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Vahid Jalili, Matteo Matteucci, Marco Masseroli, Marco J Morelli
No abstract text is available yet for this article.
March 13, 2018: Bioinformatics
Suhyung Cho, Donghui Choe, Eunju Lee, Sun Chang Kim, Bernhard Ø Palsson, Byung-Kwan Cho
Along with functional advances in the use of CRISPR/Cas9 for genome editing, endonuclease-deficient Cas9 (dCas9) has provided a versatile molecular tool for exploring gene functions. In principle, differences in cell phenotypes that result from the RNA-guided modulation of transcription levels by dCas9 are critical for inferring with gene function; however, the effect of intracellular dCas9 expression on bacterial morphology has not been systematically elucidated. Here, we observed unexpected morphological changes in Escherichia coli mediated by dCas9, which were then characterized using RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq)...
March 15, 2018: ACS Synthetic Biology
Kumaran Nagalingam, Michał T Lorenc, Sahana Manoli, Stephen L Cameron, Anthony R Clarke, Kevin J Dudley
Interactions between DNA and proteins located in the cell nucleus play an important role in controlling physiological processes by specifying, augmenting and regulating context-specific transcription events. Chromatin immunoprecipitation (ChIP) is a widely used methodology to study DNA-protein interactions and has been successfully used in various cell types for over three decades. More recently, by combining ChIP with genomic screening technologies and Next Generation Sequencing (e.g. ChIP-seq), it has become possible to profile DNA-protein interactions (including covalent histone modifications) across entire genomes...
2018: PloS One
David P Labbé, Myles Brown
Prostate cancer development involves corruption of the normal prostate transcriptional network, following deregulated expression or mutation of key transcription factors. Here, we provide an overview of the transcription factors that are important in normal prostate homeostasis (NKX3-1, p63, androgen receptor [AR]), primary prostate cancer (ETS family members, c-MYC), castration-resistant prostate cancer (AR, FOXA1), and AR-independent castration-resistant neuroendocrine prostate cancer (RB1, p53, N-MYC). We use functional (in vitro and in vivo) as well as clinical data to discuss evidence that unveils their roles in the initiation and progression of prostate cancer, with an emphasis on results of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq)...
March 12, 2018: Cold Spring Harbor Perspectives in Medicine
Marcelo Bueno Batista, Govind Chandra, Rose Adele Monteiro, Emanuel Maltempi de Souza, Ray Dixon
Bacteria adjust the composition of their electron transport chain (ETC) to efficiently adapt to oxygen gradients. This involves differential expression of various ETC components to optimize energy generation. In Herbaspirillum seropedicae, reprogramming of gene expression in response to oxygen availability is controlled at the transcriptional level by three Fnr orthologs. Here, we characterised Fnr regulons using a combination of RNA-Seq and ChIP-Seq analysis. We found that Fnr1 and Fnr3 directly regulate discrete groups of promoters (Groups I and II, respectively), and that a third group (Group III) is co-regulated by both transcription factors...
February 26, 2018: Nucleic Acids Research
Georgi K Marinov, Anshul Kundaje
Advances in the methods for detecting protein-DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput sequencing (ChIP-seq) as a readout for ChIP assays. In addition to the numerous other ways in which it is superior to arrays, by eliminating the need to design and manufacture them, sequencing also opened the door to carrying out comparative analyses of genome-wide transcription factor occupancy across species and studying chromatin biology in previously less accessible model and nonmodel organisms, thus allowing us to understand the evolution and diversity of regulatory mechanisms in unprecedented detail...
February 26, 2018: Briefings in Functional Genomics
Ryuichiro Nakato, Katsuhiko Shirahige
Motivation: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) can detect read-enriched DNA loci for point-source (e.g., transcription factor binding) and broad-source factors (e.g., various histone modifications). Although numerous quality metrics for ChIP-seq data have been developed, the 'peaks' thus obtained are still difficult to assess with respect to signal-to-noise ratio (S/N) and the percentage of false positives. Results: We developed a quality-assessment tool for ChIP-seq data, SSP (strand-shift profile), that quantifies S/N and peak reliability without peak calling...
