Characterizing and annotating the genome using RNA-seq data

doi:10.1007/s11427-015-0349-4

Review

. 2017 Feb;60(2):116-125.

doi: 10.1007/s11427-015-0349-4. Epub 2016 Jun 13.

Characterizing and annotating the genome using RNA-seq data

Geng Chen¹, Tieliu Shi², Leming Shi^{1

3

4

5}

Affiliations

¹ Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China.
² The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China. tlshi@bio.ecnu.edu.cn.
³ State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
⁴ Fudan-Zhangjiang Center for Clinical Genomics, Shanghai, 201203, China.
⁵ Zhangjiang Center for Translational Medicine, Shanghai, 201203, China.

PMID: 27294835
DOI: 10.1007/s11427-015-0349-4

Review

Characterizing and annotating the genome using RNA-seq data

Geng Chen et al. Sci China Life Sci. 2017 Feb.

. 2017 Feb;60(2):116-125.

doi: 10.1007/s11427-015-0349-4. Epub 2016 Jun 13.

Authors

Geng Chen¹, Tieliu Shi², Leming Shi^{1

3

4

5}

Affiliations

¹ Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China.
² The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China. tlshi@bio.ecnu.edu.cn.
³ State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
⁴ Fudan-Zhangjiang Center for Clinical Genomics, Shanghai, 201203, China.
⁵ Zhangjiang Center for Translational Medicine, Shanghai, 201203, China.

PMID: 27294835
DOI: 10.1007/s11427-015-0349-4

Abstract

Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts (especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome- guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.

Keywords: RNA-seq; de novo assembly; genetic variants; genome-guided transcriptome reconstruction; long noncoding RNA.

PubMed Disclaimer

Cited by

Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton.
Shahzad K, Zhang M, Mubeen I, Zhang X, Guo L, Qi T, Feng J, Tang H, Qiao X, Wu J, Xing C. Shahzad K, et al. Funct Integr Genomics. 2024 Sep 4;24(5):156. doi: 10.1007/s10142-024-01420-0. Funct Integr Genomics. 2024. PMID: 39230785
Water stress modulates terpene biosynthesis and morphophysiology at different ploidal levels in Lippia alba (Mill.) N. E. Brown (Verbenaceae).
Lopes JML, Nascimento LSQ, Souza VC, de Matos EM, Fortini EA, Grazul RM, Santos MO, Soltis DE, Soltis PS, Otoni WC, Viccini LF. Lopes JML, et al. Protoplasma. 2024 Mar;261(2):227-243. doi: 10.1007/s00709-023-01890-2. Epub 2023 Sep 4. Protoplasma. 2024. PMID: 37665420
Serum Long Noncoding RNA H19 and CKD Progression in IgA Nephropathy.
He L, Wang H, He P, Jiang Y, Ma F, Wang J, Hu J. He L, et al. J Nephrol. 2023 Mar;36(2):397-406. doi: 10.1007/s40620-022-01536-1. Epub 2022 Dec 27. J Nephrol. 2023. PMID: 36574208
Differentially expressed genes against Colletotrichum lindemuthiamum in a bean genotype carrying the Co-2 gene revealed by RNA-sequencing analysis.
Jurado M, Campa A, Ferreira JJ. Jurado M, et al. Front Plant Sci. 2022 Sep 15;13:981517. doi: 10.3389/fpls.2022.981517. eCollection 2022. Front Plant Sci. 2022. PMID: 36311094 Free PMC article.
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing.
Ye MS, Zhang JY, Yu DD, Xu M, Xu L, Lv LB, Zhu QY, Fan Y, Yao YG. Ye MS, et al. Zool Res. 2021 Nov 18;42(6):692-709. doi: 10.24272/j.issn.2095-8137.2021.272. Zool Res. 2021. PMID: 34581030 Free PMC article.

See all "Cited by" articles

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions

LinkOut - more resources

Full Text Sources
- Springer
Other Literature Sources
- scite Smart Citations

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Characterizing and annotating the genome using RNA-seq data

Affiliations

Characterizing and annotating the genome using RNA-seq data

Authors

Affiliations

Abstract

Similar articles

Cited by

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources