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ChIP-Seq

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https://www.readbyqxmd.com/read/28922390/identifying-novel-transcription-factors-involved-in-the-inflammatory-response-by-using-binding-site-motif-scanning-in-genomic-regions-defined-by-histone-acetylation
#1
Peter S Askovich, Stephen A Ramsey, Alan H Diercks, Kathleen A Kennedy, Theo A Knijnenburg, Alan Aderem
The innate immune response to pathogenic challenge is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that act as master regulators of this response have been identified, the temporal complexity of gene expression changes in response to pathogen-associated molecular pattern receptor stimulation strongly suggest that additional layers of regulation remain to be uncovered. The evolved pathogen response program in mammalian innate immune cells is understood to reflect a compromise between the probability of clearing the infection and the extent of tissue damage and inflammatory sequelae it causes...
2017: PloS One
https://www.readbyqxmd.com/read/28921929/tumor-suppressive-mir-145-co-repressed-by-tcf4-%C3%AE-catenin-and-prc2-complexes-forms-double-negative-regulation-loops-with-its-negative-regulators-in-colorectal-cancer
#2
Wei Wang, Xin Xiao, Xu Chen, Yi Huo, Wen-Jin Xi, Zhi-Feng Lin, Dan Zhang, Yu-Fang Li, Fan Yang, Wei-Hong Wen, An-Gang Yang, Tao Wang
The frequently dysregulated Wnt/β-catenin signaling in different malignancies, by activation of its own or orchestration with other co-factors, regulates various oncogenic or tumor-suppressive genes. Among these genes, miRNAs, which are negative posttranscriptional regulators, are also embedded in the Wnt signaling network. Different from the Wnt-induced oncogenic miRNAs, the specific mechanism underlying the Wnt-repressed tumor-suppressive miRNAs is much less understood. In the present study, firstly by analyzing a ChIP-seq dataset against TCF4, the core transcription factor for initiation of Wnt signaling in colorectal cancer (CRC) cells, we screened out several tumor-suppressive miRNAs potentially regulated by Wnt signaling...
September 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28916725/characterization-of-enhancers-and-the-role-of-the-transcription-factor-klf7-in-regulating-corneal-epithelial-differentiation
#3
Rachel Herndon Klein, William Hu, Ghaidaa Kashgari, Ziguang Lin, Tuyen Nguyen, Michael Doan, Bogi Andersen
During tissue development, transcription factors bind regulatory DNA regions called enhancers, often located at great distances from the genes they regulate, to control gene expression. The enhancer landscape during embryonic stem cell differentiation has been well characterized. By contrast, little is known about the shared and unique enhancer regulatory mechanisms in different ectodermally derived epithelial cells. Here, we use ChIP-seq to identify domains enriched for histone marks H3K4me3, H3K4me1, and H3K27ac, and define for the first time the super enhancers and typical enhancers active in primary human corneal epithelial cells...
