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https://www.readbyqxmd.com/read/29036702/a-hyperdynamic-h3-3-nucleosome-marks-promoter-regions-in-pluripotent-embryonic-stem-cells
#1
Sharon Schlesinger, Binyamin Kaffe, Shai Melcer, Jose D Aguilera, Divya M Sivaraman, Tommy Kaplan, Eran Meshorer
Histone variants and their chaperones are key regulators of eukaryotic transcription, and are critical for normal development. The histone variant H3.3 has been shown to play important roles in pluripotency and differentiation, and although its genome-wide patterns have been investigated, little is known about the role of its dynamic turnover in transcriptional regulation. To elucidate the role of H3.3 dynamics in embryonic stem cell (ESC) biology, we generated mouse ESC lines carrying a single copy of a doxycycline (Dox)-inducible HA-tagged version of H3...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036481/identification-of-the-direct-regulon-of-ntca-during-early-acclimation-to-nitrogen-starvation-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#2
Joaquín Giner-Lamia, Rocío Robles-Rengel, Miguel A Hernández-Prieto, M Isabel Muro-Pastor, Francisco J Florencio, Matthias E Futschik
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29030827/genome-wide-identification-of-transcription-factor-binding-sites-in-quiescent-adult-neural-stem-cells
#3
Shradha Mukherjee, Jenny Hsieh
Transcription factors bind to specific DNA sequences and control the transcription rate of nearby genes in the genome. This activation or repression of gene expression is further potentiated by epigenetic modifications of histones with active and silent marks, respectively. Resident adult stem cells in the hematopoietic system, skin, and brain exist in a non-proliferative quiescent resting state. When quiescent stem cells become activated and transition to dividing progenitors and distinct cell types, they can replenish and repair tissue...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29030824/distinguishing-states-of-arrest-genome-wide-descriptions-of-cellular-quiescence-using-chip-seq-and-rna-seq-analysis
#4
Surabhi Srivastava, Hardik P Gala, Rakesh K Mishra, Jyotsna Dhawan
Regenerative potential in adult stem cells is closely associated with the establishment of-and exit from-a temporary state of quiescence. Emerging evidence not only provides a rationale for the link between lineage determination programs and cell cycle regulation but also highlights the understanding of quiescence as an actively maintained cellular program, encompassing networks and mechanisms beyond mitotic inactivity or metabolic restriction. Interrogating the quiescent genome and transcriptome using deep-sequencing technologies offers an unprecedented view of the global mechanisms governing this reversibly arrested cellular state and its importance for cell identity...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29030344/cell-type-specific-chromatin-signatures-underline-regulatory-dna-elements-in-human-induced-pluripotent-stem-cells-and-somatic-cells
#5
Mingtao Zhao, Ning-Yi Shao, Shijun Hu, Ning Ma, Rajini Srinivasan, Fereshteh Jahanbani, Jaecheol Lee, Sophia L Zhang, Michael P Snyder, Joseph C Wu
Rationale: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is a mystery how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. Objective: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression...
October 13, 2017: Circulation Research
https://www.readbyqxmd.com/read/29028882/enzymatic-methods-for-genome-wide-profiling-of-protein-binding-sites
#6
Robert A Policastro, Gabriel E Zentner
Genome-wide mapping of protein-DNA interactions is a staple approach in many areas of modern molecular biology. Genome-wide profiles of protein-binding sites are most commonly generated by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). Although ChIP-seq has played a central role in studying genome-wide protein binding, recent work has highlighted systematic biases in the technique that warrant technical and interpretive caution and underscore the need for orthogonal techniques to both confirm the results of ChIP-seq studies and uncover new insights not accessible to ChIP...
