Methods for ChIP-seq analysis: A practical workflow and advanced applications

Nakato, Ryuichiro; Sakata, Toyonori

doi:10.1016/j.ymeth.2020.03.005

Cited by 159 publications

(81 citation statements)

References 107 publications

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“…Notably, adenylate cyclase was identified as one of the most highly downregulated proteins following long-term exposure of human embryonic carcinoma cells to low levels of arsenite ( Das et al., 2011 ). Future experiments will utilize ChIP-sequencing (ChIP-seq) ( Nakato and Sakata, 2020 ) and/or CUT&Tag ( Kaya-Okur et al., 2019 ) approaches to identify additional nucSF target genes and determine whether, like SGs, there are stress-specific differences.…”

Section: Resultsmentioning

confidence: 99%

A Nuclear Stress Pathway that Parallels Cytoplasmic Stress Granule Formation

et al. 2020

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Summary Stress adaptation is exploited by cancer cells to survive and proliferate under adverse conditions. Survival pathways induced by stress are thus highly promising therapeutic targets. One key pathway involves formation of cytoplasmic stress granules, which regulate the location, stability, and translation of specific mRNAs. Here, we describe a transcriptional stress response that is triggered by similar stressors and characterized by accumulation of RepoMan (cell division cycle associated 2) at nuclear stress foci (nucSF). Formation of these structures is reversible, and they are distinct from known nuclear organelles and stress bodies. Immunofluorescence analysis revealed accumulation of heterochromatic markers, and increased association of RepoMan with the adenylate cyclase 2 (ADCY2) gene locus in stressed cells accompanied reduced levels of ADCY2 mRNA and protein. Quantitative comparison of the RepoMan interactome in stressed vs. unstressed cells identified condensin II as a nucSF factor, suggesting their functional association in the establishment and/or maintenance of these facultative heterochromatic domains.

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Section: Resultsmentioning

confidence: 99%

A Nuclear Stress Pathway that Parallels Cytoplasmic Stress Granule Formation

et al. 2020

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“…Following knock down or overexpression of lncRNAs, DNA-FISH experiments should be used to observe the effect of lncRNAs on the chromatin state of the target genes (87-89); (3) LncRNAs role in histone modification. Following knock down or overexpression of lncRNAs, chromatin immunoprecipitation (ChIP) (90,91) and chromatin isolation by RNA purification (ChIRP) (92) experiments should be used to analyze the effect of lncRNAs on histone modification. The RNA-pull down and RNA immunoprecipitation (RIP) (92) experiments can provide information regarding the binding ability of lncRNAs to the histone modification enzyme; (4) The role of lncRNAs in the regulation of DNA methylation modification.…”

Section: Lncrnas Affect the Expression Of Downstream Genes By Mediatimentioning

confidence: 99%

Long Non-Coding RNAs: The Regulatory Mechanisms, Research Strategies, and Future Directions in Cancers

et al. 2020

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The development and application of whole genome sequencing technology has greatly broadened our horizons on the capabilities of long non-coding RNAs (lncRNAs). LncRNAs are more than 200 nucleotides in length and lack protein-coding potential. Increasing evidence indicates that lncRNAs exert an irreplaceable role in tumor initiation, progression, as well as metastasis, and are novel molecular biomarkers for diagnosis and prognosis of cancer patients. Furthermore, lncRNAs and the pathways they influence might represent promising therapeutic targets for a number of tumors. Here, we discuss the recent advances in understanding of the specific regulatory mechanisms of lncRNAs. We focused on the signal, decoy, guide, and scaffold functions of lncRNAs at the epigenetic, transcription, and post-transcription levels in cancer cells. Additionally, we summarize the research strategies used to investigate the roles of lncRNAs in tumors, including lncRNAs screening, lncRNAs characteristic analyses, functional studies, and molecular mechanisms of lncRNAs. This review will provide a short but comprehensive description of the lncRNA functions in tumor development and progression, thus accelerating the clinical implementation of lncRNAs as tumor biomarkers and therapeutic targets.

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“…The Encyclopedia of DNA Elements (ENCODE) consortium performs data curation and also offers standardized processing pipelines for various assay types online ( https://www.encodeproject.org/ ), with regular updates [ 28 ]. Specific pitfalls, e.g., during sequence analysis, peak calling, or differential methylation detection, can be obtained in dedicated review articles [ 29 – 32 ]. Novel analysis methods can also be utilized entirely online on dedicated data processing servers, such as Galaxy [ 33 ].…”

Section: Tools For Biostatisticsmentioning

confidence: 99%

The role of epigenetic modifications for the pathogenesis of Crohn's disease

et al. 2021

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Epigenetics has become a promising field for finding new biomarkers and improving diagnosis, prognosis, and drug response in inflammatory bowel disease. The number of people suffering from inflammatory bowel diseases, especially Crohn's disease, has increased remarkably. Crohn's disease is assumed to be the result of a complex interplay between genetic susceptibility, environmental factors, and altered intestinal microbiota, leading to dysregulation of the innate and adaptive immune response. While many genetic variants have been identified to be associated with Crohn's disease, less is known about the influence of epigenetics in the pathogenesis of this disease. In this review, we provide an overview of current epigenetic studies in Crohn's disease. In particular, we enable a deeper insight into applied bioanalytical and computational tools, as well as a comprehensive update toward the cell-specific evaluation of DNA methylation and histone modifications.

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Methods for ChIP-seq analysis: A practical workflow and advanced applications

Cited by 159 publications

References 107 publications

A Nuclear Stress Pathway that Parallels Cytoplasmic Stress Granule Formation

A Nuclear Stress Pathway that Parallels Cytoplasmic Stress Granule Formation

Long Non-Coding RNAs: The Regulatory Mechanisms, Research Strategies, and Future Directions in Cancers

The role of epigenetic modifications for the pathogenesis of Crohn's disease

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