Utilizing Sequence Intrinsic Composition to Classify Protein-coding and Long Non-coding Transcripts

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2013 Jul 30

PMID 23892401

Citations 947

Authors

Liang Sun

Haitao Luo

Dechao Bu

Guoguang Zhao

Kuntao Yu

Changhai Zhang

Yuanning Liu

Runsheng Chen

Yi Zhao

Affiliations

Soon will be listed here.

Abstract

It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense-antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci.

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References

Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M . Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5. PMC: 3146043. DOI: 10.1038/nbt.1621. View

Kersey P, Staines D, Lawson D, Kulesha E, Derwent P, Humphrey J . Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 2011; 40(Database issue):D91-7. PMC: 3245118. DOI: 10.1093/nar/gkr895. View

Guo X, Gao L, Liao Q, Xiao H, Ma X, Yang X . Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. Nucleic Acids Res. 2012; 41(2):e35. PMC: 3554231. DOI: 10.1093/nar/gks967. View

. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; 489(7414):57-74. PMC: 3439153. DOI: 10.1038/nature11247. View

Burge C, Karlin S . Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997; 268(1):78-94. DOI: 10.1006/jmbi.1997.0951. View

Wang L, Park H, Dasari S, Wang S, Kocher J, Li W . CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013; 41(6):e74. PMC: 3616698. DOI: 10.1093/nar/gkt006. View

Mukherjee S, Zhang Y . MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Res. 2009; 37(11):e83. PMC: 2699532. DOI: 10.1093/nar/gkp318. View

Cabili M, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A . Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011; 25(18):1915-27. PMC: 3185964. DOI: 10.1101/gad.17446611. View

Liao Q, Liu C, Yuan X, Kang S, Miao R, Xiao H . Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res. 2011; 39(9):3864-78. PMC: 3089475. DOI: 10.1093/nar/gkq1348. View

10.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D . Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012; 7(3):562-78. PMC: 3334321. DOI: 10.1038/nprot.2012.016. View

11.

Lin M, Jungreis I, Kellis M . PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics. 2011; 27(13):i275-82. PMC: 3117341. DOI: 10.1093/bioinformatics/btr209. View

12.

Djebali S, Davis C, Merkel A, Dobin A, Lassmann T, Mortazavi A . Landscape of transcription in human cells. Nature. 2012; 489(7414):101-8. PMC: 3684276. DOI: 10.1038/nature11233. View

13.

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H . The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012; 22(9):1775-89. PMC: 3431493. DOI: 10.1101/gr.132159.111. View

14.

Guttman M, Rinn J . Modular regulatory principles of large non-coding RNAs. Nature. 2012; 482(7385):339-46. PMC: 4197003. DOI: 10.1038/nature10887. View

15.

Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, Harrigan P . The evolution of gene expression levels in mammalian organs. Nature. 2011; 478(7369):343-8. DOI: 10.1038/nature10532. View

16.

Re M, Pesole G, Horner D . Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics. BMC Bioinformatics. 2009; 10:282. PMC: 2758873. DOI: 10.1186/1471-2105-10-282. View

17.

Bu D, Yu K, Sun S, Xie C, Skogerbo G, Miao R . NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res. 2011; 40(Database issue):D210-5. PMC: 3245065. DOI: 10.1093/nar/gkr1175. View

18.

Liao Q, Xiao H, Bu D, Xie C, Miao R, Luo H . ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res. 2011; 39(Web Server issue):W118-24. PMC: 3125796. DOI: 10.1093/nar/gkr432. View

19.

Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E . BlastR--fast and accurate database searches for non-coding RNAs. Nucleic Acids Res. 2011; 39(16):6886-95. PMC: 3167602. DOI: 10.1093/nar/gkr335. View

20.

Kong L, Zhang Y, Ye Z, Liu X, Zhao S, Wei L . CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007; 35(Web Server issue):W345-9. PMC: 1933232. DOI: 10.1093/nar/gkm391. View