March 8, 2018: Bioinformatics
Melda Onal, Alex H Carlson, Jeff D Thostenson, Nancy A Benkusky, Mark B Meyer, Seong M Lee, J Wesley Pike
Fibroblast growth factor 23 (FGF23) production is regulated by both calciotropic hormones and inflammation. Consistent with this, elevated FGF23 levels are associated with inflammatory markers as well as parathyroid hormone (PTH) in various disease states, including chronic kidney disease (CKD). However, the molecular mechanisms underpinning Fgf23 transcription in response to these regulators are largely unknown. We therefore utilized chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) data from an osteocyte cell line to identify potential regulatory regions of the Fgf23 gene...
January 2018: JBMR Plus
Chengjian Zhao, Gustavo A Gomez, Yuwei Zhao, Yu Yang, Dan Cao, Jing Lu, Hanshuo Yang, Shuo Lin
Glioblastoma multiforme (GBM) is characterized by extensive endothelial hyperplasia. Recent studies suggest that a subpopulation of endothelial cells originates via vasculogenesis by the transdifferentiation of GBM tumor cells into endothelial cells (endo-transdifferentiation). The molecular mechanism underlying this process remains poorly defined. Here, we show that the expression of ETS variant 2 (ETV2), a master regulator of endothelial cell development, is highly correlated with malignancy. Functional studies demonstrate that ETV2 is sufficient and necessary for the transdifferentiation of a subpopulation of CD133+/Nestin+ GBM/neural stem cells to an endothelial lineage...
2018: Signal Transduction and Targeted Therapy
Alessia Para, Ying Li, Gloria M Coruzzi
Chromatin immunoprecipitation (ChIP) is a widely used method to map the position of DNA-binding proteins such as histones and transcription factors (TFs) upon their interaction with particular regions of the genome. To examine the genomic distribution of a TF in specific cell types in response to a change in nitrogen concentration, we developed a micro-ChIP (μChIP) protocol that requires only ~5000 Arabidopsis cells transiently expressing the Arabidopsis TF Basic Leucine Zipper 1 (bZIP1) fused to the glucocorticoid receptor (GR) domain that mediates nuclear import in the presence of dexamethasone...
2018: Methods in Molecular Biology
Sandra Cortijo, Varodom Charoensawan, François Roudier, Philip A Wigge
Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) is a powerful technique to investigate in vivo transcription factor (TF) binding to DNA, as well as chromatin marks. Here we provide a detailed protocol for all the key steps to perform ChIP-seq in Arabidopsis thaliana roots, also working on other A. thaliana tissues and in most non-ligneous plants. We detail all steps from material collection, fixation, chromatin preparation, immunoprecipitation, library preparation, and finally computational analysis based on a combination of publicly available tools...
2018: Methods in Molecular Biology
Darren K Patten, Giacomo Corleone, Luca Magnani
Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become an essential tool for epigenetic scientists. ChIP-seq is used to map protein-DNA interactions and epigenetic marks such as histone modifications at the genome-wide level. Here we describe a complete ChIP-seq laboratory protocol (tailored toward processing tissue samples as well as cell lines) and the bioinformatic pipelines utilized for handling raw sequencing files through to peak calling.
2018: Methods in Molecular Biology
Alejandro Saettone, Jyoti Garg, Jean-Philippe Lambert, Syed Nabeel-Shah, Marcelo Ponce, Alyson Burtch, Cristina Thuppu Mudalige, Anne-Claude Gingras, Ronald E Pearlman, Jeffrey Fillingham
BACKGROUND: The chromatin remodelers of the SWI/SNF family are critical transcriptional regulators. Recognition of lysine acetylation through a bromodomain (BRD) component is key to SWI/SNF function; in most eukaryotes, this function is attributed to SNF2/Brg1. RESULTS: Using affinity purification coupled to mass spectrometry (AP-MS) we identified members of a SWI/SNF complex (SWI/SNFTt ) in Tetrahymena thermophila. SWI/SNFTt is composed of 11 proteins, Snf5Tt , Swi1Tt , Swi3Tt , Snf12Tt , Brg1Tt , two proteins with potential chromatin-interacting domains and four proteins without orthologs to SWI/SNF proteins in yeast or mammals...
