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Chromatin modulation

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https://www.readbyqxmd.com/read/28106321/conserved-two-component-hik34-rre1-module-directly-activates-heat-stress-inducible-transcription-of-major-chaperone-and-other-genes-in-synechococcus-elongatus-pcc-7942
#1
Ikki Kobayashi, Satoru Watanabe, Yu Kanesaki, Tomohiro Shimada, Hirofumi Yoshikawa, Kan Tanaka
Bacteria and other organisms, including cyanobacteria, employ two-component signal transducing modules comprising histidine kinases and response regulators to acclimate to changing environments. While the number and composition of these modules differ among cyanobacteria, two response regulators that contain DNA binding domains, RpaB and Rre1, are conserved in all sequenced cyanobacterial genomes and are essential for viability. Although RpaB negatively or positively regulates high light and other stress-responsive gene expression, little is known about the function of Rre1...
January 20, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28106169/inhibition-of-nucks-facilitates-corneal-recovery-following-alkali-burn
#2
Ming-Wai Poon, Dan Jiang, Peng Qin, Yuelin Zhang, Beiying Qiu, Sumit Chanda, Vinay Tergaonkar, Qing Li, Ian Y Wong, Zhendong Yu, Hung-Fat Tse, David S H Wong, Qizhou Lian
Corneal wound healing involves a complex cascade of cytokine-controlled cellular events, including inflammatory and angiogenesis responses that are regulated by transcriptional chromatin remodeling. Nuclear Ubiquitous Casein and cyclin-dependent Kinase Substrate (NUCKS) is a key chromatin modifier and transcriptional regulator of metabolic signaling. In this study, we investigated the role of NUCKS in corneal wound healing by comparing its effects on corneal alkali burn in NUCKS knockout (NKO) and NUCKS wild-type (NWT) mice...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28104302/stat5-drives-abnormal-proliferation-in-autosomal-dominant-polycystic-kidney-disease
#3
Maria Fragiadaki, Morgane Lannoy, Madeleine Themanns, Barbara Maurer, Wouter N Leonhard, Dorien J M Peters, Richard Moriggl, Albert C M Ong
Autosomal dominant polycystic kidney disease (ADPKD) leads to renal failure. The hallmark of ADPKD is increased epithelial proliferation, which has been proposed to be due to atypical signaling including abnormal JAK-STAT activity. However, the relative contribution of JAK-STAT family members in promoting proliferation in ADPKD is unknown. Here, we present siRNA JAK-STAT-focused screens discovering a previously unknown proliferative role for multiple JAK-STAT components (including STAT1, STAT2, STAT4, STAT5a, and STAT5b)...
January 16, 2017: Kidney International
https://www.readbyqxmd.com/read/28103509/3-5-dihydroxy-3-4-7-trimethoxyflavone-induces-er-stress-associated-hct-116-programmed-cell-death-via-redox-signaling
#4
Mahendra Pal Singh, Jaehong Han, Sun Chul Kang
Quercetin, a well cognized bioactive flavone possessing great medicinal value, has limited usage. The rapid gastrointestinal digestion of quercetin is also a major obstacle for its clinical implementation due to low bioavailability and poor aqueous solubility. 3',5-dihydroxy-3,4',7-trimethoxyflavone (DTMF), a novel semi-synthetic derivative of quercetin, is known to modulate several biological activities. Therefore, in the present study we examined the cytotoxic mechanism of DTMF in concentration-dependent manner (25, 50, and 100μM; 24h) against HCT-116 human colon carcinoma cells...
January 16, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28103242/genome-wide-binding-of-posterior-hoxa-d-transcription-factors-reveals-subgrouping-and-association-with-ctcf
#5
Ivana Jerković, Daniel M Ibrahim, Guillaume Andrey, Stefan Haas, Peter Hansen, Catrin Janetzki, Irene González Navarrete, Peter N Robinson, Jochen Hecht, Stefan Mundlos
Homeotic genes code for key transcription factors (HOX-TFs) that pattern the animal body plan. During embryonic development, Hox genes are expressed in overlapping patterns and function in a partially redundant manner. In vitro biochemical screens probing the HOX-TF sequence specificity revealed largely overlapping sequence preferences, indicating that co-factors might modulate the biological function of HOX-TFs. However, due to their overlapping expression pattern, high protein homology, and insufficiently specific antibodies, little is known about their genome-wide binding preferences...
