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https://www.readbyqxmd.com/read/28199849/quantitative-flim-fret-microscopy-to-monitor-nanoscale-chromatin-compaction-in%C3%A2-vivo-reveals-structural-roles-of-condensin-complexes
#1
David Llères, Aymeric P Bailly, Aurélien Perrin, David G Norman, Dimitris P Xirodimas, Robert Feil
How metazoan genomes are structured at the nanoscale in living cells and tissues remains unknown. Here, we adapted a quantitative FRET (Förster resonance energy transfer)-based fluorescence lifetime imaging microscopy (FLIM) approach to assay nanoscale chromatin compaction in living organisms. Caenorhabditis elegans was chosen as a model system. By measuring FRET between histone-tagged fluorescent proteins, we visualized distinct chromosomal regions and quantified the different levels of nanoscale compaction in meiotic cells...
February 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28180290/kdm2a-integrates-dna-and-histone-modification-signals-through-a-cxxc-phd-module-and-direct-interaction-with-hp1
#2
Julie Borgel, Marek Tyl, Karin Schiller, Zsofia Pusztai, Christopher M Dooley, Wen Deng, Carol Wooding, Richard J White, Tobias Warnecke, Heinrich Leonhardt, Elisabeth M Busch-Nentwich, Till Bartke
No abstract text is available yet for this article.
February 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28177254/experimental-and-numerical-investigations-of-silver-nanoparticle-transport-under-variable-flow-and-ionic-strength-in-soil
#3
Joanna Makselon, Dan Zhou, Irina Engelhardt, Diederik Jacques, Erwin Klumpp
Unsaturated column experiments were conducted with an undisturbed loamy sand soil to investigate the influence of flow interruption (FI) and ionic strength (IS) on the transport and retention of surfactant-stabilized silver nanoparticles (AgNP) and the results were compared to those obtained under continuous flow conditions. AgNP concentrations for breakthrough curves (BTCs) and retention profiles (RPs) were analyzed by ICP-MS. Experimental results were simulated by the numerical code HP1 (Hydrus-PhreeqC) with the DLVO theory, extended colloid filtration theory and colloid release model...
February 8, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28167679/independent-mechanisms-recruit-the-cohesin-loader-protein-nipbl-to-sites-of-dna-damage
#4
Christopher Bot, Annika Pfeiffer, Fosco Giordano, Dharani Manjeera Edara, Nico P Dantuma, Lena Ström
NIPBL is required to load the cohesin complex on to DNA. While the canonical role of cohesin is to couple replicated sister chromatids together until the onset of mitosis, it also promotes tolerance to DNA damage. Here we show that NIPBL is recruited to DNA damage throughout the cell cycle via independent mechanisms, influenced by type of damage. Firstly, the heterochromatin protein HP1γ recruits NIPBL to DSBs through the corresponding HP1-binding motif within the N-terminus. In contrast, the C-terminal HEAT repeat domain is unable to recruit NIPBL to DSBs but independently targets NIPBL to laser microirradiation induced DNA damage...
February 6, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28078437/senescence-in-the-lesional-fibroblasts-of-non-segmental-vitiligo-patients
#5
Seema Rani, Supriya Bhardwaj, Niharika Srivastava, Vijay Lakshmi Sharma, Davinder Parsad, Ravinder Kumar
Dermal fibroblasts secrete various growth factors which are important for skin pigmentation. Imbalance in the synchronization of epidermal and dermal cells in the skin can play vital role in the pathogenesis of pigmentary disorder vitiligo. Therefore, our objective was to check the lesional fibroblasts for any abnormality and senescence in non-segmental vitiligo patients (NSV). Skin punch biopsies were taken from NSV patients and healthy controls. Explant culture of fibroblast from lesional dermis, non-lesional dermis, and control was analyzed...
January 11, 2017: Archives of Dermatological Research
https://www.readbyqxmd.com/read/28059589/an-hp1-isoform-specific-feedback-mechanism-regulates-suv39h1-activity-under-stress-conditions
#6
Helena Raurell-Vila, Laia Bosch-Presegue, Jessica Gonzalez, Noriko Kane-Goldsmith, Carmen Casal, Jeremy P Brown, Anna Marazuela-Duque, Prim B Singh, Lourdes Serrano, Alejandro Vaquero
The presence of H3K9me3 and heterochromatin protein 1 (HP1) are hallmarks of heterochromatin conserved in eukaryotes. The spreading and maintenance of H3K9me3 is effected by the functional interplay between the H3K9me3-specific histone methyltransferase Suv39h1 and HP1. This interplay is complex in mammals because the three HP1 isoforms, HP1α, β, and γ, are thought to play a redundant role in Suv39h1-dependent deposition of H3K9me3 in pericentric heterochromatin (PCH). Here, we demonstrate that despite this redundancy, HP1α and, to a lesser extent, HP1γ have a closer functional link to Suv39h1, compared to HP1β...
