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ChIP-Seq

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https://www.readbyqxmd.com/read/29331085/verification-of-dna-motifs-in-arabidopsis-using-crispr-cas9-mediated-mutagenesis
#1
Chenlong Li, Chen Chen, Huhui Chen, Suikang Wang, Xuemei Chen, Yuhai Cui
Transcription factors (TFs) and chromatin-modifying factors (CMFs) access chromatin by recognizing specific DNA motifs in their target genes. Chromatin Immunoprecipitation followed by next generation sequencing (ChIP-seq) has been widely used to discover the potential DNA binding motifs for both TFs and CMFs. Yet, an in vivo method for verifying DNA motifs captured by ChIP-seq is lacking in plants. Here, we describe the use of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) to verify DNA motifs in their native genomic context in Arabidopsis...
January 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29330416/virtual-genome-walking-across-the-32%C3%A2-gb-ambystoma-mexicanum-genome-assembling-gene-models-and-intronic-sequence
#2
Teri Evans, Andrew D Johnson, Matthew Loose
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329517/genome-wide-analyses-of-direct-target-genes-of-four-rice-nac-domain-transcription-factors-involved-in-drought-tolerance
#3
Pil Joong Chung, Harin Jung, Yang Do Choi, Ju-Kon Kim
BACKGROUND: Plant stress responses and mechanisms determining tolerance are controlled by diverse sets of genes. Transcription factors (TFs) have been implicated in conferring drought tolerance under drought stress conditions, and the identification of their target genes can elucidate molecular regulatory networks that orchestrate tolerance mechanisms. RESULTS: We generated transgenic rice plants overexpressing the 4 rice TFs, OsNAC5, 6, 9, and 10, under the control of the root-specific RCc3 promoter...
January 12, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29325932/riboflavin-attenuates-myocardial-injury-via-lsd1-mediated-crosstalk-between-phospholipid-metabolism-and-histone-methylation-in-mice-with-experimental-myocardial-infarction
#4
Peng Wang, Fan Fan, Xiao Li, Xiaolei Sun, Leilei Ma, Jian Wu, Cheng Shen, Hong Zhu, Zhen Dong, Cong Wang, Shuqi Zhang, Xiaona Zhao, Xin Ma, Yunzeng Zou, Kai Hu, Aijun Sun, Junbo Ge
The underlying mechanisms responsible for the cardioprotective effects of riboflavin remain elusive. Current study tested the hypothesis that riboflavin protects injured myocardium via epigenetic modification of LSD1. Here we showed that myocardial injury was attenuated and cardiac function was improved in riboflavin-treated mice with experimental myocardial infarction (MI), while these protective effects of riboflavin could be partly blocked by cotreatment with LSD1 inhibitor. Riboflavin also reduced apoptosis in hypoxic (1% oxygen) H9C2 cell lines...
January 8, 2018: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/29325558/systematic-target-function-annotation-of-human-transcription-factors
#5
Yong Fuga Li, Russ B Altman
BACKGROUND: Transcription factors (TFs), the key players in transcriptional regulation, have attracted great experimental attention, yet the functions of most human TFs remain poorly understood. Recent capabilities in genome-wide protein binding profiling have stimulated systematic studies of the hierarchical organization of human gene regulatory network and DNA-binding specificity of TFs, shedding light on combinatorial gene regulation. We show here that these data also enable a systematic annotation of the biological functions and functional diversity of TFs...
January 10, 2018: BMC Biology
https://www.readbyqxmd.com/read/29325176/dynamic-motif-occupancy-dynamo-analysis-identifies-transcription-factors-and-their-binding-sites-driving-dynamic-biological-processes
#6
Zheng Kuang, Zhicheng Ji, Jef D Boeke, Hongkai Ji
Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. However, most methods are designed to predict TF binding sites only. We present a computational method, dynamic motif occupancy analysis (DynaMO), to infer important TFs and their spatiotemporal binding activities in dynamic biological processes using chromatin profiling data from multiple biological conditions such as time-course histone modification ChIP-seq data...
