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Chromatin-associated RNA

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https://www.readbyqxmd.com/read/29908064/unconventional-rna-binding-proteins-an-uncharted-zone-in-rna-biology
#1
REVIEW
Waleed S Albihlal, André P Gerber
RNA-binding proteins play essential roles in the post-transcriptional regulation of gene expression. While hundreds of RNA-binding proteins can be predicted computationally, the recent introduction of proteome-wide approaches has dramatically expanded the repertoire of proteins interacting with RNA. Besides canonical RNA-binding proteins that contain characteristic RNA-binding domains, many proteins that lack such domains but have other well-characterised cellular functions were identified; including metabolic enzymes, heat shock proteins, kinases, as well as transcription factors and chromatin-associated proteins...
June 16, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29907651/lncrna-papas-tethered-to-the-rdna-enhancer-recruits-hypophosphorylated-chd4-nurd-to-repress-rrna-synthesis-at-elevated-temperatures
#2
Zhongliang Zhao, Nevcin Sentürk, Chenlin Song, Ingrid Grummt
Attenuation of pre-rRNA synthesis in response to elevated temperature is accompanied by increased levels of PAPAS ("promoter and pre-rRNA antisense") , a long noncoding RNA (lncRNA) that is transcribed in an orientation antisense to pre-rRNA. Here we show that PAPAS interacts directly with DNA, forming a DNA-RNA triplex structure that tethers PAPAS to a stretch of purines within the enhancer region, thereby guiding associated CHD4/NuRD (nucleosome remodeling and deacetylation) to the rDNA promoter...
June 15, 2018: Genes & Development
https://www.readbyqxmd.com/read/29905868/casein-kinase-2-mediated-phosphorylation-of-spt6-modulates-histone-dynamics-and-regulates-spurious-transcription
#3
Emmanuelle Gouot, Wajid Bhat, Anne Rufiange, Eric Fournier, Eric Paquet, Amine Nourani
CK2 is an essential protein kinase implicated in various cellular processes. In this study, we address a potential role of this kinase in chromatin modulations associated with transcription. We found that CK2 depletion from yeast cells leads to replication-independent increase of histone H3K56 acetylation and global activation of H3 turnover in coding regions. This suggests a positive role of CK2 in maintenance/recycling of the histone H3/H4 tetramers during transcription. Interestingly, strand-specific RNA-seq analyses show that CK2 inhibits global cryptic promoters driving both sense and antisense transcription...
June 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29899857/role-of-p27-kip1-as-a-transcriptional-regulator
#4
REVIEW
Oriol Bachs, Edurne Gallastegui, Serena Orlando, Anna Bigas, José Manuel Morante-Redolat, Joan Serratosa, Isabel Fariñas, Rosa Aligué, Maria Jesús Pujol
The protein p27Kip1 is a member of the Cip/Kip family of cyclin-dependent kinase (Cdk) inhibitors. It interacts with both the catalytic and the regulatory subunit (cyclin) and introduces a region into the catalytic cleave of the Cdk inducing its inactivation. Its inhibitory capacity can be modulated by specific tyrosine phosphorylations. p27Kip1 also behaves as a transcriptional regulator. It associates with specific chromatin domains through different transcription factors. ChIP on chip, ChIP-seq and expression microarray analysis allowed the identification of the transcriptional programs regulated by p27Kip1 ...
May 25, 2018: Oncotarget
https://www.readbyqxmd.com/read/29899136/neural-differentiation-selection-and-transcriptomic-profiling-of-human-neuromesodermal-progenitors-like-cells-in-vitro
#5
Laure Verrier, Lindsay Davidson, Marek Gierliński, Alwyn Dady, Kate G Storey
Robust protocols for directed differentiation of human pluripotent cells are required to determine whether mechanisms operating in model organisms are relevant to our own development. Recent work in vertebrate embryos has identified neuromesodermal progenitors as a bipotent cell population that contributes to paraxial mesoderm and spinal cord. However, precise protocols for in vitro differentiation of human spinal cord progenitors are lacking. Informed by signalling in amniote embryos, we show here that transient dual-SMAD inhibition, together with retinoic acid (dSMADi-RA), provides rapid and reproducible induction of human spinal cord progenitors from neuromesodermal progenitor-like cells...
