keyword
MENU ▼
Read by QxMD icon Read
search

chromatin interaction

keyword
https://www.readbyqxmd.com/read/29469819/the-long-noncoding-rna-hotair-in-breast-cancer-does-autophagy-play-a-role
#1
Elżbieta Pawłowska, Joanna Szczepanska, Janusz Blasiak
HOTAIR (HOX transcript antisense RNA) plays a critical role in chromatin dynamics through the interaction with histone modifiers resulting in transcriptional gene silencing. The promoter of the HOTAIR gene contains multiple estrogen response elements (EREs) and is transcriptionally activated by estradiol in estrogen receptor-positive breast cancer cells. HOTAIR competes with BRCA1, a critical protein in breast cancer and is a critical regulator of genes involved in epithelial-to-mesenchymal transition. It mediates an oncogenic action of c-Myc, essential for breast carcinogenesis...
November 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29469144/identification-of-a-novel-ligand-for-the-atad2-bromodomain-with-selectivity-over-brd4-through-a-fragment-growing-approach
#2
Duncan C Miller, Mathew P Martin, Santosh Adhikari, Alfie Brennan, Jane A Endicott, Bernard T Golding, Ian R Hardcastle, Amy Heptinstall, Stephen Hobson, Claire Jennings, Lauren Molyneux, Yvonne Ng, Stephen R Wedge, Martin E M Noble, Celine Cano
ATAD2 is an ATPase that is overexpressed in a variety of cancers and associated with a poor patient prognosis. This protein has been suggested to function as a cofactor for a range of transcription factors, including the proto-oncogene MYC and the androgen receptor. ATAD2 comprises an ATPase domain, implicated in chromatin remodelling, and a bromodomain which allows it to interact with acetylated histone tails. Dissection of the functional roles of these two domains would benefit from the availability of selective, cell-permeable pharmacological probes...
February 22, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29468159/il-1%C3%AE-promotes-a-new-function-of-dnase-i-as-a-transcription-factor-for-the-fas-receptor-gene
#3
Dhivya Thiyagarajan, Hege L Pedersen, Natalya Seredkina, Kjersti D Horvei, Lorena Arranz, Ramon Sonneveld, Tom Nijenhuis, Johan van der Vlag, Ole P Rekvig
Recently we described that endonuclease inactive DNase I translocated into the nucleus in response to increased endogenous IL-1β expression. Here, we demonstrate impact and function of translocated DNase I in tubular cells. Effect of cytokines on expression level and nuclear localisation of DNase I and corresponding levels of Fas receptor (FasR) and IL-1β were determined by confocal microscopy, qPCR and western blot analyses, in presence or absence of siRNA against IL-1β and DNase I mRNA. Nuclear DNase I bound to the FAS promotor region as determined by chromatin immuno-precipitation analysis...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29467493/c-jun-ap-1-overexpression-reprograms-er%C3%AE-signaling-related-to-tamoxifen-response-in-er%C3%AE-positive-breast-cancer
#4
Huan He, Indranil Sinha, Rongrong Fan, Lars-Arne Haldosen, Feifei Yan, Chunyan Zhao, Karin Dahlman-Wright
A critical mechanism that has been proposed for transcription regulation by estrogen receptor α (ER) is the tethering of ER to DNA via other transcription factors, such as AP-1. However, genome-wide assessment of the overlap in chromatin binding repertoires of these two transcription factors has not been reported. Here, we show that the AP-1 transcription factor c-Jun interacts with ER and that c-Jun chromatin binding shows extensive overlap with ER binding at the global level. Further, we show that c-Jun overexpression reprograms ER chromatin binding and modulates ER-mediated gene regulation...
February 22, 2018: Oncogene
https://www.readbyqxmd.com/read/29467363/enhancing-hi-c-data-resolution-with-deep-convolutional-neural-network-hicplus
#5
Yan Zhang, Lin An, Jie Xu, Bo Zhang, W Jim Zheng, Ming Hu, Jijun Tang, Feng Yue
Although Hi-C technology is one of the most popular tools for studying 3D genome organization, due to sequencing cost, the resolution of most Hi-C datasets are coarse and cannot be used to link distal regulatory elements to their target genes. Here we develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data. We demonstrate that HiCPlus can impute interaction matrices highly similar to the original ones, while only using 1/16 of the original sequencing reads...