January 9, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29322784/bioinformatic-analysis-of-changes-in-rna-polymerase-ii-transcription-stimulated-by-estradiol-in-mcf7-cells
#7
J Wu, Y Cai, G Zhao
Estradiol (E2) is the most potent estrogen and RNA polymerase II (Pol II) regulates a great mass of gene expression. This study was designed to illustrate the mechanisms of estrogen-dependent human breast cancer (BC) through Pol II. ChIP-seq data, DNase-seq data and other sequencing data of human BC MCF-7 cells were downloaded from Gene Expression Omnibus database. Each of these datasets included one control and one E2 treated sample. Sequence alignment was performed and Pol II factor binding signal was determined...
2018: Neoplasma
https://www.readbyqxmd.com/read/29322418/analysis-of-histone-modifications-in-acute-myeloid-leukaemia-using-chromatin-immunoprecipitation
#8
Benjamin J Shields, Andrew Keniry, Marnie E Blewitt, Matthew P McCormack
Chromatin Immunoprecipitation (ChIP) using antibodies specific for histone modifications is a powerful technique for assessing the epigenetic states of cell populations by either quantitative PCR (ChIP-PCR) or next generation sequencing analysis (ChIP-Seq). Here we describe the procedure for ChIP of histone marks in myeloid leukaemia cell lines and the subsequent purification of genomic DNA associated with repressive and activating histone modifications for further analysis. This procedure can be widely applied to a variety of histone marks to assess both activating and repressive modifications in the context of myeloid leukaemia...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321660/activated-alk-signals-through-the-erk-etv5-ret-pathway-to-drive-neuroblastoma-oncogenesis
#9
Lucille Lopez-Delisle, Cécile Pierre-Eugène, Caroline Louis-Brennetot, Didier Surdez, Virginie Raynal, Sylvain Baulande, Valentina Boeva, Sandrine Grossetête-Lalami, Valérie Combaret, Michel Peuchmaur, Olivier Delattre, Isabelle Janoueix-Lerosey
Activating mutations of the ALK receptor occur in a subset of neuroblastoma tumors. We previously demonstrated that Alk mutations cooperate with MYCN overexpression to induce neuroblastoma in mice and identified Ret as being strongly upregulated in MYCN/Alkmut tumors. By a genetic approach in vivo, we now document an oncogenic cooperation between activated Ret and MYCN overexpression in neuroblastoma formation. We show that MYCN/RetM919T tumors exhibit histological features and expression profiles close to MYCN/Alkmut tumors...
January 11, 2018: Oncogene
https://www.readbyqxmd.com/read/29316219/characterization-of-a-foxg1-tle1-transcriptional-network-in-glioblastoma-initiating-cells
#10
Rola Dali, Federica Verginelli, Albena Pramatarova, Robert Sladek, Stefano Stifani
Glioblastoma (GBM) is the most common and deadly malignant brain cancer of glial cell origin, with a median patient survival of less than 20 months. Transcription factors FOXG1 and TLE1 promote GBM propagation by supporting maintenance of brain tumour initiating cells with stem-like properties. Here, we characterize FOXG1 and TLE1 target genes in glioblastoma patient-derived brain tumour initiating cells using ChIP-Seq and RNA-Seq approaches. These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival, chemotaxis and angiogenesis...
