ArticleNucleic acids research2014
metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
- Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3, and SIRT1.Life science alliance · 2022Article
- Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling.Nature communications · 2021Article
- Overlapping but Distinct Sequences Play Roles in the Insulator and Promoter Activities of theGenetics · 2020Article
- The cryptic unstable transcripts are associated with developmentally regulated gene expression in blood-stageRNA biology · 2020Article
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- SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina.Nucleic acids research · 2019Article
- Shep RNA-Binding Capacity Is Required for Antagonism ofG3 (Bethesda, Md.) · 2019Article
- Article
- Shep regulatesDevelopment (Cambridge, England) · 2018Article
- Survey of gene splicing algorithms based on reads.Bioengineered · 2017Article
- Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data.BMC genomics · 2016Article
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- Article
- iTagPlot: an accurate computation and interactive drawing tool for tag density plot.Bioinformatics (Oxford, England) · 2015Article
- Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis.Computational and structural biotechnology journal · 2015Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.