keyword
MENU ▼
Read by QxMD icon Read
search

Chromatin structure regulation

keyword
https://www.readbyqxmd.com/read/29456179/the-chromatin-remodeler-bptf-activates-a-stemness-gene-expression-program-essential-for-the-maintenance-of-adult-hematopoietic-stem-cells
#1
Bowen Xu, Ling Cai, Jason M Butler, Dongliang Chen, Xiongdong Lu, David F Allison, Rui Lu, Shahin Rafii, Joel S Parker, Deyou Zheng, Gang Greg Wang
Self-renewal and differentiation of adult stem cells are tightly regulated partly through configuration of chromatin structure by chromatin remodelers. Using knockout mice, we here demonstrate that bromodomain PHD finger transcription factor (BPTF), a component of the nucleosome remodeling factor (NURF) chromatin-remodeling complex, is essential for maintaining the population size of hematopoietic stem/progenitor cells (HSPCs), including long-term hematopoietic stem cells (HSCs). Bptf-deficient HSCs are defective in reconstituted hematopoiesis, and hematopoietic-specific knockout of Bptf caused profound defects including bone marrow failure and anemia...
February 8, 2018: Stem Cell Reports
https://www.readbyqxmd.com/read/29452958/brca1-mutation-spectrum-functions-and-therapeutic-strategies-the-story-so-far
#2
REVIEW
Babita Sharma, Raman Preet Kaur, Sonali Raut, Anjana Munshi
BRCA1 gene mutations account for about 25-28% of hereditary Breast Cancer as BRCA1 is included in the category of high penetrance genes. Except for few commonmutations, there is a heterogenous spectrum of BRCA1 mutations in various ethnic groups. 185AGdel and 5382ins Care the most common BRCA1 alterations (founder mutations) which have been identified in most of the population. This review has been compiled with an aim to consolidate the information on genetic variants reported in BRCA1 found in various ethnic groups, their functional implications if known; involvement of BRCA1 in various cellular pathways/processes and potential BRCA1 targeted therapies...
January 8, 2018: Current Problems in Cancer
https://www.readbyqxmd.com/read/29452937/epigenetic-chromatin-modification-by-amber-suppression-technology
#3
REVIEW
Heinz Neumann, Petra Neumann-Staubitz, Anna Witte, Daniel Summerer
The genetic incorporation of unnatural amino acids (UAAs) into proteins by amber suppression technology provides unique avenues to study protein structure, function and interactions both in vitro and in living cells and organisms. This approach has been particularly useful for studying mechanisms of epigenetic chromatin regulation, since these extensively involve dynamic changes in structure, complex formation and posttranslational modifications that are difficult to access by traditional approaches. Here, we review recent achievements in this field, emphasizing UAAs that help to unravel protein-protein interactions in cells by photo-crosslinking or that allow the biosynthesis of proteins with defined posttranslational modifications for studying their function and turnover in vitro and in cells...
February 13, 2018: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29450107/macrogenomic-engineering-via-modulation-of-the-scaling-of-chromatin-packing-density
#4
Luay M Almassalha, Greta M Bauer, Wenli Wu, Lusik Cherkezyan, Di Zhang, Alexis Kendra, Scott Gladstein, John E Chandler, David VanDerway, Brandon-Luke L Seagle, Andrey Ugolkov, Daniel D Billadeau, Thomas V O'Halloran, Andrew P Mazar, Hemant K Roy, Igal Szleifer, Shohreh Shahabi, Vadim Backman
Many human diseases result from the dysregulation of the complex interactions between tens to thousands of genes. However, approaches for the transcriptional modulation of many genes simultaneously in a predictive manner are lacking. Here, through the combination of simulations, systems modelling and in vitro experiments, we provide a physical regulatory framework based on chromatin packing-density heterogeneity for modulating the genomic information space. Because transcriptional interactions are essentially chemical reactions, they depend largely on the local physical nanoenvironment...
November 2017: Nature Biomedical Engineering
https://www.readbyqxmd.com/read/29442041/the-interaction-between-atrip-and-mcm-complex-is-essential-for-atrip-chromatin-loading-and-its-phosphorylation-in-mantle-cell-lymphoma-cells
#5
Yuling Nie, Tao Lang
AIM: The ATR-interacting protein (ATRIP) is responsible for the recognition of DNA damage-induced structure and regulation of cellular responses to DNA damage and replication stress. The purpose of our study was to identify the underlying mechanism with respect to chromatin loading and phosphorylation of ATRIP in mantle cell lymphoma (MCL). METHODS: JeKo cells were used in our study. Differently tagged ATRIP (Myc-, hemaglutinin (HA) or Flag) and minichromosome maintenance (MCM) complex (MCM2, MCM3, MCM5, and MCM6) were transfected into 293T cells...
November 1, 2017: Die Pharmazie
https://www.readbyqxmd.com/read/29441061/profiling-of-human-molecular-pathways-affected-by-retrotransposons-at-the-level-of-regulation-by-transcription-factor-proteins
#6
Daniil Nikitin, Dmitry Penzar, Andrew Garazha, Maxim Sorokin, Victor Tkachev, Nicolas Borisov, Alexander Poltorak, Vladimir Prassolov, Anton A Buzdin
Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS)...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29440232/noncoding-rnas-long-non-coding-rnas-and-micrornas-in-endocrine-related-cancers
#7
Carolyn M Klinge
The human genome is 'pervasively transcribed' leading to a complex array of non-coding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~ 22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation...
February 12, 2018: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29435515/the-smyd-family-of-methyltransferases-role-in-cardiac-and-skeletal-muscle-physiology-and-pathology
#8
Christopher Tracy, Junco S Warren, Marta Szulik, Li Wang, June Garcia, Aman Makaju, Kristi Russell, Mickey Miller, Sarah Franklin
Protein methylation plays a pivotal role in the regulation of various cellular processes including chromatin remodeling and gene expression. SET and MYND domain-containing proteins (Smyd) are a special class of lysine methyltransferases whose catalytic SET domain is split by an MYND domain. The hallmark feature of this family was thought to be the methylation of histone H3 (on lysine 4). However, several studies suggest that the role of the Smyd family is dynamic, targeting unique histone residues associated with both transcriptional activation and repression...
February 2018: Current Opinion in Physiology
https://www.readbyqxmd.com/read/29434999/functions-of-nuclear-actin-binding-proteins-in-human-cancer
#9
Xinyi Yang, Ying Lin
Nuclear actin-binding proteins (ABPs) perform distinguishable functions compared with their cytoplasmic counterparts in extensive activities of living cells. In addition to the ability to regulate actin cytoskeleton dynamics, nuclear ABPs are associated with multiple nuclear biological processes, including chromatin remodeling, gene transcriptional regulation, DNA damage response, nucleocytoplasmic trafficking and nuclear structure maintenance. The nuclear translocation of ABPs is affected by numerous intracellular or extracellular stimuli, which may lead to developmental malformation, tumor initiation, tumor progression and metastasis...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29434220/the-plant-specific-histone-residue-phe41-is-important-for-genome-wide-h3-1-distribution
#10
Li Lu, Xiangsong Chen, Shuiming Qian, Xuehua Zhong
The dynamic incorporation of histone variants influences chromatin structure and many biological processes. In Arabidopsis, the canonical variant H3.1 differs from H3.3 in four residues, one of which (H3.1Phe41) is unique and conserved in plants. However, its evolutionary significance remains unclear. Here, we show that Phe41 first appeared in H3.1 in ferns and became stable during land plant evolution. Unlike H3.1, which is specifically enriched in silent regions, H3.1F41Y variants gain ectopic accumulation at actively transcribed regions...