January 9, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/29312534/the-pax8-cistrome-in-epithelial-ovarian-cancer
#11
Emily K Adler, Rosario I Corona, Janet M Lee, Norma Rodriguez-Malave, Paulette Mhawech-Fauceglia, Heidi Sowter, Dennis J Hazelett, Kate Lawrenson, Simon A Gayther
PAX8 is a lineage-restricted transcription factor that is expressed in epithelial ovarian cancer (EOC) precursor tissues, and in the major EOC histotypes. Frequent overexpression of PAX8 in primary EOCs suggests this factor functions as an oncogene during tumorigenesis, however, the biological role of PAX8 in EOC development is poorly understood. We found that stable knockdown of PAX8 in EOC models significantly reduced cell proliferation and anchorage dependent growth in vitro, and attenuated tumorigenicity in vivo...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29305858/identification-of-a-candidate-enhancer-for-dmrt3-involved-in-spastic-cerebral-palsy-pathogenesis
#12
Naoto Kubota, Toshifumi Yokoyama, Nobuhiko Hoshi, Mikita Suyama
Cerebral palsy (CP) is a major neuronal disease and the most common movement disorder in children. Although environmental factors leading to CP have been greatly investigated, the genetic mechanism underlying CP is not well understood. Here we focused on two clinical reports that characterized a deletion involving the KANK1 gene locus in the 9p24.3 region. One report shows spastic CP and the other shows no spastic CP phenotype. Based on the epigenetic status and evolutionary conservation, we first found a functional genomic element at the noncoding region that was deleted only in patients with spastic CP...
January 3, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29298679/sequence-motif-finder-using-memetic-algorithm
#13
Jader M Caldonazzo Garbelini, André Y Kashiwabara, Danilo S Sanches
BACKGROUND: De novo prediction of Transcription Factor Binding Sites (TFBS) using computational methods is a difficult task and it is an important problem in Bioinformatics. The correct recognition of TFBS plays an important role in understanding the mechanisms of gene regulation and helps to develop new drugs. RESULTS: We here present Memetic Framework for Motif Discovery (MFMD), an algorithm that uses semi-greedy constructive heuristics as a local optimizer. In addition, we used a hybridization of the classic genetic algorithm as a global optimizer to refine the solutions initially found...
January 3, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29290775/nuclear-egfr-and-integrator-super-elongation-complex-concurrently-binds-to-immediate-early-genes-for-gene-transactivation
#14
Victor Chun-Lam Wong
The gene transactivation function of nuclear EGFR (nEGFR) has been studied by investigating the genomic co-occupancies of nEGFR and RNA Polymerase II (RNAPII). However, due to RNAPII pausing, the co-recruitment of RNAPII and nEGFR does not necessarily represent productive transactivation. In this study, we integrated gatekeepers of productive transcriptional elongation such as Integrator and Super Elongation Complex (SEC) to interrogate the function of nEGFR. By analyzing publicly available ChIP-seq and RNA-seq data, we aims to 1) explore the function of nEGFR, 2) unravel nEGFR target genes, and 3) discuss potential mechanisms of nEGFR chromatin recruitment...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29286469/generation-of-native-chromatin-immunoprecipitation-sequencing-libraries-for-nucleosome-density-analysis
#15
Alireza Lorzadeh, Rodrigo Lopez Gutierrez, Linda Jackson, Michelle Moksa, Martin Hirst
We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) experimental protocol compatible with a Gaussian mixture distribution based analysis methodology (nucleosome density ChIP-seq; ndChIP-seq) that enables the generation of combined measurements of micrococcal nuclease (MNase) accessibility with histone modification genome-wide. Nucleosome position and local density, and the posttranslational modification of their histone subunits, act in concert to regulate local transcription states...