January 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28100789/complex-evolutionary-history-of-the-mammalian-histone-h1-1-h1-5-gene-family
#6
Inma Ponte, Devani Romero, Daniel Yero, Pedro Suau, Alicia Roque
H1 is involved in chromatin higher-order structure and gene regulation. H1 has a tripartite structure. The central domain is stably folded in solution, while the N- and C-terminal domains are intrinsically disordered. The terminal domains are encoded by DNA of low sequence complexity, and are thus prone to short insertions/deletions (indels). We have examined the evolution of the H1.1-H1.5 gene family from 27 mammalian species. Multiple sequence alignment has revealed a strong preferential conservation of the number and position of basic residues among paralogs, suggesting that overall H1 basicity is under a strong purifying selection...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28096468/o-glcnac-expression-levels-epigenetically-regulate-colon-cancer-tumorigenesis-by-affecting-the-cancer-stem-cell-compartment-via-modulating-expression-of-transcriptional-factor-mybl1
#7
Huabei Guo, Bing Zhang, Alison V Nairn, Tamas Nagy, Kelley W Moremen, Phillip Buckhaults, Michael Pierce
To study the regulation of colorectal adenocarcinoma progression by O-GlcNAc, we have focused on the O-GlcNAc-mediated epigenetic regulation of human colon cancer stem cells (CCSC). Xenograft tumors from colon tumor cells with OGT knockdown grew significantly slower than those formed from control cells, indicating a reduced proliferation of tumor cells due to inhibition of OGT expression. Significant reduction of CCSC population was observed in the tumor cells after OGT knockdown, while tumor cells treated with O-GlcNAcase inhibitor showed an increased CCSC population, indicating that O-GlcNAc levels regulated the CCSC compartment...
January 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28094813/a-methylome-wide-mqtl-analysis-reveals-associations-of-methylation-sites-with-gad1-and-hdac3-snps-and-a-general-psychiatric-risk-score
#8
D M Ciuculete, A E Boström, S Voisin, H Philipps, O E Titova, M Bandstein, L Nikontovic, M J Williams, J Mwinyi, H B Schiöth
Genome-wide association studies have identified a number of single-nucleotide polymorphisms (SNPs) that are associated with psychiatric diseases. Increasing body of evidence suggests a complex connection of SNPs and the transcriptional and epigenetic regulation of gene expression, which is poorly understood. In the current study, we investigated the interplay between genetic risk variants, shifts in methylation and mRNA levels in whole blood from 223 adolescents distinguished by a risk for developing psychiatric disorders...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28093838/fusaric-acid-contributes-to-virulence-of-fusarium-oxysporum-on-plant-and-mammalian-hosts
#9
Cristina López-Díaz, Vahid Rahjoo, Michael Sulyok, Veronica Ghionna, Adela Martín-Vicente, Javier Capilla, Antonio Di Pietro, Manuel S López-Berges
Fusaric acid (FA) is among the oldest identified secondary metabolites produced by Fusarium species, known for a long time to display strong phytotoxicity and moderate toxicity to animal cells; however, the cellular targets of FA as well as its function in fungal pathogenicity remain unknown. Here, we investigated the role of FA in Fusarium oxysporum, a soil-borne cross-kingdom pathogen that causes vascular wilt on more than a hundred plant species and opportunistic infections in humans. Targeted deletion of fub1, encoding a predicted orthologue of the polyketide synthase involved in FA biosynthesis in F...
January 17, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28093507/mosaic-expression-of-atrx-in-the-central-nervous-system-causes-memory-deficits
#10
Renee J Tamming, Jennifer R Siu, Yan Jiang, Marco A M Prado, Frank Beier, Nathalie G Bérubé
The rapid modulation of chromatin organization is thought to play a critical role in cognitive processes such as memory consolidation. This is supported in part by the dysregulation of many chromatin remodeling proteins in neurodevelopmental and psychiatric disorders. A key example is ATRX, an X-linked gene commonly mutated in individuals with syndromic and non-syndromic intellectual disability (ID). The consequences of Atrx inactivation on learning and memory have been difficult to evaluate due to the early lethality of hemizygous-null animals...