February 21, 2018: Nature Communications
https://www.readbyqxmd.com/read/29467333/chd7-represses-the-retinoic-acid-synthesis-enzyme-aldh1a3-during-inner-ear-development
#6
Hui Yao, Sophie F Hill, Jennifer M Skidmore, Ethan D Sperry, Donald L Swiderski, Gilson J Sanchez, Cynthia F Bartels, Yehoash Raphael, Peter C Scacheri, Shigeki Iwase, Donna M Martin
CHD7, an ATP-dependent chromatin remodeler, is disrupted in CHARGE syndrome, an autosomal dominant disorder characterized by variably penetrant abnormalities in craniofacial, cardiac, and nervous system tissues. The inner ear is uniquely sensitive to CHD7 levels and is the most commonly affected organ in individuals with CHARGE. Interestingly, upregulation or downregulation of retinoic acid (RA) signaling during embryogenesis also leads to developmental defects similar to those in CHARGE syndrome, suggesting that CHD7 and RA may have common target genes or signaling pathways...
February 22, 2018: JCI Insight
https://www.readbyqxmd.com/read/29467285/angiogenic-patterning-by-steel-an-endothelial-enriched-long-noncoding-rna
#7
H S Jeffrey Man, Aravin N Sukumar, Gabrielle C Lam, Paul J Turgeon, Matthew S Yan, Kyung Ha Ku, Michelle K Dubinsky, J J David Ho, Jenny Jing Wang, Sunit Das, Nora Mitchell, Peter Oettgen, Michael V Sefton, Philip A Marsden
Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell type-specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for s pliced- t ranscript e ndothelial- e nriched lncRNA (STEEL) in angiogenic potential, macrovascular/microvascular identity, and shear stress responsiveness...
February 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29467217/hp1%C3%AE-targets-the-chromosomal-passenger-complex-for-activation-at-heterochromatin-before-mitotic-entry
#8
Jan G Ruppert, Kumiko Samejima, Melpomeni Platani, Oscar Molina, Hiroshi Kimura, A Arockia Jeyaprakash, Shinya Ohta, William C Earnshaw
The chromosomal passenger complex (CPC) is directed to centromeres during mitosis via binding to H3T3ph and Sgo1. Whether and how heterochromatin protein 1α (HP1α) influences CPC localisation and function during mitotic entry is less clear. Here, we alter HP1α dynamics by fusing it to a CENP-B DNA-binding domain. Tethered HP1 strongly recruits the CPC, destabilising kinetochore-microtubule interactions and activating the spindle assembly checkpoint. During mitotic exit, the tethered HP1 traps active CPC at centromeres...
February 21, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29466992/the-hnf1%C3%AE-regulated-lncrna-hnf1a-as1-reverses-the-malignancy-of-hepatocellular-carcinoma-by-enhancing-the-phosphatase-activity-of-shp-1
#9
Chen-Hong Ding, Chuan Yin, Shi-Jie Chen, Liang-Zhi Wen, Kai Ding, Shu-Juan Lei, Jin-Pei Liu, Jian Wang, Kai-Xian Chen, Hua-Liang Jiang, Xin Zhang, Cheng Luo, Wei-Fen Xie
BACKGROUND: Our previous study has demonstrated that hepatocyte nuclear factor 1α (HNF1α) exerts potent therapeutic effects on hepatocellular carcinoma (HCC). However, the molecular mechanisms by which HNF1α reverses HCC malignancy need to be further elucidated. METHODS: lncRNA microarray was performed to identify the long noncoding RNAs (lncRNAs) regulated by HNF1α. Chromatin immunoprecipitation and luciferase reporter assays were applied to clarify the mechanism of the transcriptional regulation of HNF1α to HNF1A antisense RNA 1 (HNF1A-AS1)...
February 21, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29466755/transformation-of-accessible-chromatin-and-3d-nucleome-underlies-lineage-commitment-of-early-t-cells
#10
Gangqing Hu, Kairong Cui, Difeng Fang, Satoshi Hirose, Xun Wang, Darawalee Wangsa, Wenfei Jin, Thomas Ried, Pentao Liu, Jinfang Zhu, Ellen V Rothenberg, Keji Zhao
How chromatin reorganization coordinates differentiation and lineage commitment from hematopoietic stem and progenitor cells (HSPCs) to mature immune cells has not been well understood. Here, we carried out an integrative analysis of chromatin accessibility, topologically associating domains, AB compartments, and gene expression from HSPCs to CD4+ CD8+ T cells. We found that abrupt genome-wide changes at all three levels of chromatin organization occur during the transition from double-negative stage 2 (DN2) to DN3, accompanying the T lineage commitment...
