title: metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA.
abstract: Here we introduce metaseq, a software library written in Python, which enables loading multiple genomic data formats into standard Python data structures and allows flexible, customized manipulation and visualization of data from high-throughput sequencing studies. We demonstrate its practical use by analyzing multiple datasets related to chromatin insulators, which are DNA-protein complexes proposed to organize the genome into distinct transcriptional domains. Recent studies in Drosophila and mammals have implicated RNA in the regulation of chromatin insulator activities. Moreover, the Drosophila RNA-binding protein Shep has been shown to antagonize gypsy insulator activity in a tissue-specific manner, but the precise role of RNA in this process remains unclear. Better understanding of chromatin insulator regulation requires integration of multiple datasets, including those from chromatin-binding, RNA-binding, and gene expression experiments. We use metaseq to integrate RIP- and ChIP-seq data for Shep and the core gypsy insulator protein Su(Hw) in two different cell types, along with publicly available ChIP-chip and RNA-seq data. Based on the metaseq-enabled analysis presented here, we propose a model where Shep associates with chromatin cotranscriptionally, then is recruited to insulator complexes in trans where it plays a negative role in insulator activity.
authors: Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA dalerr@niddk.nih.gov.
authors: Ryan K
authors: RK
authors: Dale
authors: Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA.
authors: Leah H
authors: LH
authors: Matzat
authors: Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA leielissa@niddk.nih.gov.
authors: Elissa P
authors: EP
authors: Lei
mesh_terms: D024506:5' Flanking Region; D001665:Binding Sites; D002460:Cell Line; D002467:Cell Nucleus / Q000235:genetics; D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D029721:Drosophila Proteins / Q000378:metabolism*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D047468:Immunoprecipitation; D038101:Insulator Elements; D012333:RNA, Messenger / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012097:Repressor Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D029721:Drosophila Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012097:Repressor Proteins; C000592804:Shep protein, Drosophila; C083738:su(Hw) protein, Drosophila