June 13, 2018: Development
https://www.readbyqxmd.com/read/29898995/ews-ets-driven-ewing-sarcoma-requires-bet-bromodomain-proteins
#6
Paradesi Naidu Gollavilli, Aishwarya Pawar, Kari Wilder-Romans, Natesan Ramakrishnan, Carl G Engelke, Vijaya L Dommeti, Pranathi M Krishnamurthy, Archana Nallasivam, Ingrid J Apel, Tianlei Xu, Zhaohui Qin, Felix Y Feng, Irfan A Asangani
The EWS/ETS fusion transcription factors drive Ewing sarcoma (EWS) by orchestrating an oncogenic transcription program. Therapeutic targeting of EWS/ETS has been unsuccessful; however, identifying mediators of the EWS/ETS function could offer new therapeutic options. Here we describe the dependency of EWS/ETS-driven transcription upon chromatin reader BET bromdomain proteins and investigate the potential of BET inhibitors in treating EWS. EWS/FLI1 and EWS/ERG were found in a transcriptional complex with BRD4, and knockdown of BRD2/3/4 significantly impaired the oncogenic phenotype of EWS cells...
June 13, 2018: Cancer Research
https://www.readbyqxmd.com/read/29898919/overexpression-of-pp1-nipp1-limits-the-repair-capacity-of-dna-double-strand-breaks
#7
Claudia Winkler, Raphael Rouget, Dan Wu, Monique Beullens, Aleyde Van Eynde, Mathieu Bollen
The ubiquitously expressed nuclear protein NIPP1 recruits phosphoproteins for regulated dephosphorylation by associated protein phosphatase PP1. To bypass PP1 titration artifacts of NIPP1 overexpression we have engineered covalently linked fusions of PP1 and NIPP1, and demonstrate their potential to selectively explore the function of the PP1:NIPP1 holoenzyme. Using inducible stable cell lines we show that PP1-NIPP1 fusions cause replication stress in a manner that requires both PP1 activity and substrate recruitment via the ForkHead Associated domain of NIPP1...
June 13, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29898790/an-enchip-system-for-the-analysis-of-bacterial-genome-functions
#8
Toshitsugu Fujita, Miyuki Yuno, Hodaka Fujii
OBJECTIVE: The engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) technology enables purification of specific genomic regions interacting with their associated molecules. In enChIP, the locus to be purified is first tagged with engineered DNA-binding molecules. An example of such engineered DNA-binding molecules to tag the locus of interest is the clustered regularly interspaced short palindromic repeats (CRISPR) system, consisting of a catalytically-inactive form of Cas9 (dCas9) and guide RNA (gRNA)...
June 14, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29895332/long-noncoding-rna-hulc-accelerates-liver-cancer-by-inhibiting-pten-via-autophagy-cooperation-to-mir15a
#9
Xiaoru Xin, Mengying Wu, Qiuyu Meng, Chen Wang, Yanan Lu, Yuxin Yang, Xiaonan Li, Qidi Zheng, Hu Pu, Xin Gui, Tianming Li, Jiao Li, Song Jia, Dongdong Lu
BACKGROUND: Long noncoding RNA HULC is highly up-regulation in human hepatocellular carcinoma (HCC). However, the functions of HULC in hepatocarcinogenesis remains unclear. METHODS: RT-PCR, Western blotting, Chromatin immunoprecipitation (CHIP) assay, RNA Immunoprecipitation (RIP) and tumorignesis test in vitro and in vivo were performed. RESULTS: HULC is negatively associated with expression of PTEN or miR15a in patients of human liver cancer...
June 12, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29889205/carip-seq-and-chip-seq-methods-to-identify-chromatin-associated-rnas-and-protein-dna-interactions-in-embryonic-stem-cells
#10
Benjamin L Kidder
Embryonic stem (ES) cell self-renewal and differentiation is governed by extrinsic signals and intrinsic networks of transcription factors, epigenetic regulators, and post-translation modifications of histones that combinatorially influence the gene expression state of nearby genes. RNA has also been shown to interact with various proteins to regulate chromatin dynamics and gene expression. Chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) is a novel method to survey RNAs associated with chromatin proteins, while chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) is a powerful genomics technique to map the location of post-translational modification of histones, transcription factors, and epigenetic modifiers on a global-scale in ES cells...