September 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28915555/identification-of-a-p53-repressed-gene-module-in-breast-cancer-cells
#4
Takafumi Miyamoto, Chizu Tanikawa, Varalee Yodsurang, Yao-Zhong Zhang, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Koichi Matsuda
The p53 protein is a sophisticated transcription factor that regulates dozens of target genes simultaneously in accordance with the cellular circumstances. Although considerable efforts have been made to elucidate the functions of p53-induced genes, a holistic understanding of the orchestrated signaling network repressed by p53 remains elusive. Here, we performed a systematic analysis to identify simultaneously regulated p53-repressed genes in breast cancer cells. Consequently, 28 genes were designated as the p53-repressed gene module, whose gene components were simultaneously suppressed in breast cancer cells treated with Adriamycin...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28911122/data-exploration-quality-control-and-statistical-analysis-of-chip-exo-nexus-experiments
#5
Rene Welch, Dongjun Chung, Jeffrey Grass, Robert Landick, Sündüz Keles
ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28911105/a-novel-nucleoid-associated-protein-coordinates-chromosome-replication-and-chromosome-partition
#6
James A Taylor, Gaël Panis, Patrick H Viollier, Gregory T Marczynski
We searched for regulators of chromosome replication in the cell cycle model Caulobacter crescentus and found a novel DNA-binding protein (GapR) that selectively aids the initiation of chromosome replication and the initial steps of chromosome partitioning. The protein binds the chromosome origin of replication (Cori) and has higher-affinity binding to mutated Cori-DNA that increases Cori-plasmid replication in vivo. gapR gene expression is essential for normal rapid growth and sufficient GapR levels are required for the correct timing of chromosome replication...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28899340/regulatory-network-changes-between-cell-lines-and-their-tissues-of-origin
#7
Camila M Lopes-Ramos, Joseph N Paulson, Cho-Yi Chen, Marieke L Kuijjer, Maud Fagny, John Platig, Abhijeet R Sonawane, Dawn L DeMeo, John Quackenbush, Kimberly Glass
BACKGROUND: Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tissues, a systematic overview of the differences between the regulatory processes of a cell line and those of its tissue of origin has not been conducted. The RNA-Seq data generated by the GTEx project is the first available data resource in which it is possible to perform a large-scale transcriptional and regulatory network analysis comparing cell lines with their tissues of origin...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28894735/navigating-the-functional-landscape-of-transcription-factors-via-non-negative-tensor-factorization-analysis-of-medline-abstracts
#8
Sujoy Roy, Daqing Yun, Behrouz Madahian, Michael W Berry, Lih-Yuan Deng, Daniel Goldowitz, Ramin Homayouni
In this study, we developed and evaluated a novel text-mining approach, using non-negative tensor factorization (NTF), to simultaneously extract and functionally annotate transcriptional modules consisting of sets of genes, transcription factors (TFs), and terms from MEDLINE abstracts. A sparse 3-mode term × gene × TF tensor was constructed that contained weighted frequencies of 106,895 terms in 26,781 abstracts shared among 7,695 genes and 994 TFs. The tensor was decomposed into sub-tensors using non-negative tensor factorization (NTF) across 16 different approximation ranks...
2017: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/28894104/nfatc1-controls-the-cytotoxicity-of-cd8-t-cells
#9
Stefan Klein-Hessling, Khalid Muhammad, Matthias Klein, Tobias Pusch, Ronald Rudolf, Jessica Flöter, Musga Qureischi, Andreas Beilhack, Martin Vaeth, Carsten Kummerow, Christian Backes, Rouven Schoppmeyer, Ulrike Hahn, Markus Hoth, Tobias Bopp, Friederike Berberich-Siebelt, Amiya Patra, Andris Avots, Nora Müller, Almut Schulze, Edgar Serfling
Cytotoxic T lymphocytes are effector CD8(+) T cells that eradicate infected and malignant cells. Here we show that the transcription factor NFATc1 controls the cytotoxicity of mouse cytotoxic T lymphocytes. Activation of Nfatc1 (-/-) cytotoxic T lymphocytes showed a defective cytoskeleton organization and recruitment of cytosolic organelles to immunological synapses. These cells have reduced cytotoxicity against tumor cells, and mice with NFATc1-deficient T cells are defective in controlling Listeria infection...
September 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28891464/concentration-dependent-chromatin-states-induced-by-the-bicoid-morphogen-gradient
#10
Colleen E Hannon, Shelby A Blythe, Eric F Wieschaus
In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context...
September 11, 2017: ELife
https://www.readbyqxmd.com/read/28889076/genesurv-an-interactive-web-based-tool-for-survival-analysis-in-genomics-research
#11
Selcuk Korkmaz, Dincer Goksuluk, Gokmen Zararsiz, Sevilay Karahan
Survival analysis methods are often used in cancer studies. It has been shown that the combination of clinical data with genomics increases the predictive performance of survival analysis methods. But, this leads to a high-dimensional data problem. Fortunately, new methods have been developed in the last decade to overcome this problem. However, there is a strong need for easily accessible, user-friendly and interactive tool to perform survival analysis in the presence of genomics data. We developed an open-source and freely available web-based tool for survival analysis methods that can deal with high-dimensional data...
