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The Cyclophilin AtCYP71 Interacts with CAF-1 and LHP1 and Functions in Multiple Chromatin Remodeling Processes

Molecular Plant 2011年第4期4卷 748-758页

作者： Hong Li Sheng Luan Department of Plant and Microbial Biology University of California Berkeley CA 94720 USA

Chromatin is the primary carrier of epigenetic information in higher eukaryotes. AtCYP71 contains both cyclophilin domain and WD40 repeats. Loss of AtCYP71 function causes drastic pleiotropic phenotypic defects. Here, we show that AtCYP71 physically interacts with FAS1 and LHP1, respectively, to modulate their distribution on chromatin. The Ihpl cyp71 double mutant showed more severe phenotypes than the single mutants, suggesting that AtCYP71 and LHP1 synergistically control plant development. Such synergism was in part illustrated by the observation that LHP1 association with its specific target loci requires AtCYP71 function. We also demonstrate that AtCYP71 physically interacts with FAS1 and is indispensable for FAS1 targeting to the KNAT1 locus. Together, our data suggest that AtCYP71 is involved in fundamental processes of chromatin assembly and histone modification in plants.

关键词： Arabidopsis cyclophilin like heterochromatin protein 1 histone mark chromatin assembly factor Chromatin Immunoprecipitation.

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Computational methodology for ChlP-seq analysis

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Frontiers of Electrical and Electronic Engineering in China 2013年第1期8卷 54-70页

作者： Hyunjin Shin Tao Liu Xikun Duan Yong Zhang X. Shirley Liu Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute/Harvard School of Public Health Boston MA 02115 USA Department of Bioinformatics School of Life Science and Technology Tongji University Shanghai 200092 China

Chromatin immunoprecipitation coupled with massive parallel sequencing （ChlP-seq） is a powerful technology to identify the genome-wide locations of DNA binding proteins such as transcription factors or modified histones. As more and more experimental laboratories are adopting ChlP-seq to unravel the transcriptional and epigenetic regulatory mechanisms, computational analyses of ChlP-seq also become increasingly comprehensive and sophisticated. In this article, we review current computational methodology for ChlP-seq analysis, recommend useful algorithms and workflows, and introduce quality control measures at different analytical steps. We also discuss how ChlP-seq could be integrated with other types of genomic assays, such as gene expression profiling and genome-wide association studies, to provide a more comprehensive view of gene regulatory mechanisms in important physiological and pathological processes.

关键词： histone mark Nucleosome Occupancy Peak Calling Chromatin Signature Target Gene Prediction

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