis. The nuclear versus NuMat proportion of RNA, DNA, and proteins is yet another relatively convenient parameter for reliable preparation (21). Retention of RNA (ϳ45%), a small fraction of DNA (ϳ0.92%), and proteins (ϳ10%) in the NuMat preparation from Drosophila cells/embryos is considered acceptable (21).…”

Section: Numat Preparation and Qualitymentioning

confidence: 99%

“…NuMat and its associated proteins are likely to be involved in the nuclear transport and may also play a vital role by providing a scaffold for the transport machinery. In addition, post-translational modifications appear to be important for NuMat proteins (21,22). The presence of protein kinases in the NuMat may be relevant in this context.…”

Section: Figmentioning

confidence: 99%

Nuclear Matrix Proteome Analysis of Drosophila melanogaster

Kallappagoudar

Varma

Pathak

et al. 2010

Molecular & Cellular Proteomics

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The nucleus is a highly structured organelle and contains many functional compartments. Although the structural basis for this complex spatial organization of compartments is unknown, a major component of this organization is likely to be the non-chromatin scaffolding called nuclear matrix (NuMat). Experimental evidence over the past decades indicates that most of the nuclear functions are at least transiently associated with the NuMat, although the components of NuMat itself are poorly known. Here, we report NuMat proteome analysis from Drosophila melanogaster embryos and discuss its links with nuclear architecture and functions. In the NuMat proteome, we found structural proteins, chaperones, DNA/RNAbinding proteins, chromatin remodeling and transcription factors. This complexity of NuMat proteome is an indicator of its structural and functional significance. The eukaryotic cell nucleus contains a number of structural features like heterochromatin, nucleolus, nuclear lamina, and nuclear territories and functional features like transcription foci, replication foci, Cajal bodies, stress-induced foci, etc.(1-7). Packaging of the genome on the other hand also results in non-random distribution of a variety of structural features like chromatin domains that help to regulate expression of genes (8). How these complex structural and functional domains are established and maintained is not known. It is likely that the non-chromatin scaffolding called nuclear matrix (9) plays an important role in this process. Nuclear matrix (NuMat) 1 mainly consists of the nuclear lamina, the nucleolar remnants, and an internal nuclear meshwork of fibers of unknown constitution that can be seen by electron microscopy (10). These fibers have ultrastructural features reminiscent of intermediate filaments of the cytosol (11). The protein component of nucleoplasmic filaments, however, is largely unknown. Earlier studies on a few proteins isolated from nuclear matrix from different organisms have shown them to be DNA-and RNA-binding and structural components of the nuclear pore complex (12), enzymes (13), and nuclear membrane proteins (14). This diversity among the small number of identified NuMat constituents reflects the link of nuclear architecture with the variety of nuclear functions. The importance of NuMat constituents in nuclear processes has been apparent for a long time, and several studies have been carried out to identify the proteins of this complex structure in different organisms (15-18). Major advancements in the field of proteomics now provide further scope for extensive analysis of NuMat in this context.Here, we present a comprehensive analysis of the NuMat proteome of Drosophila melanogaster. NuMat preparations from D. melanogaster embryos were separated by one-dimensional gel electrophoresis, and the proteins were identified by LC-MS/MS. We also report a remarkable variation in the NuMat proteome depending on developmental stages, indicating a link between embryonic development and nuclear architecture. Finally, immunos...

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Boundary Element-Associated Factor 32B Connects Chromatin Domains to the Nuclear Matrix

Cited by 37 publications

References 43 publications

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

Construction and Characterization of a Repetitive DNA Library in Parodontidae (Actinopterygii: Characiformes): A Genomic and Evolutionary Approach to the Degeneration of the W Sex Chromosome

Nuclear Matrix Proteome Analysis of Drosophila melanogaster

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