January 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27939293/telomeric-retrotransposon-het-a-contains-a-bidirectional-promoter-that-initiates-divergent-transcription-of-pirna-precursors-in-drosophila-germline
#7
Elizaveta Radion, Sergei Ryazansky, Natalia Akulenko, Yakov Rozovsky, Dmitry Kwon, Valeriya Morgunova, Ivan Olovnikov, Alla Kalmykova
PIWI-interacting RNAs (piRNAs) provide the silencing of transposable elements in the germline. Drosophila telomeres are maintained by transpositions of specialized telomeric retroelements. piRNAs generated from sense and antisense transcripts of telomeric elements provide telomere length control in the germline. Previously, we have found that antisense transcription of the major telomeric retroelement HeT-A is initiated upstream of the HeT-A sense transcription start site. Here, we performed a deletion analysis of the HeT-A promoter and show that common regulatory elements are shared by sense and antisense promoters of HeT-A...
December 7, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27924040/kdm2a-integrates-dna-and-histone-modification-signals-through-a-cxxc-phd-module-and-direct-interaction-with-hp1
#8
Julie Borgel, Marek Tyl, Karin Schiller, Zsofia Pusztai, Christopher M Dooley, Wen Deng, Carol Wooding, Richard J White, Tobias Warnecke, Heinrich Leonhardt, Elisabeth M Busch-Nentwich, Till Bartke
Functional genomic elements are marked by characteristic DNA and histone modification signatures. How combinatorial chromatin modification states are recognized by epigenetic reader proteins and how this is linked to their biological function is largely unknown. Here we provide a detailed molecular analysis of chromatin recognition by the lysine demethylase KDM2A. Using biochemical approaches we identify a nucleosome interaction module within KDM2A consisting of a CXXC type zinc finger, a PHD domain and a newly identified Heterochromatin Protein 1 (HP1) interaction motif that mediates direct binding between KDM2A and HP1...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903903/novel-roles-of-hp1a-and-mcm10-in-dna-replication-genome-maintenance-and-photoreceptor-cell-differentiation
#9
Nicole Vo, Dang Ngoc Anh Suong, Natsuki Yoshino, Hideki Yoshida, Sue Cotterill, Masamitsu Yamaguchi
Both Mcm10 and HP1a are known to be required for DNA replication. However, underlying mechanism is not clarified yet especially for HP1. Knockdown of both HP1a and Mcm10 genes inhibited the progression of S phase in Drosophila eye imaginal discs. Proximity Ligation Assay (PLA) demonstrated that HP1a is in close proximity to DNA replication proteins including Mcm10, RFC140 and DNA polymerase ϵ 255 kDa subunit in S-phase. This was further confirmed by co-immunoprecipitation assay. The PLA signals between Mcm10 and HP1a are specifically observed in the mitotic cycling cells, but not in the endocycling cells...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895715/protein-kinase-msk1-physically-and-functionally-interacts-with-the-kmt2a-mll1-methyltransferase-complex-and-contributes-to-the-regulation-of-multiple-target-genes
#10
Maaike Wiersma, Marianne Bussiere, John A Halsall, Nil Turan, Robert Slany, Bryan M Turner, Karl P Nightingale
BACKGROUND: The KMT2A/MLL1 lysine methyltransferase complex is an epigenetic regulator of selected developmental genes, in part through the SET domain-catalysed methylation of H3K4. It is essential for normal embryonic development and haematopoiesis and frequently mutated in cancer. The catalytic properties and targeting of KMT2A/MLL1 depend on the proteins with which it complexes and the post-translational protein modifications which some of these proteins put in place, though detailed mechanisms remain unclear...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27865105/sensitive-and-rapid-detection-of-micrornas-using-hairpin-probes-mediated-exponential-isothermal-amplification
#11
Haiyun Liu, Tian Tian, Yuhan Zhang, Longhua Ding, Jinghua Yu, Mei Yan
MicroRNAs (miRNAs) play significant roles in a diverse range of biological progress and have been regarded as biomarkers and therapeutic targets in cancer treatment. Here, we develop a rapid and sensitive miRNA assay on the basis of exponential isothermal amplification in combination with the hairpin probes, which was designed for sensitive detection of miRNA. The binding of target miRNA with a linear DNA template initiates exponential isothermal amplification reaction (EXPAR) and generates the universal triggers which are complementary to the 3' protruding end of hairpin probe1(HP1)...