May 25, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29877135/aging-in-the-brain-new-roles-of-epigenetics-in-cognitive-decline
#11
Jolie D Barter, Thomas C Foster
Gene expression in the aging brain depends on transcription signals generated by senescent physiology, interacting with genetic and epigenetic programs. In turn, environmental factors influence epigenetic mechanisms, such that an epigenetic-environmental link may contribute to the accumulation of cellular damage, susceptibility or resilience to stressors, and variability in the trajectory of age-related cognitive decline. Epigenetic mechanisms, DNA methylation and histone modifications, alter chromatin structure and the accessibility of DNA...
June 1, 2018: Neuroscientist: a Review Journal Bringing Neurobiology, Neurology and Psychiatry
https://www.readbyqxmd.com/read/29875794/chromatin-landscape-distinguishes-the-genomic-loci-of-hundreds-of-androgen-receptor-associated-lincrnas-from-the-loci-of-non-associated-lincrnas
#12
Lucas F daSilva, Felipe C Beckedorff, Ana C Ayupe, Murilo S Amaral, Vinícius Mesel, Alexandre Videira, Eduardo M Reis, João C Setubal, Sergio Verjovski-Almeida
Cell signaling events triggered by androgen hormone in prostate cells is dependent on activation of the androgen receptor (AR) transcription factor. Androgen hormone binding to AR promotes its displacement from the cytoplasm to the nucleus and AR binding to DNA motifs, thus inducing activatory and inhibitory transcriptional programs through a complex regulatory mechanism not yet fully understood. In this work, we performed RNA-seq deep-sequencing of LNCaP prostate cancer cells and found over 7000 expressed long intergenic non-coding RNAs (lincRNAs), of which ∼4000 are novel lincRNAs, and 258 lincRNAs have their expression activated by androgen...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29875274/redistribution-of-chh-methylation-and-small-interfering-rnas-across-the-genome-of-tomato-ddm1-mutants
#13
Shira Corem, Adi Doron-Faigenboim, Ophélie Jouffroy, Florian Maumus, Tzahi Arazi, Nicolas Bouché
In plants, cytosine methylation, an epigenetic mark critical for transposon silencing, is maintained over generations by key enzymes that directly methylate DNA and is facilitated by chromatin remodelers, like DECREASE IN DNA METHYLATION 1 (DDM1). Short-interfering RNAs (siRNAs) also mediate transposon DNA methylation through a process called RNA-directed DNA methylation (RdDM). In tomato (Solanum lycopersicum), siRNAs are primarily mapped to gene-rich chromosome arms, and not to pericentromeric regions as in Arabidopsis thaliana...
June 6, 2018: Plant Cell
https://www.readbyqxmd.com/read/29875242/-arabidopsis-histone-reader-emsy-like-1-binds-h3k36-and-suppresses-geminivirus-infection
#14
Tami Coursey, Milica Milutinovic, Elizabeth Regedanz, Jelena Brkljacic, David M Bisaro
Histone post-translational modifications (PTMs) impart information that regulates chromatin structure and activity. Their effects are mediated by histone reader proteins that bind specific PTMs to modify chromatin and/or recruit appropriate effectors to alter the chromatin landscape. Despite their crucial juxtaposition between information and functional outcome, relatively few plant histone readers have been identified, and nothing is known about their impact on viral chromatin and pathogenesis. We used the geminivirus Cabbage leaf curl virus (CaLCuV) as a model to functionally characterize two recently identified reader proteins, EMSY-LIKE 1 and 3 (EML1 and EML3), which contain Tudor-like Agenet domains predictive of histone PTM binding function...
June 6, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29874575/tau-activates-transposable-elements-in-alzheimer-s-disease
#15
Caiwei Guo, Hyun-Hwan Jeong, Yi-Chen Hsieh, Hans-Ulrich Klein, David A Bennett, Philip L De Jager, Zhandong Liu, Joshua M Shulman
Aging and neurodegenerative disease are characterized by genomic instability in neurons, including aberrant activation and mobilization of transposable elements (TEs). Integrating studies of human postmortem brain tissue and Drosophila melanogaster models, we investigate TE activation in association with Tau pathology in Alzheimer's disease (AD). Leveraging RNA sequencing from 636 human brains, we discover differential expression for several retrotransposons in association with neurofibrillary tangle burden and highlight evidence for global TE transcriptional activation among the long interspersed nuclear element 1 and endogenous retrovirus clades...
