RECOGNICER:A coarse-graining approach for identifying broad domains from ChIP-seq data

作     者：Chongzhi Zang Yiren Wang Weiqun Peng Chongzhi Zang;Yiren Wang;Weiqun Peng

作者机构：Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVA 22908USA Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVA 22908USA Department of PhysicsThe George Washington UniversityWashingtonDC 20052USA 

出 版 物：《Quantitative Biology》 (定量生物学（英文版）)

年 卷 期：2020年第8卷第4期

页      面：359-368页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 08[工学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种] 

基　　金：the U.S.National Institutes of Health(NIH)R35GM133712 to C.Z R01 AI121080 and R01AI139874 to W.P 

主　　题：coarse-graining ChIP-seq peak calling histone modification 

摘      要：Background:Histone modifications are major factors that define chromatin states and have functions in regulating gene expression in eukaryotic *** immunoprecipitation coupled with high-throughput sequencing(ChIP-seq)technique has been widely used for profiling the genome-wide distribution of chromatin-associating protein *** histone modifications,such as H3K27me3 and H3K9me3,usually mark broad domains in the genome ranging from kilobases(kb)to megabases(Mb)long,resulting in diffuse patterns in the ChIP-seq data that are challenging for signal *** most existing ChIP-seq peak-calling algorithms are based on local statistical models without account of multi-scale features,a principled method to identify scale-free board domains has been ***:Here we present RECOGNICER(Recursive coarse-graining identification for ChIP-seq enriched regions),a computational method for identifying ChIP-seq enriched domains on a large range of *** algorithm is based on a coarse-graining approach,which uses recursive block transformations to determine spatial clustering of local enriched elements across multiple length ***:We apply RECOGNICER to call H3K27me3 domains from ChIP-seq data,and validate the results based on H3K27me3 s association with repressive gene *** show that RECOGNICER outperforms existing ChIP-seq broad domain calling tools in identifying more whole domains than separated ***:RECOGNICER can be a useful bioinformatics tool for next-generation sequencing data analysis in epigenomics research.