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enChIP-Seq Analyzer: A Software Program to Analyze and Interpret enChIP-Seq Data for the Detection of Physical Interactions between Genomic Regions

1
Research Institute of Bio-System Informatics, Tohoku Chemical Co., Ltd., 6-15-5 Mitake, Morioka 020-0122, Iwate, Japan
2
Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
*
Author to whom correspondence should be addressed.
Academic Editors: Stefano Lonardi and Cenk Sahinalp
Genes 2022, 13(3), 472; https://doi.org/10.3390/genes13030472
Received: 13 December 2021 / Revised: 25 February 2022 / Accepted: 2 March 2022 / Published: 7 March 2022
(This article belongs to the Section Bioinformatics)
Accumulating evidence suggests that the physical interactions between genomic regions play critical roles in the regulation of genome functions, such as transcription and epigenetic regulation. Various methods to detect the physical interactions between genomic regions have been developed. We recently developed a method to search for genomic regions interacting with a locus of interest in a non-biased manner that combines pull-down of the locus using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and next-generation sequencing (NGS) analysis (enChIP-Seq). The clustered regularly interspaced short palindromic repeats (CRISPR) system, consisting of a nuclease-dead form of Cas9 (dCas9) and a guide RNA (gRNA), or transcription activator-like (TAL) proteins, can be used for enChIP. In enChIP-Seq, it is necessary to compare multiple datasets of enChIP-Seq data to unambiguously detect specific interactions. However, it is not always easy to analyze enChIP-Seq datasets to subtract non-specific interactions or identify common interactions. To facilitate such analysis, we developed the enChIP-Seq analyzer software. It enables easy extraction of common signals as well as subtraction of non-specific signals observed in negative control samples, thereby streamlining extraction of specific enChIP-Seq signals. enChIP-Seq analyzer will help users analyze enChIP-Seq data and identify physical interactions between genomic regions. View Full-Text
Keywords: enChIP-Seq; CRISPR; intergenomic interactions; 3-D genomics; enChIP-Seq analyzer enChIP-Seq; CRISPR; intergenomic interactions; 3-D genomics; enChIP-Seq analyzer
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MDPI and ACS Style

Sarudate, A.; Fujita, T.; Nakayama, T.; Fujii, H. enChIP-Seq Analyzer: A Software Program to Analyze and Interpret enChIP-Seq Data for the Detection of Physical Interactions between Genomic Regions. Genes 2022, 13, 472. https://doi.org/10.3390/genes13030472

AMA Style

Sarudate A, Fujita T, Nakayama T, Fujii H. enChIP-Seq Analyzer: A Software Program to Analyze and Interpret enChIP-Seq Data for the Detection of Physical Interactions between Genomic Regions. Genes. 2022; 13(3):472. https://doi.org/10.3390/genes13030472

Chicago/Turabian Style

Sarudate, Ashita, Toshitsugu Fujita, Takahiro Nakayama, and Hodaka Fujii. 2022. "enChIP-Seq Analyzer: A Software Program to Analyze and Interpret enChIP-Seq Data for the Detection of Physical Interactions between Genomic Regions" Genes 13, no. 3: 472. https://doi.org/10.3390/genes13030472

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