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https://www.readbyqxmd.com/read/28910574/o-glcnacylation-of-boundary-element-associated-factor-beaf-32-in-drosophila-melanogaster-correlates-with-active-histone-marks-at-the-promoters-of-its-target-genes
#1
Debaditya De, Satish Kallappagoudar, Jae-Min Lim, Rashmi U Pathak, Rakesh K Mishra
Boundary Element-Associated Factor 32 (BEAF 32) is a sequence specific DNA binding protein involved in functioning of chromatin domain boundaries in Drosophila. Several studies also show it to be involved in transcriptional regulation of a large number of genes, many of which are annotated to have cell cycle, development and differentiation related function. Since post-translational modifications (PTMs) of proteins add to their functional capacity, we investigated the PTMs on BEAF 32. The protein is known to be phosphorylated and O-GlcNAcylated...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28910569/hierarchical-recruitment-of-polycomb-complexes-revisited
#2
Eshagh Dorafshan, Tatyana G Kahn, Yuri B Schwartz
Polycomb Group (PcG) proteins epigenetically repress key developmental genes and thereby control alternative cell fates. PcG proteins act as complexes that can modify histones and these histone modifications play a role in transmitting the "memory" of the repressed state as cells divide. Here we consider mainstream models that link histone modifications to hierarchical recruitment of PcG complexes and compare them to results of a direct test of interdependence between PcG complexes for recruitment to Drosophila genes...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28910411/molecular-population-genetics-of-the-polycomb-genes-in-drosophila-subobscura
#3
Juan M Calvo-Martín, Montserrat Papaceit, Carmen Segarra
Polycomb group (PcG) proteins are important regulatory factors that modulate the chromatin state. They form protein complexes that repress gene expression by the introduction of posttranslational histone modifications. The study of PcG proteins divergence in Drosophila revealed signals of coevolution among them and an acceleration of the nonsynonymous evolutionary rate in the lineage ancestral to the obscura group species, mainly in subunits of the Pcl-PRC2 complex. Herein, we have studied the nucleotide polymorphism of PcG genes in a natural population of D...
2017: PloS One
https://www.readbyqxmd.com/read/28891464/concentration-dependent-chromatin-states-induced-by-the-bicoid-morphogen-gradient
#4
Colleen E Hannon, Shelby A Blythe, Eric F Wieschaus
In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context...
September 11, 2017: ELife
https://www.readbyqxmd.com/read/28887412/enzymatic-modules-of-the-saga-chromatin-modifying-complex-play-distinct-roles-in-drosophila-gene-expression-and-development
#5
Xuanying Li, Christopher W Seidel, Leanne T Szerszen, Jeffrey J Lange, Jerry L Workman, Susan M Abmayr
The Spt-Ada-Gcn5-acetyltransferase (SAGA) chromatin-modifying complex is a transcriptional coactivator that contains four different modules of subunits. The intact SAGA complex has been well characterized for its function in transcription regulation and development. However, little is known about the roles of individual modules within SAGA and whether they have any SAGA-independent functions. Here we demonstrate that the two enzymatic modules of Drosophila SAGA are differently required in oogenesis. Loss of the histone acetyltransferase (HAT) activity blocks oogenesis, while loss of the H2B deubiquitinase (DUB) activity does not...
September 8, 2017: Genes & Development
https://www.readbyqxmd.com/read/28878066/cytological-analysis-of-cytoplasmic-incompatibility-induced-by-cardinium-suggests-convergent-evolution-with-its-distant-cousin-wolbachia
#6
Marco Gebiola, Massimo Giorgini, Suzanne E Kelly, Matthew R Doremus, Patrick M Ferree, Martha S Hunter
Cytoplasmic incompatibility (CI) is a conditional sterility in numerous arthropods that is caused by inherited, intracellular bacteria such as Wolbachia Matings between males carrying CI-inducing Wolbachia and uninfected females, or between males and females infected with different Wolbachia strains, result in progeny that die during very early embryogenesis. Multiple studies in diploid (Drosophila) and haplodiploid (Nasonia) insects have shown that CI-Wolbachia cause a failure of the paternally derived chromatin from resolving into distinct chromosomes...
September 13, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28871058/the-hox-proteins-ubx-and-abda-collaborate-with-the-transcription-pausing-factor-m1bp-to-regulate-gene-transcription
#7
Amel Zouaz, Ankush Auradkar, Marie Claire Delfini, Meiggie Macchi, Marine Barthez, Serge Ela Akoa, Leila Bastianelli, Gengqiang Xie, Wu-Min Deng, Stuart S Levine, Yacine Graba, Andrew J Saurin
In metazoans, the pausing of RNA polymerase II at the promoter (paused Pol II) has emerged as a widespread and conserved mechanism in the regulation of gene transcription. While critical in recruiting Pol II to the promoter, the role transcription factors play in transitioning paused Pol II into productive Pol II is, however, little known. By studying how Drosophila Hox transcription factors control transcription, we uncovered a molecular mechanism that increases productive transcription. We found that the Hox proteins AbdA and Ubx target gene promoters previously bound by the transcription pausing factor M1BP, containing paused Pol II and enriched with promoter-proximal Polycomb Group (PcG) proteins, yet lacking the classical H3K27me3 PcG signature...