October 6, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29028833/merkel-cell-polyomavirus-recruits-mycl-to-the-ep400-complex-to-promote-oncogenesis
#7
Jingwei Cheng, Donglim Esther Park, Christian Berrios, Elizabeth A White, Reety Arora, Rosa Yoon, Timothy Branigan, Tengfei Xiao, Thomas Westerling, Alexander Federation, Rhamy Zeid, Benjamin Strober, Selene K Swanson, Laurence Florens, James E Bradner, Myles Brown, Peter M Howley, Megha Padi, Michael P Washburn, James A DeCaprio
Merkel cell carcinoma (MCC) frequently contains integrated copies of Merkel cell polyomavirus DNA that express a truncated form of Large T antigen (LT) and an intact Small T antigen (ST). While LT binds RB and inactivates its tumor suppressor function, it is less clear how ST contributes to MCC tumorigenesis. Here we show that ST binds specifically to the MYC homolog MYCL (L-MYC) and recruits it to the 15-component EP400 histone acetyltransferase and chromatin remodeling complex. We performed a large-scale immunoprecipitation for ST and identified co-precipitating proteins by mass spectrometry...
October 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29028265/stereogene-rapid-estimation-of-genome-wide-correlation-of-continuous-or-interval-feature-data
#8
Elena D Stavrovskaya, Tejasvi Niranjan, Elana J Fertig, Sarah J Wheelan, Alexander V Favorov, Andrey A Mironov
Motivation: Genomics features with similar genome-wide distributions are generally hypothesized to be functionally related, for example, colocalization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genome-wide correlation among genomic features are required. Results: Here, we propose a method, StereoGene, that rapidly estimates genome-wide correlation among pairs of genomic features...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29027176/analysis-of-chip-seq-data-in-r-bioconductor
#9
Ines de Santiago, Thomas Carroll
The development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation in multiple conditions at unprecedented resolution and scale. Proactive quality-control and appropriate data analysis techniques are of critical importance to extract the most meaningful results from the data. Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source Bioconductor project...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027175/multiplexed-chip-seq-using-direct-nucleosome-barcoding-a-tool-for-high-throughput-chromatin-analysis
#10
Christophe D Chabbert, Sophie H Adjalley, Lars M Steinmetz, Vicent Pelechano
Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027173/native-chromatin-immunoprecipitation-sequencing-chip-seq-from-low-cell-numbers
#11
Teodora Ribarska, Gregor D Gilfillan
ChIP-seq is the current method of choice for genome-wide protein location analysis. Here, we present a native (non-cross-linked) ChIP procedure suitable for histone proteins, coupled with an efficient library preparation technique for subsequent next-generation sequencing. The method enables ChIP-seq starting with 50,000 or more cells.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027171/chromatin-immunoprecipitation-assay-in-the-hyperthermoacidophilic-crenarchaeon-sulfolobus-acidocaldarius
#12
Kun Wang, Ann-Christin Lindås
Chromatin immunoprecipitation (ChIP) is a powerful method used for identifying genome-wide DNA-protein interactions in vivo. A large number of essential intracellular processes such as DNA replication, transcription regulation, chromatin stability, and others are all dependent on protein interactions with DNA. The DNA fragments enriched from the ChIP assay are analyzed by downstream applications, for example, microarray hybridization (ChIP-chip), quantitative PCR (ChIP-qPCR), or deep sequencing (ChIP-seq). This chapter presents a stepwise protocol for ChIP performed in hyperthermophilic archaea that we have successfully used in the hyperthermoacidophilic crenarchaeon Sulfolobus acidocaldarius...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027170/chromatin-immunoprecipitation-of-skeletal-muscle-tissue
#13
Amarjit Saini, Carl Johan Sundberg
Chromatin immunoprecipitation (ChIP) is an invaluable method for studying interactions between histone proteins and genomic DNA regions and transcriptional regulation using antibodies to enrich genomic regions associated with these epitopes. Either to monitor the presence of histones with post-translational modifications at specific genomic locations or to measure transcription factor interactions with a candidate target gene, protein-DNA complexes are most commonly crosslinked using formaldehyde, which stabilizes these transient interactions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027167/characterization-of-the-nucleosome-landscape-by-micrococcal-nuclease-sequencing-mnase-seq
#14
Wieteke Anna Maria Hoeijmakers, Richárd Bártfai