January 12, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28093207/p53-mediates-the-suppression-of-cancer-cell-invasion-by-inducing-lima1-eplin
#11
Tomoko Ohashi, Masashi Idogawa, Yasushi Sasaki, Takashi Tokino
The tumor suppressor gene p53 is frequently mutated in human cancer. p53 executes various functions, such as apoptosis induction and cell cycle arrest, by modulating transcriptional regulation. In this study, LIM domain and Actin-binding protein 1 (LIMA1) was identified as a target of the p53 family using a cDNA microarray. We also evaluated genome-wide occupancy of the p53 protein by performing chromatin immunoprecipitation-sequencing (ChIP-seq) and identified two p53 response elements in the LIMA1 gene. LIMA1 protein levels were increased by treatment with nutlin-3a, a small molecule that activates endogenous p53...
January 13, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28090287/transcription-factors-transcriptional-coregulators-and-epigenetic-modulation-in-the-control-of-pulmonary-vascular-cell-phenotype-therapeutic-implications-for-pulmonary-hypertension-2015-grover-conference-series
#12
REVIEW
Soni S Pullamsetti, Frédéric Perros, Prakash Chelladurai, Jason Yuan, Kurt Stenmark
Pulmonary hypertension (PH) is a complex and multifactorial disease involving genetic, epigenetic, and environmental factors. Numerous stimuli and pathological conditions facilitate severe vascular remodeling in PH by activation of a complex cascade of signaling pathways involving vascular cell proliferation, differentiation, and inflammation. Multiple signaling cascades modulate the activity of certain sequence-specific DNA-binding transcription factors (TFs) and coregulators that are critical for the transcriptional regulation of gene expression that facilitates PH-associated vascular cell phenotypes, as demonstrated by several studies summarized in this review...
December 2016: Pulmonary Circulation
https://www.readbyqxmd.com/read/28087711/ctcf-mediated-topological-boundaries-during-development-foster-appropriate-gene-regulation
#13
Varun Narendra, Milica Bulajić, Job Dekker, Esteban O Mazzoni, Danny Reinberg
The genome is organized into repeating topologically associated domains (TADs), each of which is spatially isolated from its neighbor by poorly understood boundary elements thought to be conserved across cell types. Here, we show that deletion of CTCF (CCCTC-binding factor)-binding sites at TAD and sub-TAD topological boundaries that form within the HoxA and HoxC clusters during differentiation not only disturbs local chromatin domain organization and regulatory interactions but also results in homeotic transformations typical of Hox gene misregulation...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28079155/dietary-phytochemical-peitc-restricts-tumor-development-via-modulation-of-epigenetic-writers-and-erasers
#14
Jung Eun Park, Yang Sun, Sai Kiang Lim, James P Tam, Matthijs Dekker, Hong Chen, Siu Kwan Sze
Dietary intake of bioactive phytochemicals including the cruciferous vegetable derivative phenethyl isothiocyanate (PEITC) can reduce risk of human cancers, but possible epigenetic mechanisms of these effects are yet unknown. We therefore sought to identify the molecular basis of PEITC-mediated epigenetic tumor restriction. Colon cancer cells treated with low-dose PEITC for >1 month exhibited stable alterations in expression profile of epigenetic writers/erasers and chromatin-binding of histone deacetylases (HDACs) and Polycomb-group (PcG) proteins...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077316/chromatin-dynamics-regulate-mesenchymal-stem-cell-lineage-specification-and-differentiation-to-osteogenesis
#15
Hai Wu, Jonathan A R Gordon, Troy W Whitfield, Phillip W L Tai, Andre J van Wijnen, Janet L Stein, Gary S Stein, Jane B Lian
Multipotent mesenchymal stromal cells (MSCs) are critical for regeneration of multiple tissues. Epigenetic mechanisms are fundamental regulators of lineage specification and cell fate, and as such, we addressed the question of which epigenetic modifications characterize the transition of nascent MSCs to a tissue specific MSC-derived phenotype. By profiling the temporal changes of seven histone marks correlated to gene expression during proliferation, early commitment, matrix deposition, and mineralization stages, we identified distinct epigenetic mechanisms that regulate transcriptional programs necessary for tissue-specific phenotype development...