September 4, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28856379/vertebrate-gaf-thpok-emerging-functions-in-chromatin-architecture-and-transcriptional-regulation
#8
REVIEW
Avinash Srivastava, Amitha Sampath Kumar, Rakesh K Mishra
GAGA factor of Drosophila melanogaster (DmGAF) is a multifaceted transcription factor with diverse roles in chromatin regulation. Recently, ThPOK/c-Krox was identified as its vertebrate homologue (vGAF), which has a basic domain structure similar to DmGAF and is decorated with a number of post-translationally modified residues. In vertebrate genomes, vGAF associates with purine-rich GAGA sequences and performs diverse chromatin-mediated functions, viz., gene activation, repression and enhancer blocking. Expansion of regulatory chromatin proteins with the acquisition of PTMs appears to be the general trend that facilitated the evolution of complexity in vertebrates...
August 30, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28855971/the-effect-of-nipped-b-like-nipbl-haploinsufficiency-on-genome-wide-cohesin-binding-and-target-gene-expression-modeling-cornelia-de-lange-syndrome
#9
Daniel A Newkirk, Yen-Yun Chen, Richard Chien, Weihua Zeng, Jacob Biesinger, Ebony Flowers, Shimako Kawauchi, Rosaysela Santos, Anne L Calof, Arthur D Lander, Xiaohui Xie, Kyoko Yokomori
BACKGROUND: Cornelia de Lange syndrome (CdLS) is a multisystem developmental disorder frequently associated with heterozygous loss-of-function mutations of Nipped-B-like (NIPBL), the human homolog of Drosophila Nipped-B. NIPBL loads cohesin onto chromatin. Cohesin mediates sister chromatid cohesion important for mitosis but is also increasingly recognized as a regulator of gene expression. In CdLS patient cells and animal models, expression changes of multiple genes with little or no sister chromatid cohesion defect suggests that disruption of gene regulation underlies this disorder...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28844648/drosophila-paf1-modulates-piwi-pirna-silencing-capacity
#10
Josef P Clark, Reazur Rahman, Nachen Yang, Linda H Yang, Nelson C Lau
To test the directness of factors in initiating PIWI-directed gene silencing, we employed a Piwi-interacting RNA (piRNA)-targeted reporter assay in Drosophila ovary somatic sheet (OSS) cells [1]. This assay confirmed direct silencing roles for piRNA biogenesis factors and PIWI-associated factors [2-12] but suggested that chromatin-modifying proteins may act downstream of the initial silencing event. Our data also revealed that RNA-polymerase-II-associated proteins like PAF1 and RTF1 antagonize PIWI-directed silencing...
September 11, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28841365/taf10-and-taf10b-partially-redundant-roles-during-drosophila-melanogaster-morphogenesis
#11
Z Pahi, B N Borsos, B Vedelek, Y V Shidlovskii, S G Georgieva, I M Boros, T Pankotai
Transcription of eukaryotic genes requires the cooperative action of the RNA polymerase complex, the general transcription factors (TFIIB, TFIID, TFIIE, TFIIF and TFIIH) and chromatin modifiers. The TFIID complex contributes to transcriptional activation by several mechanisms and has a subunit with associated histone acetyltransferase (HAT) activity. The histone modifier SAGA complex has both HAT and deubiquitylase (DUB) activities. TFIID and SAGA share several TBP-associated factors (TAFs), but not their HAT subunit...
August 25, 2017: Transcription
https://www.readbyqxmd.com/read/28838946/histone-locus-regulation-by-the-drosophila-dosage-compensation-adaptor-protein-clamp
#12
Leila E Rieder, Kaitlin P Koreski, Kara A Boltz, Guray Kuzu, Jennifer A Urban, Sarah K Bowman, Anna Zeidman, William T Jordan, Michael Y Tolstorukov, William F Marzluff, Robert J Duronio, Erica N Larschan
The conserved histone locus body (HLB) assembles prior to zygotic gene activation early during development and concentrates factors into a nuclear domain of coordinated histone gene regulation. Although HLBs form specifically at replication-dependent histone loci, the cis and trans factors that target HLB components to histone genes remained unknown. Here we report that conserved GA repeat cis elements within the bidirectional histone3-histone4 promoter direct HLB formation in Drosophila In addition, the CLAMP (chromatin-linked adaptor for male-specific lethal [MSL] proteins) zinc finger protein binds these GA repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation...
August 24, 2017: Genes & Development
https://www.readbyqxmd.com/read/28826674/evolutionarily-conserved-principles-predict-3d-chromatin-organization
#13
M Jordan Rowley, Michael H Nichols, Xiaowen Lyu, Masami Ando-Kuri, I Sarahi M Rivera, Karen Hermetz, Ping Wang, Yijun Ruan, Victor G Corces
Topologically associating domains (TADs), CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP, we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C...
