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BMC Genomics. 2019 Jul 8;20(1):559. doi: 10.1186/s12864-019-5903-y.

Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing.

Wan Y1,2, Liu X1,2, Zheng D3, Wang Y1,2, Chen H4, Zhao X1,2, Liang G1, Yu D5,6, Gan L7.

Author information

1
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.
2
Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China.
3
Zhejiang Academy of Medical Sciences, Hangzhou, China.
4
Key Laboratory of microbiological technology and Bioinformatics in Zhejiang Province, Hangzhou, China.
5
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China. yudl@hznu.edu.cn.
6
Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China. yudl@hznu.edu.cn.
7
Department of Ophthalmology and Flaum Eye Institute, University of Rochester, Rochester, NY, 14642, USA. lin_gan@urmc.rochester.edu.

Abstract

BACKGROUND:

A great mass of long noncoding RNAs (lncRNAs) have been identified in mouse genome and increasing evidences in the last decades have revealed their crucial roles in diverse biological processes. Nevertheless, the biological roles of lncRNAs in the mouse retina remains largely unknown due to the lack of a comprehensive annotation of lncRNAs expressed in the retina.

RESULTS:

In this study, we applied the long-reads sequencing strategy to unravel the transcriptomes of developing mouse retinas and identified a total of 940 intergenic lncRNAs (lincRNAs) in embryonic and neonatal retinas, including about 13% of them were transcribed from unannotated gene loci. Subsequent analysis revealed that function of lincRNAs expressed in mouse retinas were closely related to the physiological roles of this tissue, including 90 lincRNAs that were differentially expressed after the functional loss of key regulators of retinal ganglion cell (RGC) differentiation. In situ hybridization results demonstrated the enrichment of three class IV POU-homeobox genes adjacent lincRNAs (linc-3a, linc-3b and linc-3c) in ganglion cell layer and indicated they were potentially RGC-specific.

CONCLUSIONS:

In summary, this study systematically annotated the lincRNAs expressed in embryonic and neonatal mouse retinas and implied their crucial regulatory roles in retinal development such as RGC differentiation.

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