January 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28076901/nuclear-factor-one-transcription-factors-as-epigenetic-regulators-in-cancer
#16
REVIEW
Mitchell Fane, Lachlan Harris, Aaron G Smith, Michael Piper
Tumour heterogeneity poses a distinct obstacle to therapeutic intervention. While the initiation of tumours across various physiological systems is frequently associated with signature mutations in genes that drive proliferation and bypass senescence, increasing evidence suggests that tumour progression and clonal diversity is driven at an epigenetic level. The tumour microenvironment plays a key role in driving diversity as cells adapt to demands during tumour growth, and is thought to drive certain subpopulations back to a stem cell-like state...
January 11, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28076781/crtc1-nuclear-translocation-following-learning-modulates-memory-strength-via-exchange-of-chromatin-remodeling-complexes-on-the-fgf1-gene
#17
Shusaku Uchida, Brett J W Teubner, Charles Hevi, Kumiko Hara, Ayumi Kobayashi, Rutu M Dave, Tatsushi Shintaku, Pattaporn Jaikhan, Hirotaka Yamagata, Takayoshi Suzuki, Yoshifumi Watanabe, Stanislav S Zakharenko, Gleb P Shumyatsky
Memory is formed by synapse-to-nucleus communication that leads to regulation of gene transcription, but the identity and organizational logic of signaling pathways involved in this communication remain unclear. Here we find that the transcription cofactor CRTC1 is a critical determinant of sustained gene transcription and memory strength in the hippocampus. Following associative learning, synaptically localized CRTC1 is translocated to the nucleus and regulates Fgf1b transcription in an activity-dependent manner...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28076780/det1-and-hy5-control-pif4-mediated-thermosensory-elongation-growth-through-distinct-mechanisms
#18
Sreeramaiah N Gangappa, S Vinod Kumar
Plant growth and development are defined by environmental cues. The transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is the central signaling hub that integrates environmental cues, including light and temperature, to regulate growth and development. The thermosensory mechanisms controlling the PIF4-mediated temperature response, and its integration with other environmental responses, remain poorly understood. DE-ETIOLATED 1 (DET1) and CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1), key regulators of light signaling, have been proposed to control thermosensory growth by transcriptional regulation of PIF4, through ELONGATED HYPOCOTYL 5 (HY5)...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28074286/regulation-of-microtubule-nucleation-mediated-by-%C3%AE-tubulin-complexes
#19
REVIEW
Vadym Sulimenko, Zuzana Hájková, Anastasiya Klebanovych, Pavel Dráber
The microtubule cytoskeleton is critically important for spatio-temporal organization of eukaryotic cells. The nucleation of new microtubules is typically restricted to microtubule organizing centers (MTOCs) and requires γ-tubulin that assembles into multisubunit complexes of various sizes. γ-Tubulin ring complexes (TuRCs) are efficient microtubule nucleators and are associated with large number of targeting, activating and modulating proteins. γ-Tubulin-dependent nucleation of microtubules occurs both from canonical MTOCs, such as spindle pole bodies and centrosomes, and additional sites such as Golgi apparatus, nuclear envelope, plasma membrane-associated sites, chromatin and surface of pre-existing microtubules...
January 10, 2017: Protoplasma
https://www.readbyqxmd.com/read/28073943/kdm4b-jmjd2b-is-a-p53-target-gene-that-modulates-the-amplitude-of-p53-response-after-dna-damage
#20
Laura Castellini, Eui Jung Moon, Olga V Razorenova, Adam J Krieg, Rie von Eyben, Amato J Giaccia
The p53 tumor suppressor protein plays a critical role in orchestrating the genomic response to various stress signals by acting as a master transcriptional regulator. Differential gene activity is controlled by transcription factors but also dependent on the underlying chromatin structure, especially on covalent histone modifications. After screening different histone lysine methyltransferases and demethylases, we identified JMJD2B/KDM4B as a p53-inducible gene in response to DNA damage. p53 directly regulates JMJD2B gene expression by binding to a canonical p53-consensus motif in the JMJD2B promoter...
January 9, 2017: Nucleic Acids Research
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