Literature DB >> 34495502

Genome-Wide Identification and Functional Characterization of Noncoding RNAs (ncRNAs) Differentially Expressed During Insect Development.

Yue Wang1,2,3, Minsheng You1,2,3, Weiyi He4,5,6.   

Abstract

MicroRNAs (miRNAs) are important regulatory noncoding RNAs (ncRNAs) at the posttranscriptional level of gene expression. Linear long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) can function as competing endogenous RNAs (ceRNAs) of miRNAs and regulate the expression of protein-coding genes. This chapter presents a procedure for the bioinformatic analysis of these three ncRNAs that are differentially expressed during insect development. In the first step, lncRNAs and circRNAs are identified based on RNA-sequencing data. In the second step, miRNAs are identified based on small RNA-sequencing data and combined with the two ncRNAs from the previous step for functional characterization.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Noncoding RNAs; Target gene prediction; Transcriptome analysis

Mesh：

Substances：

Year:  2022        PMID： 34495502     DOI： 10.1007/978-1-0716-1633-8_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  24 in total

1.  STAR: ultrafast universal RNA-seq aligner.

Authors:  Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras
Journal:  Bioinformatics       Date:  2012-10-25       Impact factor: 6.937

2.  Fast gapped-read alignment with Bowtie 2.

Authors:  Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

3.  FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.

Authors:  Valentin Wucher; Fabrice Legeai; Benoît Hédan; Guillaume Rizk; Lætitia Lagoutte; Tosso Leeb; Vidhya Jagannathan; Edouard Cadieu; Audrey David; Hannes Lohi; Susanna Cirera; Merete Fredholm; Nadine Botherel; Peter A J Leegwater; Céline Le Béguec; Hille Fieten; Jeremy Johnson; Jessica Alföldi; Catherine André; Kerstin Lindblad-Toh; Christophe Hitte; Thomas Derrien
Journal:  Nucleic Acids Res       Date:  2017-05-05       Impact factor: 16.971

4.  Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation.

Authors:  Jakub O Westholm; Pedro Miura; Sara Olson; Sol Shenker; Brian Joseph; Piero Sanfilippo; Susan E Celniker; Brenton R Graveley; Eric C Lai
Journal:  Cell Rep       Date:  2014-11-26       Impact factor: 9.423

Review 5.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

6.  Discovering microRNAs from deep sequencing data using miRDeep.

Authors:  Marc R Friedländer; Wei Chen; Catherine Adamidi; Jonas Maaskola; Ralf Einspanier; Signe Knespel; Nikolaus Rajewsky
Journal:  Nat Biotechnol       Date:  2008-04       Impact factor: 54.908

7.  Diverse alternative back-splicing and alternative splicing landscape of circular RNAs.

Authors:  Xiao-Ou Zhang; Rui Dong; Yang Zhang; Jia-Lin Zhang; Zheng Luo; Jun Zhang; Ling-Ling Chen; Li Yang
Journal:  Genome Res       Date:  2016-06-30       Impact factor: 9.043

8.  Transcriptome assembly from long-read RNA-seq alignments with StringTie2.

Authors:  Sam Kovaka; Aleksey V Zimin; Geo M Pertea; Roham Razaghi; Steven L Salzberg; Mihaela Pertea
Journal:  Genome Biol       Date:  2019-12-16       Impact factor: 13.583

9.  CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.

Authors:  Liguo Wang; Hyun Jung Park; Surendra Dasari; Shengqin Wang; Jean-Pierre Kocher; Wei Li
Journal:  Nucleic Acids Res       Date:  2013-01-17       Impact factor: 16.971

10.  Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.

Authors:  Liang Sun; Haitao Luo; Dechao Bu; Guoguang Zhao; Kuntao Yu; Changhai Zhang; Yuanning Liu; Runsheng Chen; Yi Zhao
Journal:  Nucleic Acids Res       Date:  2013-07-27       Impact factor: 16.971
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