March 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27856763/normal-chromosome-conformation-depends-on-subtelomeric-facultative-heterochromatin-in-neurospora-crassa
#12
Andrew D Klocko, Tereza Ormsby, Jonathan M Galazka, Neena A Leggett, Miki Uesaka, Shinji Honda, Michael Freitag, Eric U Selker
High-throughput chromosome conformation capture (Hi-C) analyses revealed that the 3D structure of the Neurospora crassa genome is dominated by intra- and interchromosomal links between regions of heterochromatin, especially constitutive heterochromatin. Elimination of trimethylation of lysine 9 on histone H3 (H3K9me3) or its binding partner Heterochromatin Protein 1 (HP1)-both prominent features of constitutive heterochromatin-have little effect on the Hi-C pattern. It remained possible that di- or trimethylation of lysine 27 on histone H3 (H3K27me2/3), which becomes localized in regions of constitutive heterochromatin when H3K9me3 or HP1 are lost, plays a critical role in the 3D structure of the genome...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27782152/hulc-cooperates-with-malat1-to-aggravate-liver-cancer-stem-cells-growth-through-telomere-repeat-binding-factor-2
#13
Mengying Wu, Zhuojia Lin, Xiaonan Li, Xiaoru Xin, Jiahui An, Qidi Zheng, Yuxin Yang, Dongdong Lu
The dysregulation of lncRNAs has increasingly been linked to many human diseases, especially in cancers. Our results demonstrate HULC, MALAT1 and TRF2 are highly expressed in human hepatocellular carcinoma tissues, and HULC plus MALAT1 overexpression drastically promotes the growth of liver cancer stem cells. Mechanistically, both HULC and MALAT1 overexpression enhanced RNA polII, P300, CREPT to load on the promoter region of telomere repeat-binding factor 2(TRF2), triggering the overexpression, phosphorylation and SUMOylation of TRF2...
October 26, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27777990/conformational-features-of-the-a%C3%AE-42-peptide-monomer-and-its-interaction-with-the-surrounding-solvent
#14
Prabir Khatua, Jaya C Jose, Neelanjana Sengupta, Sanjoy Bandyopadhyay
Accumulation of the amyloid beta (Aβ) peptide in the brain is responsible for debilitating neurodegenerative diseases, such as Alzheimer's disease (AD). We have carried out atomistic molecular dynamics simulations of the full-length Aβ42 peptide monomer with a wide range of conformations at room temperature. Efforts have been made to probe the conformational features of different segments of the peptide, namely the two terminal segments (N-term and C-term), the central hydrophobic regions (hp1 and hp2) and the central turn region joining hp1 and hp2, and their nonuniform influence on the spatial arrangements and binding energies of the surrounding water molecules...
October 25, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27733730/pericentric-h3k9me3-formation-by-hp1-interaction-defective-histone-methyltransferase-suv39h1
#15
Daisuke Muramatsu, Hiroshi Kimura, Kaoru Kotoshiba, Makoto Tachibana, Yoichi Shinkai
Pericentric regions form epigenetically organized, silent heterochromatin structures that accumulate histone H3 lysine 9 tri-methylation (H3K9me3) and heterochromatin protein 1 (HP1), a methylated H3K9-binding protein. At pericentric regions, Suv39h is the major enzyme that generates H3K9me3. Suv39h also interacts directly with HP1. However, the importance of HP1 interaction for Suv39h-mediated H3K9me3 formation at the pericentromere is not well characterized. To address this question, we introduced HP1 binding-defective, N-terminally truncated mouse Suv39h1 (ΔN) into Suv39h-deficient cells...