September 5, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28887412/enzymatic-modules-of-the-saga-chromatin-modifying-complex-play-distinct-roles-in-drosophila-gene-expression-and-development
#12
Xuanying Li, Christopher W Seidel, Leanne T Szerszen, Jeffrey J Lange, Jerry L Workman, Susan M Abmayr
The Spt-Ada-Gcn5-acetyltransferase (SAGA) chromatin-modifying complex is a transcriptional coactivator that contains four different modules of subunits. The intact SAGA complex has been well characterized for its function in transcription regulation and development. However, little is known about the roles of individual modules within SAGA and whether they have any SAGA-independent functions. Here we demonstrate that the two enzymatic modules of Drosophila SAGA are differently required in oogenesis. Loss of the histone acetyltransferase (HAT) activity blocks oogenesis, while loss of the H2B deubiquitinase (DUB) activity does not...
September 8, 2017: Genes & Development
https://www.readbyqxmd.com/read/28886276/systems-approach-to-the-pharmacological-actions-of-hdac-inhibitors-reveals-ep300-activities-and-convergent-mechanisms-of-regulation-in-diabetes
#13
Haloom Rafehi, Antony Kaspi, Mark Ziemann, Jun Okabe, Tom C Karagiannis, Assam El-Osta
Given the skyrocketing costs to develop new drugs, repositioning of approved drugs, such as histone deacetylase (HDAC) inhibitors, may be a promising strategy to develop novel therapies. However, a gap exists in the understanding and advancement of these agents to meaningful translation for which new indications may emerge. To address this, we performed systems-level analyses of 33 independent HDAC inhibitor microarray studies. Based on network analysis, we identified enrichment for pathways implicated in metabolic syndrome and diabetes (insulin receptor signaling, lipid metabolism, immunity and trafficking)...
September 8, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28885181/chip-seq-a-powerful-tool-for-studying-protein-dna-interactions-in-plants
#14
Xifeng Chen, Vijai Bhadauria, Bojun Ma
DNA-binding proteins, including transcription factors, epigenetic and chromatin modifiers, control gene expressions in plants. To pinpoint the binding sits of DNA-binding proteins in genome is crucial for decoding gene regulatory networks. Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-Seq) is a widely used approach to identify the DNA regions bound by a specific protein in vivo. The information generated from ChIP-Seq has tremendously advanced our understanding on the mechanism of transcription factors, cofactors and histone modifications in regulating gene expression...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28881977/denoising-genome-wide-histone-chip-seq-with-convolutional-neural-networks
#15
Pang Wei Koh, Emma Pierson, Anshul Kundaje
Motivation: Chromatin immune-precipitation sequencing (ChIP-seq) experiments are commonly used to obtain genome-wide profiles of histone modifications associated with different types of functional genomic elements. However, the quality of histone ChIP-seq data is affected by many experimental parameters such as the amount of input DNA, antibody specificity, ChIP enrichment and sequencing depth. Making accurate inferences from chromatin profiling experiments that involve diverse experimental parameters is challenging...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881808/cxcl13-is-androgen-responsive-and-involved-in-androgen-induced-prostate-cancer-cell-migration-and-invasion
#16
Long Fan, Qingyi Zhu, Li Liu, Cuicui Zhu, Haojie Huang, Shan Lu, Ping Liu
Androgen receptor (AR) is a key transcription factor playing a critical role in prostate cancer (PCa) initiation and progression. However, the molecular mechanisms of AR action in prostate cancer are not very clear. CXCL13, known as B cell attracting chemokine1 (BCA-1), is a member of CXC chemokine family and relevant to cancer metastasis. This study shows that CXCL13 is an androgen-responsive gene and involved in AR-induced PCa cell migration and invasion. In clinical specimens, expression of CXCL13 in PCa tissues is markedly higher than that in adjacent normal tissues...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28874528/ein2-mediates-direct-regulation-of-histone-acetylation-in-the-ethylene-response