MNase-seq allows the genome-wide examination of the nucleosome landscape by determination of nucleosome positioning and occupancy. Typically, native or formaldehyde fixed chromatin is subjected to digestion by micrococcal nuclease (MNase), which degrades linker DNA and yields mainly mono-nucleosomes. The resulting material can be processed directly or can be subjected to an optional chromatin immunoprecipitation step (MNase-ChIP-seq). De-crosslinked and purified DNA is then subjected to next-generation sequencing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027164/chromatin-immunoprecipitation-from-mouse-embryonic-tissue-or-adherent-cells-in-culture-followed-by-next-generation-sequencing
#15
Mário A F Soares, Diogo S Castro
Chromatin immunoprecipitation (ChIP) is considered the method of choice for characterizing interactions between a protein of interest and specific genomic regions. It is of paramount importance in gene-regulation studies, as it can be used to map the target regions of sequence-specific transcription factors and cofactors, or histone marks that characterize distinct chromatin states. ChIP can be used directly to probe interactions with candidate regions (ChIP-PCR), or coupled to Next-Generation Sequencing (ChIP-seq) to generate genome-wide information...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027163/analysis-of-protein-dna-interaction-by-chromatin-immunoprecipitation-and-dna-tiling-microarray-chip-on-chip
#16
Hui Gao, Chunyan Zhao
Chromatin immunoprecipitation (ChIP) has become the most effective and widely used tool to study the interactions between specific proteins or modified forms of proteins and a genomic DNA region. Combined with genome-wide profiling technologies, such as microarray hybridization (ChIP-on-chip) or massively parallel sequencing (ChIP-seq), ChIP could provide a genome-wide mapping of in vivo protein-DNA interactions in various organisms. Here, we describe a protocol of ChIP-on-chip that uses tiling microarray to obtain a genome-wide profiling of ChIPed DNA...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027161/considerations-on-experimental-design-and-data-analysis-of-chromatin-immunoprecipitation-experiments
#17
Antonio Jordán-Pla, Neus Visa
Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29026837/binding-site-analysis-of-the-caenorhabditis-elegans-nr4a-nuclear-receptor-nhr-6-during-development
#18
Brandon Praslicka, Jeremy S Harmson, Joohyun Kim, Vittobai Rashika Rangaraj, Aikseng Ooi, Chris R Gissendanner
Members of the NR4A subfamily of nuclear receptors make up a highly conserved, functionally diverse group of transcription factors implicated in a multitude of cellular processes such as proliferation, differentiation, apoptosis, metabolism and DNA repair. The gene nhr-6, which encodes the sole C. elegans NR4A nuclear receptor homolog, has a critical role in organogenesis and regulates the development of the spermatheca organ system. Our previous work revealed that nhr-6 is required for spermatheca cell divisions in late L3 and early L4 and spermatheca cell differentiation during the mid L4 stage...
2017: Nuclear Receptor Research
https://www.readbyqxmd.com/read/29025895/accounting-for-gc-content-bias-reduces-systematic-errors-and-batch-effects-in-chip-seq-data
#19
Mingxiang Teng, Rafael A Irizarry
The main application of ChIP-seq technology is the detection of genomic regions that bind to a protein of interest. A large part of functional genomics' public catalogs is based on ChIP-seq data. These catalogs rely on peak calling algorithms that infer protein-binding sites by detecting genomic regions associated with more mapped reads (coverage) than expected by chance, as a result of the experimental protocol's lack of perfect specificity. We find that GC-content bias accounts for substantial variability in the observed coverage for ChIP-seq experiments and that this variability leads to false-positive peak calls...
October 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29025389/chromatin-states-responsible-for-the-regulation-of-differentially-expressed-genes-under-60-co-%C3%AE-ray-radiation-in-rice
#20
Xiucai Pan, Yuan Fang, Xueming Yang, Dongyang Zheng, Lifen Chen, Lei Wang, Jin Xiao, Xiu-E Wang, Kai Wang, Zhukuan Cheng, Hengxiu Yu, Wenli Zhang
BACKGROUND: The role of histone modifications in the DNA damage response has been extensively studied in non-plant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant DNA damage response. RESULTS: In this study, we used RNA-seq and ChIP-seq to show that differentially expressed genes (DEGs), in response to ionizing radiation (IR), might be involved in different pathways responsible for the DNA damage response...
October 12, 2017: BMC Genomics
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