Advanced search
Publication Cover
RNA Biology Volume 18, 2021 - Issue 11
Submit an article Journal homepage
1,153
Views
3
CrossRef citations to date
0
Altmetric
Technical Paper

Target-capture full-length double-strand cDNA sequencing for alternative splicing analysis

Hiroki Uraa Center for Clinical Genomics, Kanazawa Medical University Hospital, Ishikawa, Japan;b Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, JapanCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0002-7600-3481View further author information
ORCID Icon,
Sumihito Togia Center for Clinical Genomics, Kanazawa Medical University Hospital, Ishikawa, Japan;b Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, JapanORCID Iconhttps://orcid.org/0000-0002-3189-8111View further author information
ORCID Icon &
Yo Niidaa Center for Clinical Genomics, Kanazawa Medical University Hospital, Ishikawa, Japan;b Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, JapanORCID Iconhttps://orcid.org/0000-0001-5641-7962View further author information
ORCID Icon
Pages 1600-1607 | Received 29 Sep 2020, Accepted 04 Jan 2021, Published online: 20 Jan 2021

References

  • Shi Y. Mechanistic insights into precursor messenger RNA splicing by the spliceosome. Nat Rev Mol Cell Biol. 2017;18(11):655–670.
  • Bush SJ, Chen L, Tovar-Corona JM, et al. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc London, Ser B. 2017;372. DOI:10.1098/rstb.2015.0474
  • Pan Q, Shai O, Lee LJ, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008;40:1413–1415.
  • Wang ET, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008;456:470–476.
  • Kim MS, Pinto SM, Getnet D, et al. A draft map of the human proteome. Nature. 2014;509:575–581.
  • Martinez NM, Pan Q, Cole BS, et al. Alternative splicing networks regulated by signaling in human T cells. RNA. 2012;18:1029–1040.
  • Singh RK, Xia Z, Bland CS, et al. Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis. Mol Cell. 2014;55:592–603.
  • Bhate A, Parker DJ, Bebee TW, et al. ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation. Nat Commun. 2015;6:8768.
  • Dillman AA, Hauser DN, Gibbs JR, et al. mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex. Nat Neurosci. 2013;16:499–506.
  • Giudice J, Xia Z, Wang ET, et al. Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nat Commun. 2014;5:3603.
  • Llorian M, Gooding C, Bellora N, et al. The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators. Nucleic Acids Res. 2016;44:8933–8950.
  • Srebrow A, Kornblihtt AR. The connection between splicing and cancer. J Cell Sci. 2006;119:2635–2641.
  • Brinkman BM. Splice variants as cancer biomarkers. Clin Biochem. 2004;37:584–594.
  • Venables JP. Aberrant and alternative splicing in cancer. Cancer Res. 2004;64:7647–7654.
  • Byron SA, Van Keuren-Jensen KR, Engelthaler DM, et al. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet. 2016;17:257–271.
  • Picelli S, Faridani OR, Björklund AK, et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc. 2014;9:171–181.
  • Song Y, Milon B, Ott S, et al. A comparative analysis of library prep approaches for sequencing low input translatome samples. BMC Genomics. 2018;19:696.
  • Ura H, Togi S, Niida Y. Dual deep sequencing improves the accuracy of low-frequency somatic mutation detection in cancer gene panel testing. Int J Mol Sci. 2020;21:21.
  • Andrews S FastQC a qurality control tool for high throughput sequence data. 2010.
  • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357–360.
  • Pertea M, Pertea GM, Antonescu CM, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–295.
  • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–140.
  • Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–2079.
  • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–842.
  • Shen W, Le S, Li Y, et al. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PloS One. 2016;11:e0163962.
  • Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012;28:2184–2185.
  • Kahles A, Ong CS, Zhong Y, et al. SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data. Bioinformatics. 2016;32:1840–1847.
  • Kono N, Arakawa K. Nanopore sequencing: review of potential applications in functional genomics. Dev Growth Differ. 2019;61:316–326.
  • Rhoads A, Au KF. PacBio sequencing and its applications. Genomics Proteomics Bioinformatics. 2015;13:278–289.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.