December 3, 2016: Cell Structure and Function
https://www.readbyqxmd.com/read/27729944/expression-and-chromatin-structures-of-cellulolytic-enzyme-gene-regulated-by-heterochromatin-protein-1
#16
Xiujun Zhang, Yinbo Qu, Yuqi Qin
BACKGROUND: Heterochromatin protein 1 (HP1, homologue HepA in Penicillium oxalicum) binding is associated with a highly compact chromatin state accompanied by gene silencing or repression. HP1 loss leads to the derepression of gene expression. We investigated HepA roles in regulating cellulolytic enzyme gene expression, as an increasingly number of studies have suggested that cellulolytic enzyme gene expression is not only regulated by transcription factors, but is also affected by the chromatin status...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27715020/marine-phages-as-tracers-effects-of-size-morphology-and-physico-chemical-surface-properties-on-transport-in-a-porous-medium
#17
Nawras Ghanem, Bärbel Kiesel, René Kallies, Hauke Harms, Antonis Chatzinotas, Lukas Y Wick
Although several studies examined the transport of viruses in terrestrial systems only few studies exist on the use of marine phages (i.e., nonterrestrial viruses infecting marine host bacteria) as sensitively detectable microbial tracers for subsurface colloid transport and water flow. Here, we systematically quantified and compared for the first time the effects of size, morphology and physicochemical surface properties of six marine phages and two coliphages (MS2, T4) on transport in sand-filled percolated columns...
December 6, 2016: Environmental Science & Technology
https://www.readbyqxmd.com/read/27681634/dual-chromatin-recognition-by-the-histone-deacetylase-complex-hchc-is-required-for-proper-dna-methylation-in-neurospora-crassa
#18
Shinji Honda, Vincent T Bicocca, Jordan D Gessaman, Michael R Rountree, Ayumi Yokoyama, Eun Y Yu, Jeanne M L Selker, Eric U Selker
DNA methylation, heterochromatin protein 1 (HP1), histone H3 lysine 9 (H3K9) methylation, histone deacetylation, and highly repeated sequences are prototypical heterochromatic features, but their interrelationships are not fully understood. Prior work showed that H3K9 methylation directs DNA methylation and histone deacetylation via HP1 in Neurospora crassa and that the histone deacetylase complex HCHC is required for proper DNA methylation. The complex consists of the chromodomain proteins HP1 and chromodomain protein 2 (CDP-2), the histone deacetylase HDA-1, and the AT-hook motif protein CDP-2/HDA-1-associated protein (CHAP)...
11, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27619474/characterization-of-phloroglucinol-enriched-fractions-of-brazilian-hypericum-species-and-evaluation-of-their-effect-on-human-keratinocytes-proliferation
#19
Henrique Bridi, Aline Beckenkamp, Gari Vidal Ccana-Ccapatinta, Sérgio Augusto de Loreto Bordignon, Andréia Buffon, Gilsane Lino von Poser
In this study, a phytochemical and biological investigation on five South Brazilian Hypericum species (Hypericum caprifoliatum, Hypericum carinatum, Hypericum connatum, Hypericum myrianthum, and Hypericum polyanthemum) was carried out. The phloroglucinol-enriched fractions (PEF) of the flowering aerial parts were analyzed by high-performance liquid chromatography for the content of uliginosin A (1), japonicin A (2), uliginosin B (3), hyperbrasilol B (4), and the three benzopyrans, that is, 6-isobutyryl-5,7-dimethoxy-2,2-dimethyl-benzopyran (HP1) (5), 7-hydroxy-6-isobutyryl-5-methoxy-2,2-dimethyl-benzopyran (HP2) (6), and 5-hydroxy-6-isobutyryl-7-methoxy-2,2-dimethyl-benzopyran (HP3) (7)...
January 2017: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/27614332/genome-wide-identification-evolution-of-chromobox-family-genes-and-their-expression-in-nile-tilapia
#20
Xing-Yong Liu, Xian-Bo Zhang, Ming-Hui Li, Shu-Qing Zheng, Zhi-Long Liu, Yun-Ying Cheng, De-Shou Wang
Chromobox (Cbx) family proteins are transcriptional repressors that involved in epigenetic and developmental processes. In this study, comprehensive analyses of Cbxs were performed using available genome databases from representative animal species. The Cbx family were originated from one Polycomb (Pc) gene like the yeast Pc, which duplicated into two and gave rise to the Pc and the Heterochromatin protein 1 (Hp1) identified in invertebrates from protozoon to lancelet. Rapid expansion of Cbx family members was observed in vertebrates as ~8 (5 Pc and 3 Hp1) were identified in spotted gar, coelacanth and tetrapods...
January 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
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