February 20, 2018: Immunity
https://www.readbyqxmd.com/read/29466355/epigenome-comparisons-reveal-linkage-between-gene-expression-and-postnatal-remodeling-of-chromatin-domain-topology
#11
Bruce H Howard, Tazuko H Hirai, Valya R Russanova
Substantial evidence has accumulated linking epigenome change to alterations in stem cell function during postnatal development and aging. Yet much remains to be learned about causal relationships, and large gaps remain in our understanding of epigenome-transcriptome interactions. Here we investigate structural features of large histone H3K27me3-enriched regions in human stem cell-like monocytes and their dendritic cell derivatives, where the H3K27me3 modification is considered to demarcate Polycomb (PcG) domains...
2018: PloS One
https://www.readbyqxmd.com/read/29466322/environmental-temperature-controls-accumulation-of-transacting-sirnas-involved-in-heterochromatin-formation
#12
Marcello Pirritano, Ulrike Götz, Sivarajan Karunanithi, Karl Nordström, Marcel H Schulz, Martin Simon
Genes or alleles can interact by small RNAs in a homology dependent manner meaning that short interfering (siRNAs) can act in trans at the chromatin level producing stable and heritable silencing phenotypes. Because of the puzzling data on endogenous paramutations, their impact contributing to adaptive evolution in a Lamarckian manner remains unknown. An increasing number of studies characterizes the underlying siRNA accumulation pathways using transgene experiments. Also in the ciliate Paramecium tetraurelia , we induce trans silencing on the chromatin level by injection of truncated transgenes...
February 21, 2018: Genes
https://www.readbyqxmd.com/read/29465771/site-specific-studies-of-nucleosome-interactions-by-solid-state-nmr
#13
ShengQi Xiang, Ulric B le Paige, Velten Horn, Klaartje Houben, Marc Baldus, Hugo van Ingen
Chromatin function depends on a dense network of interactions between nucleosomes and wide range of proteins. A detailed description of these protein-nucleosome interactions is required to reach a full molecular understanding of chromatin function in both genetics and epigenetics. Here, we show that the structure, dynamics and interactions of nucleosomes can be interrogated in a residue-specific manner using state-of-the-art solid-state NMR. Using sedimented nucleosomes, high-resolution spectra are obtained for both flexible histone tails and the non-mobile histone core...
February 21, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29465625/spinal-bromodomain-containing-protein-4-contributes-to-neuropathic-pain-induced-by-hiv-glycoprotein-120-with-morphine-in-rats
#14
Keiya Takahashi, Hyun Yi, Ching-Hang Liu, Shue Liu, Yuta Kashiwagi, Dennis J Patin, Shuanglin Hao
The symptoms of HIV-sensory neuropathy are dominated by neuropathic pain. Recent data show that repeated use of opiates enhances the chronic pain states in HIV patients. Limited attention has so far been devoted to exploring the exact pathogenesis of HIV painful disorder and opiate abuse in vivo, for which there is no effective treatment. Bromodomain-containing protein 4 (Brd4) is a member of the bromodomain and extraterminal domain protein (BET) family and functions as a chromatin 'reader' that binds acetylated lysines in histones in brain neurons to mediate the transcriptional regulation underlying learning and memory...
February 20, 2018: Neuroreport
https://www.readbyqxmd.com/read/29463681/bromodomian-containing-protein-4-independent-transcriptional-activation-by-autoimmune-regulator-aire-and-nf-%C3%AE%C2%BAb
#15
Fang Huang, Wei Shao, Koh Fujinaga, B Matija Peterlin
Autoimmune regulator (AIRE) and nu-clear factor-kappa B (NF-κB) are transcription factors (TFs) that direct the expression of individual genes and gene clusters. Bromodomain-containing protein 4 (BRD4) is an epigenetic regulator that recognizes and binds to acetylated histones. BRD4 also has been reported to promote interactions between the positive elongation factor b (P-TEFb) and AIRE or P-TEFb and NF-κB subunit p65. Here, we report that AIRE and p65 bind to P-TEFb independently of BRD4. JQ1, a compound that disrupts interactions between BRD4 and acetylated proteins, does not decrease transcriptional activities of AIRE or p65...
