nASAP: A Nascent RNA Profiling Data Analysis Platform.

Data Analysis Gene Expression Profiling Gene Expression Regulation RNA, Messenger / genetics Sequence Analysis, RNA Software
gene expression gene regulatory network nascent RNA profiling pausing quality assessment web server

Journal

Journal of molecular biology
ISSN: 1089-8638
Titre abrégé: J Mol Biol
Pays: Netherlands
ID NLM: 2985088R

Informations de publication

Date de publication:
15 07 2023
Historique:
received: 13 11 2022
revised: 19 04 2023
accepted: 30 04 2023
medline: 27 6 2023
pubmed: 26 6 2023
entrez: 25 6 2023
Statut: ppublish

Résumé

Although nascent RNA profiling data are widely used in transcriptional regulation studies, the development and standardization of data processing pipeline lags far behind RNA-seq. We are filling this gap by establishing the nASAP web server (https://grobase.top/nasap/) to provide practical quality evaluation and comprehensive analysis of nascent RNA datasets. In nASAP, four customized analysis modules are provided, including i) quality assessment, which summarizes the sequencing statistics, mapping ratio, and evaluates RNA integrity and mRNA contamination; ii) quantification analysis for mRNAs, lncRNAs and eRNAs; iii) pausing analysis across the whole genome based on sequencing reads distribution; and iv) network analysis to better understand the gene regulatory mechanism by obtaining annotated enhancer-promoter interactomes. The nASAP is user-friendly and outperforms the existing pipeline for quality control of nascent RNA profiling data. We anticipate that nASAP, which eases both basic and advanced analysis of nascent RNA data, will be extremely useful in various fields.

Identifiants

DOI: 10.1016/j.jmb.2023.168142 PMID: 37356907
pubmed: 37356907
pii: S0022-2836(23)00220-6
doi: 10.1016/j.jmb.2023.168142
pii:
doi:

Substances chimiques

RNA, Messenger 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

168142

Informations de copyright

Copyright © 2023 Elsevier Ltd. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Auteurs

Zhi Wang (Z)

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

Peng Ge (P)

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

Xiao-Long Zhou (XL)

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

Kun-Ming Shui (KM)

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.

Huichao Geng (H)

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.

Jie Yang (J)

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China. Electronic address: yangjie@nju.edu.cn.

Jia-Yu Chen (JY)

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China. Electronic address: jiayuchen@nju.edu.cn.

Jin Wang (J)

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; NJU Advanced Institute for Life Sciences (NAILS), Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing 210023, China. Electronic address: jwang@nju.edu.cn.

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Classifications MeSH

questionsmedicales.fr › Disciplines des sciences naturelles › Mathématiques › Analyse de données › nASAP: A Nascent RNA Profiling Data Analysis Platform.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › nASAP: A Nascent RNA Profiling Data Analysis Platform.
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › nASAP: A Nascent RNA Profiling Data Analysis Platform.
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN messager › nASAP: A Nascent RNA Profiling Data Analysis Platform.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › nASAP: A Nascent RNA Profiling Data Analysis Platform.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › nASAP: A Nascent RNA Profiling Data Analysis Platform.