June 5, 2018: Cell Reports
https://www.readbyqxmd.com/read/29868581/a-decade-of-exploring-the-mammalian-sperm-epigenome-paternal-epigenetic-and-transgenerational-inheritance
#16
REVIEW
Alexandre Champroux, Julie Cocquet, Joëlle Henry-Berger, Joël R Drevet, Ayhan Kocer
The past decade has seen a tremendous increase in interest and progress in the field of sperm epigenetics. Studies have shown that chromatin regulation during male germline development is multiple and complex, and that the spermatozoon possesses a unique epigenome. Its DNA methylation profile, DNA-associated proteins, nucleo-protamine distribution pattern and non-coding RNA set up a unique epigenetic landscape which is delivered, along with its haploid genome, to the oocyte upon fertilization, and therefore can contribute to embryogenesis and to the offspring health...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29868118/rna-sequencing-of-primary-retinoblastoma-tumors-provides-new-insights-and-challenges-into-tumor-development
#17
Sailaja V Elchuri, Swetha Rajasekaran, Wayne O Miles
Retinoblastoma is rare tumor of the retina caused by the homozygous loss of the Retinoblastoma 1 tumor suppressor gene (RB1). Loss of the RB1 protein, pRB, results in de-regulated activity of the E2F transcription factors, chromatin changes and developmental defects leading to tumor development. Extensive microarray profiles of these tumors have enabled the identification of genes sensitive to pRB disruption, however, this technology has a number of limitations in the RNA profiles that they generate. The advent of RNA-sequencing has enabled the global profiling of all of the RNA within the cell including both coding and non-coding features and the detection of aberrant RNA processing events...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29864419/cigarette-smoke-induces-stem-cell-features-of-pancreatic-cancer-cells-via-paf1
#18
Rama Krishna Nimmakayala, Parthasarathy Seshacharyulu, Imayavaramban Lakshmanan, Satyanarayana Rachagani, Seema Chugh, Saswati Karmakar, Sanchita Rauth, Raghupathy Vengoji, Pranita Atri, Geoffrey A Talmon, Subodh M Lele, Lynette M Smith, Ishwor Thapa, Dhundy Bastola, Michel M Ouellette, Surinder K Batra, Moorthy P Ponnusamy
BACKGROUND & AIMS: Cigarette smoking is a major risk factor for pancreatic cancer. Aggressive pancreatic tumors contain cancer cells with stem cell features. We investigated whether cigarette smoke induces stem cell features in pancreatic cancer cells. METHODS: KrasG12D ; Pdx1-Cre (KC) mice were exposed to cigarette smoke or clean air (controls) for up to 20 weeks; pancreata were collected and analyzed by histology, quantitative reverse transcription PCR, and confocal immunofluorescence microscopy...
June 1, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29860334/swi-snf-interacts-with-cleavage-and-polyadenylation-factors-and-facilitates-pre-mrna-3-end-processing
#19
Simei Yu, Antonio Jordán-Pla, Antoni Gañez-Zapater, Shruti Jain, Anna Rolicka, Ann-Kristin Östlund Farrants, Neus Visa
SWI/SNF complexes associate with genes and regulate transcription by altering the chromatin at the promoter. It has recently been shown that these complexes play a role in pre-mRNA processing by associating at alternative splice sites. Here, we show that SWI/SNF complexes are involved also in pre-mRNA 3' end maturation by facilitating 3' end cleavage of specific pre-mRNAs. Comparative proteomics show that SWI/SNF ATPases interact physically with subunits of the cleavage and polyadenylation complexes in fly and human cells...
May 31, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29859899/long-non-coding-rnas-as-molecular-players-in-plant-defense-against-pathogens
#20
REVIEW
Madiha Zaynab, Mahpara Fatima, Safdar Abbas, Muhammad Umair, Yasir Sharif, Muhammad Ammar Raza
Long non-coding RNAs (lncRNAs) has significant role in of gene expression and silencing pathways for several biological processes in eukaryotes. lncRNAs has been reported as key player in remodeling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Host lncRNAs are reckoned as compulsory elements of plant defense. In response to pathogen attack, plants protect themselves with the help of lncRNAs -dependent immune systems in which lncRNAs regulate pathogen-associated molecular patterns (PAMPs) and other effectors...
May 31, 2018: Microbial Pathogenesis
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