September 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28819201/linker-histone-h1-prevents-r-loop-accumulation-and-genome-instability-in-heterochromatin
#14
Aleix Bayona-Feliu, Anna Casas-Lamesa, Oscar Reina, Jordi Bernués, Fernando Azorín
Linker histone H1 is an important structural component of chromatin that stabilizes the nucleosome and compacts the nucleofilament into higher-order structures. The biology of histone H1 remains, however, poorly understood. Here we show that Drosophila histone H1 (dH1) prevents genome instability as indicated by the increased γH2Av (H2AvS137P) content and the high incidence of DNA breaks and sister-chromatid exchanges observed in dH1-depleted cells. Increased γH2Av occurs preferentially at heterochromatic elements, which are upregulated upon dH1 depletion, and is due to the abnormal accumulation of DNA:RNA hybrids (R-loops)...
August 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28815537/from-heterochromatin-to-long-noncoding-rnas-in-drosophila-expanding-the-arena-of-gene-function-and-regulation
#15
Subhash C Lakhotia
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28807902/h2av-facilitates-h3s10-phosphorylation-but-is-not-required-for-heat-shock-induced-chromatin-decondensation-or-transcriptional-elongation
#16
Yeran Li, Chao Wang, Weili Cai, Saheli Sengupta, Michael Zavortink, Huai Deng, Jack Girton, Jørgen Johansen, Kristen M Johansen
A model has been proposed where JIL-1 kinase-mediated H3S10 and H2Av phosphorylation is required for transcriptional elongation and heat shock-induced chromatin decondensation to occur. However, here we show that while H3S10 phosphorylation is indeed compromised in the H2Av null mutant we find that chromatin decondensation at heat shock loci is unaffected both in the absence of JIL-1 as well as of H2Av and that there is no discernable decrease in the elongating form of Pol II in either mutant. Furthermore, mRNA for the major heat shock protein Hsp70 is transcribed at robust levels in both H2Av and JIL-1 null mutants...
August 14, 2017: Development
https://www.readbyqxmd.com/read/28795356/drosophila-studies-on-autism-spectrum-disorders
#17
REVIEW
Yao Tian, Zi Chao Zhang, Junhai Han
In the past decade, numerous genes associated with autism spectrum disorders (ASDs) have been identified. These genes encode key regulators of synaptogenesis, synaptic function, and synaptic plasticity. Drosophila is a prominent model system for ASD studies to define novel genes linked to ASDs and decipher their molecular roles in synaptogenesis, synaptic function, synaptic plasticity, and neural circuit assembly and consolidation. Here, we review Drosophila studies on ASD genes that regulate synaptogenesis, synaptic function, and synaptic plasticity through modulating chromatin remodeling, transcription, protein synthesis and degradation, cytoskeleton dynamics, and synaptic scaffolding...
August 9, 2017: Neuroscience Bulletin
https://www.readbyqxmd.com/read/28794204/chromosome-topology-guides-the-drosophila-dosage-compensation-complex-for-target-gene-activation
#18
Tamás Schauer, Yad Ghavi-Helm, Tom Sexton, Christian Albig, Catherine Regnard, Giacomo Cavalli, Eileen Em Furlong, Peter B Becker
X chromosome dosage compensation in Drosophila requires chromosome-wide coordination of gene activation. The male-specific lethal dosage compensation complex (DCC) identifies and binds to X-chromosomal high-affinity sites (HAS) from which it boosts transcription. A sub-class of HAS, PionX sites, represent first contacts on the X. Here, we explored the chromosomal interactions of representative PionX sites by high-resolution 4C and determined the global chromosome conformation by Hi-C in sex-sorted embryos. Male and female X chromosomes display similar nuclear architecture, concordant with clustered, constitutively active genes...
August 9, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28771467/comprehensive-analysis-of-nucleocytoplasmic-dynamics-of-mrna-in-drosophila-cells
#19
Tao Chen, Bas van Steensel
Eukaryotic mRNAs undergo a cycle of transcription, nuclear export, and degradation. A major challenge is to obtain a global, quantitative view of these processes. Here we measured the genome-wide nucleocytoplasmic dynamics of mRNA in Drosophila cells by metabolic labeling in combination with cellular fractionation. By mathematical modeling of these data we determined rates of transcription, export and cytoplasmic decay for 5420 genes. We characterized these kinetic rates and investigated links with mRNA features, RNA-binding proteins (RBPs) and chromatin states...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28765367/polycomb-mediated-chromatin-loops-revealed-by-a-subkilobase-resolution-chromatin-interaction-map
#20
Kyle P Eagen, Erez Lieberman Aiden, Roger D Kornberg
The locations of chromatin loops in Drosophila were determined by Hi-C (chemical cross-linking, restriction digestion, ligation, and high-throughput DNA sequencing). Whereas most loop boundaries or "anchors" are associated with CTCF protein in mammals, loop anchors in Drosophila were found most often in association with the polycomb group (PcG) protein Polycomb (Pc), a subunit of polycomb repressive complex 1 (PRC1). Loops were frequently located within domains of PcG-repressed chromatin. Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
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