February 20, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29463646/mutant-idh1-disrupts-pkm2-%C3%AE-catenin-brg1-transcriptional-network-driven-cd47-expression
#16
Pruthvi Gowda, Shruti Patrick, Ankita Singh, Touseef Sheikh, Ellora Sen
Gain-of-function mutation in isocitrate dehydrogenase1 (IDH1) affects immune-surveillance in gliomas. As elevated CD47 is associated with immune evasion in cancers, its status in gliomas harboring IDH1-MT was investigated. Decreased CD47 expression in IDH1-R132H overexpressing cells was accompanied by diminished nuclear β-catenin, PKM2 and TCF4 levels as compared to IDH1-WT. Inhibition of β-catenin in IDH1-WT abrogated CD47 expression, β-catenin-TCF4 interaction and transactivational activity of β-catenin/TCF4...
February 20, 2018: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/29463645/molecular-architecture-of-the-essential-yeast-histone-acetyltransferase-complex-nua4-redefines-its-multi-modularity
#17
Dheva Setiaputra, Salar Ahmad, Udit Dalwadi, Anne-Lise Steunou, Shan Lu, James D Ross, Meng-Qiu Dong, Jacques Côté, Calvin K Yip
Conserved from yeast to humans, the NuA4 histone acetyltransferase is a large multisubunit complex essential for cell viability through regulation of gene expression, genome maintenance, metabolism, and cell fate during development and stress. How the different NuA4 subunits work in concert with one another to perform these diverse functions remains unclear, and addressing this central question requires a comprehensive understanding of NuA4's molecular architecture and subunit organization. We have determined the structure of fully assembled native yeast NuA4 by single-particle electron microscopy...
February 20, 2018: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/29462945/luminal-lncrnas-regulation-by-er%C3%AE-controlled-enhancers-in-a-ligand-independent-manner-in-breast-cancer-cells
#18
Valentina Miano, Giulio Ferrero, Valentina Rosti, Eleonora Manitta, Jamal Elhasnaoui, Giulia Basile, Michele De Bortoli
Estrogen receptor-α (ERα) is a ligand-inducible protein which mediates estrogenic hormones signaling and defines the luminal BC phenotype. Recently, we demonstrated that even in absence of ligands ERα (apoERα) binds chromatin sites where it regulates transcription of several protein-coding and lncRNA genes. Noteworthy, apoERα-regulated lncRNAs marginally overlap estrogen-induced transcripts, thus representing a new signature of luminal BC genes. By the analysis of H3K27ac enrichment in hormone-deprived MCF-7 cells, we defined a set of Super Enhancers (SEs) occupied by apoERα, including one mapped in proximity of the DSCAM-AS1 lncRNA gene...
February 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29462880/benzothiophenone-derivatives-targeting-mutant-forms-of-estrogen-receptor-%C3%AE-in-hormone-resistant-breast-cancers
#19
Kriti Singh, Ravi S N Munuganti, Nada Lallous, Kush Dalal, Ji Soo Yoon, Aishwariya Sharma, Takeshi Yamazaki, Artem Cherkasov, Paul S Rennie
Estrogen receptor-α positive (ERα⁺) breast cancers represent 75% of all invasive breast cancer cases, while de novo or acquired resistance to ER-directed therapy is also on the rise. Numerous factors contribute to this phenomenon including the recently-reported ESR1 gene mutations such as Y537S, which amplifies co-activator interactions with ERα and promotes constitutive activation of ERα function. Herein, we propose that direct targeting of the activation function-2 (AF2) site on ERα represents a promising alternative therapeutic strategy to overcome mutation-driven resistance in breast cancer...
February 15, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29459768/oncoprotein-tudor-sn-is-a-key-determinant-providing-survival-advantage-under-dna-damaging-stress
#20
Xiao Fu, Chunyan Zhang, Hao Meng, Kai Zhang, Lei Shi, Cheng Cao, Ye Wang, Chao Su, Lingbiao Xin, Yuanyuan Ren, Wei Zhang, Xiaoming Sun, Lin Ge, Olli Silvennoinen, Zhi Yao, Xi Yang, Jie Yang
Herein, Tudor-SN was identified as a DNA damage response (DDR)-related protein that plays important roles in the early stage of DDR. X-ray or laser irradiation could evoke the accumulation of Tudor-SN to DNA damage sites in a poly(ADP-ribosyl)ation-dependent manner via interaction with PARP-1. Additionally, we illustrated that the SN domain of Tudor-SN mediated the association of these two proteins. The accumulated Tudor-SN further recruited SMARCA5 (ATP-dependent chromatin remodeller) and GCN5 (histone acetyltransferase) to DNA damage sites, resulting in chromatin relaxation, and consequently activating the ATM kinase and downstream DNA repair signalling pathways to promote cell survival...
February 19, 2018: Cell Death and Differentiation
keyword
keyword
78092
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"