February 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29430581/plagioneurin-b-a-potent-isolated-compound-induces-apoptotic-signalling-pathways-and-cell-cycle-arrest-in-ovarian-cancer-cells
#11
Noraziah Nordin, Nazia Abdul Majid, Rozana Othman, Fatima Abdelmutaal Ahmed Omer, Muhammad Nazil Afiq Nasharuddin, Najihah Mohd Hashim
Plagioneurin B belongs to acetogenin group has well-established class of compounds. Acetogenin group has attracted worldwide attention in the past few years due their biological abilities as inhibitors for several types of tumour cells. Plagioneurin B was isolated via conventional chromatography and tested for thorough mechanistic apoptosis activity on human ovarian cancer cells (CAOV-3). Its structure was also docked at several possible targets using Autodock tools software. Our findings showed that plagioneurin B successfully inhibits the growth of CAOV-3 cells at IC50 of 0...
February 12, 2018: Apoptosis: An International Journal on Programmed Cell Death
https://www.readbyqxmd.com/read/29429977/zfx-acts-as-a-transcriptional-activator-in-multiple-types-of-human-tumors-by-binding-downstream-of-transcription-start-sites-at-the-majority-of-cpg-island-promoters
#12
Suhn Kyong Rhie, Lijun Yao, Zhifei Luo, Heather Witt, Shannon Schreiner, Yu Guo, Andrew A Perez, Peggy J Farnham
High expression of the transcription factor ZFX is correlated with proliferation, tumorigenesis, and patient survival in multiple types of human cancers. However, the mechanism by which ZFX influences transcriptional regulation has not been determined. We performed ChIP-seq in four cancer cell lines (representing kidney, colon, prostate, and breast cancers) to identify ZFX binding sites throughout the human genome. We identified ~9,000 ZFX binding sites and found that the majority of the sites are in CpG island promoters...
February 2, 2018: Genome Research
https://www.readbyqxmd.com/read/29422688/lc-ms-ms-based-quantitative-study-of-the-acyl-group-and-site-selectivity-of-human-sirtuins-to-acylated-nucleosomes
#13
Kana Tanabe, Jiaan Liu, Daiki Kato, Hitoshi Kurumizaka, Kenzo Yamatsugu, Motomu Kanai, Shigehiro A Kawashima
Chromatin structure and gene expression are dynamically regulated by posttranslational modifications of histones. Recent advance in mass spectrometry has identified novel types of lysine acylations, such as butyrylation and malonylation, whose functions and regulations are likely different from those of acetylation. Sirtuins, nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases, catalyze various deacylations. However, it is poorly understood how distinct sirtuins regulate the histone acylation states of nucleosomes that have many lysine residues...
February 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29422670/alterations-of-specific-chromatin-conformation-affect-atra-induced-leukemia-cell-differentiation
#14
Yanjian Li, Yi He, Zhengyu Liang, Yang Wang, Fengling Chen, Mohamed Nadhir Djekidel, Guipeng Li, Xu Zhang, Shuqin Xiang, Zejun Wang, Juntao Gao, Michael Q Zhang, Yang Chen
Chromatin conformation plays a key role in regulating gene expression and controlling cell differentiation. However, the whole-genome chromatin conformation changes that occur during leukemia cell differentiation are poorly understood. Here, we characterized the changes in chromatin conformation, histone states, chromatin accessibility, and gene expression using an all-trans retinoic acid (ATRA)-induced HL-60 cell differentiation model. The results showed that the boundaries of topological associated domains (TADs) were stable during differentiation; however, the chromatin conformations within several specific TADs were obviously changed...
February 8, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29419817/investigation-of-the-spatial-structure-and-interactions-of-the-genome-at-sub-kilobase-pair-resolution-using-t2c
#15
Petros Kolovos, Rutger W W Brouwer, Christel E M Kockx, Michael Lesnussa, Nick Kepper, Jessica Zuin, A M Ali Imam, Harmen J G van de Werken, Kerstin S Wendt, Tobias A Knoch, Wilfred F J van IJcken, Frank Grosveld
Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5C and Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, interactomes and structural changes associated with gene regulation, the cell cycle, and cell survival and development. Here, we present the protocol for T2C based on capture, describing all experimental steps and bio-informatic tools in full detail. T2C offers high resolution, a large dynamic interaction frequency range and a high signal-to-noise ratio...