March 9, 2018: Epigenetics & Chromatin
Pelin Balcik-Ercin, Metin Cetin, Irem Yalim-Camci, Gorkem Odabas, Nurettin Tokay, A Emre Sayan, Tamer Yagci
BACKGROUND: ZEB2 is a transcriptional repressor that regulates epithelial-to-mesenchymal transition (EMT) through binding to bipartite E-box motifs in gene regulatory regions. Despite the abundant presence of E-boxes within the human genome and the multiplicity of pathophysiological processes regulated during ZEB2-induced EMT, only a small fraction of ZEB2 targets has been identified so far. Hence, we explored genome-wide ZEB2 binding by chromatin immunoprecipitation-sequencing (ChIP-seq) under endogenous ZEB2 expression conditions...
March 7, 2018: Cellular Oncology (Dordrecht)
Yu Zhu, Luo Lu, Chun Qiao, Yi Shan, Huapeng Li, Sixuan Qian, Ming Hong, Huihui Zhao, Jianyong Li, Zhongfa Yang, Yaoyu Chen
Resistance to the BCR-ABL tyrosine kinase inhibitor (TKI) remains a challenge for curing the disease in chronic myeloid leukemia (CML) patients as leukemia cells may survive through BCR-ABL kinase activity-independent signal pathways. To gain insight into BCR-ABL kinase activity-independent mechanisms, we performed an initial bioinformatics screen and followed by a quantitative PCR screen of genes that were elevated in CML samples. A total of 33 candidate genes were identified to be highly expressed in TKIs resistant patients...
March 7, 2018: Oncogene
Mickael Orgeur, Marvin Martens, Georgeta Leonte, Sonya Nassari, Marie-Ange Bonnin, Stefan T Börno, Bernd Timmermann, Jochen Hecht, Delphine Duprez, Sigmar Stricker
Connective tissues support organs and play crucial roles in development, homeostasis and fibrosis, yet our understanding of their formation is still limited. To gain insight into the molecular mechanisms of connective tissue specification, we selected five zinc finger transcription factors - OSR1, OSR2, EGR1, KLF2 and KLF4 - based on their expression patterns and/or known involvement in connective tissue subtype differentiation. RNA-seq and ChIP-seq profiling revealed a set of common genes regulated by all five transcription factors, which we propose as connective tissue core expression set...
March 6, 2018: Development
Shuxiang Ruan, Gary D Stormo
BACKGROUND: Transcription factor (TF) binding site specificity is commonly represented by some form of matrix model in which the positions in the binding site are assumed to contribute independently to the site's activity. The independence assumption is known to be an approximation, often a good one but sometimes poor. Alternative approaches have been developed that use k-mers (DNA "words" of length k) to account for the non-independence, and more recently DNA structural parameters have been incorporated into the models...
March 6, 2018: BMC Bioinformatics
Zenab F Mchaourab, Andrea A Perreault, Bryan J Venters
The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as chromatin immunoprecipitation coupled to sequencing (ChIP-seq). While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions...
March 6, 2018: Scientific Data
Jialiang Huang, Kailong Li, Wenqing Cai, Xin Liu, Yuannyu Zhang, Stuart H Orkin, Jian Xu, Guo-Cheng Yuan
Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, here we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants...
March 5, 2018: Nature Communications
Vikas Yadav, Sheng Sun, R Blake Billmyre, Bhagya C Thimmappa, Terrance Shea, Robert Lintner, Guus Bakkeren, Christina A Cuomo, Joseph Heitman, Kaustuv Sanyal
The centromere DNA locus on a eukaryotic chromosome facilitates faithful chromosome segregation. Despite performing such a conserved function, centromere DNA sequence as well as the organization of sequence elements is rapidly evolving in all forms of eukaryotes. The driving force that facilitates centromere evolution remains an enigma. Here, we studied the evolution of centromeres in closely related species in the fungal phylum of Basidiomycota. Using ChIP-seq analysis of conserved inner kinetochore proteins, we identified centromeres in three closely related Cryptococcus species: two of which are RNAi-proficient, while the other lost functional RNAi...
March 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
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