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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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nASAP: A Nascent RNA Profiling Data Analysis Platform.

Zhi Wang1, Peng Ge1, Xiao-Long Zhou1

  • 1State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.

Journal of Molecular Biology
|June 25, 2023
PubMed
Summary
This summary is machine-generated.

We developed nASAP, a user-friendly web server for analyzing nascent RNA sequencing data. It provides essential quality control and comprehensive analysis, improving transcriptional regulation studies.

Keywords:
gene expressiongene regulatory networknascent RNA profilingpausingquality assessmentweb server

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Nascent RNA sequencing is crucial for studying transcriptional regulation.
  • Existing data processing pipelines for nascent RNA lack standardization and comprehensive analysis tools.
  • There is a need for accessible and robust bioinformatics solutions for nascent RNA data.

Purpose of the Study:

  • To introduce nASAP, a novel web server designed for the quality evaluation and comprehensive analysis of nascent RNA datasets.
  • To address the gap in standardized data processing pipelines for nascent RNA profiling.
  • To facilitate deeper understanding of gene regulatory mechanisms through advanced data analysis.

Main Methods:

  • Development of the nASAP web server (https://grobase.top/nasap/).
  • Implementation of four customized analysis modules: quality assessment, quantification analysis (mRNAs, lncRNAs, eRNAs), genome-wide pausing analysis, and network analysis (enhancer-promoter interactomes).
  • Utilizing sequencing read distribution for pausing analysis and annotated interactomes for network analysis.

Main Results:

  • nASAP provides practical quality assessment, including sequencing statistics, mapping ratios, RNA integrity, and mRNA contamination evaluation.
  • The server enables quantification of mRNAs, lncRNAs, and eRNAs.
  • Genome-wide pausing analysis and network analysis for gene regulatory insights are integrated.
  • nASAP demonstrates superior performance in quality control compared to existing pipelines.

Conclusions:

  • nASAP offers a user-friendly platform for both basic and advanced analysis of nascent RNA data.
  • The web server standardizes and enhances the analysis of nascent RNA profiling, filling a critical gap in the field.
  • nASAP is expected to be highly valuable across various research fields investigating transcriptional regulation.