March 2018: Nature Protocols
https://www.readbyqxmd.com/read/29415456/bet-family-protein-brd4-an-emerging-actor-in-nf%C3%AE%C2%BAb-signaling-in-inflammation-and-cancer
#16
REVIEW
Azadeh Hajmirza, Anouk Emadali, Arnaud Gauthier, Olivier Casasnovas, Rémy Gressin, Mary B Callanan
NFκB (Nuclear Factor- κ -light-chain-enhancer of activated B cells) signaling elicits global transcriptional changes by activating cognate promoters and through genome-wide remodeling of cognate regulatory elements called "super enhancers". BET (Bromodomain and Extra-Terminal domain) protein family inhibitor studies have implicated BET protein member BRD4 and possibly other BET proteins in NFκB-dependent promoter and super-enhancer modulation. Members of the BET protein family are known to bind acetylated chromatin to facilitate access by transcriptional regulators to chromatin, as well as to assist the activity of transcription elongation complexes via CDK9/pTEFb...
February 6, 2018: Biomedicines
https://www.readbyqxmd.com/read/29412139/role-of-the-visual-experience-dependent-nascent-proteome-in-neuronal-plasticity
#17
Han-Hsuan Liu, Daniel B Mcclatchy, Lucio Schiapparelli, Wanhua Shen, John R Yates, Hollis T Cline
Experience-dependent synaptic plasticity refines brain circuits during development. To identify novel protein synthesis-dependent mechanisms contributing to experience-dependent plasticity, we conducted a quantitative proteomic screen of the nascent proteome in response to visual experience in Xenopus optic tectum using bio-orthogonal metabolic labeling (BONCAT). We identified 83 differentially synthesized candidate plasticity proteins (CPPs). The CPPs form strongly interconnected networks and are annotated to a variety of biological functions, including RNA splicing, protein translation, and chromatin remodeling...
February 7, 2018: ELife
https://www.readbyqxmd.com/read/29408992/reconstructing-spatial-organizations-of-chromosomes-through-manifold-learning
#18
Guangxiang Zhu, Wenxuan Deng, Hailin Hu, Rui Ma, Sai Zhang, Jinglin Yang, Jian Peng, Tommy Kaplan, Jianyang Zeng
Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility...
February 2, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29407793/promoter-analysis-and-transcriptional-regulation-of-human-carbonic-anhydrase-viii-gene-in-a-merrf-disease-cell-model
#19
Che-Min Lo, Yi-Shing Ma, Yau-Huei Wei, Benjamin Y T Hsieh, Mingli Hsieh
Myoclonic epilepsy with ragged-red fibers (MERRF) is a maternally inherited mitochondrial neuromuscular disease. We previously reported a significant decrease of mRNA and protein levels of nuclear DNA-encoded carbonic anhydrase VIII (CA8) in MERRF cybrids harboring A8344G mutation in mitochondrial DNA (mtDNA). In this study, we established a reporter construct of luciferase gene-carrying hCA8 promoter containing several putative transcription factor-binding sites, including GC-box, AP-2 and TATA-binding element in the 5'flanking region of the hCA8 gene...
January 31, 2018: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29401683/epigenetics-and-micrornas-in-cancer
#20
REVIEW
Alice Ramassone, Sara Pagotto, Angelo Veronese, Rosa Visone
The ability to reprogram the transcriptional circuitry by remodeling the three-dimensional structure of the genome is exploited by cancer cells to promote tumorigenesis. This reprogramming occurs because of hereditable chromatin chemical modifications and the consequent formation of RNA-protein-DNA complexes that represent the principal actors of the epigenetic phenomena. In this regard, the deregulation of a transcribed non-coding RNA may be both cause and consequence of a cancer-related epigenetic alteration...
February 3, 2018: International Journal of Molecular Sciences
keyword
keyword
32590
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"