December 12, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29285296/rna-sequencing-reveals-genome-wide-long-non-coding-rnas-profiling-associated-with-early-development-of-diabetic-nephropathy
#16
Wanxin Tang, Dongmei Zhang, Xiaoke Ma
Background: Diabetic nephropathy (DN) seriously threatens the lives of patients, and the mechanism of DN remains largely unknown because of the complex regulation between long non-coding RNA (lncRNA) and protein-coding genes. In early development of diabetic nephropathy (DN), pathogenesis remains largely unknown. Results: We used RNA-sequencing to profile protein-coding and lncRNA gene transcriptome of mouse kidney proximal tubular cells during early stage of DN at various time points...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29285248/super-enhancer-associated-rai14-is-a-new-potential-biomarker-in-lung-adenocarcinoma
#17
Chongze Yuan, Hong Hu, Muyu Kuang, Zongwei Chen, Xiaoting Tao, Shengjian Fang, Yihua Sun, Yawei Zhang, Haiquan Chen
Purpose: Tyrosine kinase inhibitors (TKIs) are widely used to treat lung adenocarcinoma patients with EGFR mutations or ALK-fusions. However, patients with wild-type genes or TKIs-resistant mutations lack effective therapeutic targets. Extensive studies reveal that super enhancer (SE), a large cis-regulatory element, is associated with key oncogenes in a variety of cancers. By comparing the effect of SE on lung adenocarcinoma cell lines with normal cell line, this work attempts to find new biomarkers and potential therapeutic targets for lung adenocarcinoma...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29284660/the-modern-resource-genome-wide-binding-profiles-for-hundreds-of-drosophila-and-caenorhabditis-elegans-transcription-factors
#18
Michelle M Kudron, Alec Victorsen, Louis Gevirtzman, LaDeana W Hillier, William W Fisher, Dionne Vafeados, Matt Kirkey, Ann S Hammonds, Jeffery Gersch, Haneen Ammouri, Martha L Wall, Jennifer Moran, David Steffen, Matt Szynkarek, Samantha Seabrook-Sturgis, Nader Jameel, Madhura Kadaba, Jaeda Patton, Robert Terrell, Mitch Corson, Timothy J Durham, Soo Park, Swapna Samanta, Mei Han, Jinrui Xu, Koon-Kiu Yan, Susan E Celniker, Kevin P White, Lijia Ma, Mark Gerstein, Valerie Reinke, Robert Waterston
In order to develop a catalog of regulatory sites in two major model organisms, Drosophilia melanogaster and Caenorhabditis elegans, the modERN consortium has systematically assayed the binding sites of transcription factors (TFs). Combined with data produced by our predecessor, modENCODE, we now have data for 262 TFs identifying 1.23M sites in the fly genome and 217 TFs identifying 0.67M sites in the worm genome. Because sites from different TFs are often overlapping and tightly clustered, they fall into 91,011 and 59,150 regions in the fly and worm, respectively, and these binding sites span as little as 8...
December 28, 2017: Genetics
https://www.readbyqxmd.com/read/29282222/a-kdm5-inhibitor-increases-global-h3k4-trimethylation-occupancy-and-enhances-the-biological-efficacy-of-5-aza-2-deoxycytidine
#19
Benjamin R Leadem, Ioannis Kagiampakis, Catherine Wilson, Tommy K Cheung, David Arnott, Patrick Trojer, Marie Classon, Hariharan Easwaran, Stephen B Baylin
The H3K4 demethylase KDM5B is amplified and overexpressed in luminal breast cancer, suggesting it might constitute a potential cancer therapy target. Here we characterize, in breast cancer cells, the molecular effects of a recently developed small-molecule inhibitor of the KDM5 family of proteins (KDM5i), either alone or in combination with the DNA demethylating agent 5-aza-2'-deoxycytidine (DAC). KDM5i treatment alone increased expression of a small number of genes, whereas combined treatment with DAC enhanced the effects of the latter for increasing expression of hundreds of DAC-responsive genes...
December 27, 2017: Cancer Research
https://www.readbyqxmd.com/read/29281953/argo_cuda-exhaustive-gpu-based-approach-for-motif-discovery-in-large-dna-datasets
#20
Oleg V Vishnevsky, Andrey V Bocharnikov, Nikolay A Kolchanov
The development of chromatin immunoprecipitation sequencing (ChIP-seq) technology has revolutionized the genetic analysis of the basic mechanisms underlying transcription regulation and led to accumulation of information about a huge amount of DNA sequences. There are a lot of web services which are currently available for de novo motif discovery in datasets containing information about DNA/protein binding. An enormous motif diversity makes their finding challenging. In order to avoid the difficulties, researchers use different stochastic approaches...
December 10, 2017: Journal of Bioinformatics and Computational Biology
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