#17
Fan Zhang, Likai Wang, Bin Qi, Bo Zhao, Eun Esther Ko, Nathaniel D Riggan, Kevin Chin, Hong Qiao
Ethylene gas is essential for developmental processes and stress responses in plants. Although the membrane-bound protein EIN2 is critical for ethylene signaling, the mechanism by which the ethylene signal is transduced remains largely unknown. Here we show the levels of H3K14Ac and H3K23Ac are correlated with the levels of EIN2 protein and demonstrate EIN2 C terminus (EIN2-C) is sufficient to rescue the levels of H3K14/23Ac of ein2-5 at the target loci, using CRISPR/dCas9-EIN2-C. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and ChIP-reChIP-seq analyses revealed that EIN2-C associates with histone partially through an interaction with EIN2 nuclear-associated protein1 (ENAP1), which preferentially binds to the genome regions that are associated with actively expressed genes both with and without ethylene treatments...
September 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28872116/chromatin-immunoprecipitation-chip-protocol-for-low-abundance-embryonic-samples
#18
Rizwan Rehimi, Michaela Bartusel, Francesca Solinas, Janine Altmüller, Alvaro Rada-Iglesias
Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes at a given locus or on a genome-wide scale. The combination of ChIP assays with next-generation sequencing (i.e., ChIP-Seq) is a powerful approach to globally uncover gene regulatory networks and to improve the functional annotation of genomes, especially of non-coding regulatory sequences. ChIP protocols normally require large amounts of cellular material, thus precluding the applicability of this method to investigating rare cell types or small tissue biopsies...
August 29, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28860350/identification-of-distinct-mutational-patterns-and-new-driver-genes-in-oesophageal-squamous-cell-carcinomas-and-adenocarcinomas
#19
De-Chen Lin, Huy Q Dinh, Jian-Jun Xie, Anand Mayakonda, Tiago Chedraoui Silva, Yan-Yi Jiang, Ling-Wen Ding, Jian-Zhong He, Xiu-E Xu, Jia-Jie Hao, Ming-Rong Wang, Chunquan Li, Li-Yan Xu, En-Min Li, Benjamin P Berman, H Phillip Koeffler
OBJECTIVES: Oesophageal squamous cell carcinoma (OSCC) and adenocarcinoma (OAC) are distinct cancers in terms of a number of clinical and epidemiological characteristics, complicating the design of clinical trials and biomarker developments. We analysed 1048 oesophageal tumour-germline pairs from both subtypes, to characterise their genomic features, and biological and clinical significance. DESIGN: Previously exome-sequenced samples were re-analysed to identify significantly mutated genes (SMGs) and mutational signatures...
August 31, 2017: Gut
https://www.readbyqxmd.com/read/28859475/identification-of-slirp-as-a-g-quadruplex-binding-protein
#20
Preston Williams, Lin Li, Xiaoli Dong, Yinsheng Wang
The guanine quadruplex (G4) structure in DNA is a secondary structure motif that plays important roles in DNA replication, transcriptional regulation, and maintenance of genomic stability. Here, we employed a quantitative mass spectrometry-based approach to profile the interaction proteomes of three well-defined G4 structures derived from the human telomere and the promoters of cMYC and cKIT genes. We identified SLIRP as a novel G4-interacting protein. We also demonstrated that the protein could bind directly with G4 DNA with Kd values in the low nanomolar range and revealed that the robust binding of the protein toward G4 DNA requires its RRM domain...
September 13, 2017: Journal of the American Chemical Society
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