Stable Intronic Sequences and Exon Skipping Events in the Human RPE65 Gene: Analysis of Expression in Retinal Pigment Epithelium Cells and Cell Culture Models

Frontiers in Genetics
Olga PostnikovaT M Redmond

Abstract

Currently, there is much interest in intronic sequence-containing long non-coding RNAs and the role of intronic transcription in regulation of cellular metabolism and fate. Several stable intronic sequence RNAs (sisRNAs) were recently implicated in regulation of parental genes. To investigate transcription from introns of the RPE65 gene, we analyzed RNA-seq and Nanopore sequencing data from different cell models of human retinal pigment epithelium (RPE) and native bovine RPE. We discovered putative stable poly-adenylated transcripts with sequences corresponding to intronic regions of the RPE65 gene in the cytoplasm of RPE cells. These stable intronic sequences could be important for RPE65 transcription, splicing or translation. We also analyzed alternative splicing events in RPE65. Frequent exon skipping events involving exons 2, 3, and 7 were detected. The rate of these events was much higher in human RPE cell cultures compared with native RPE , consistent with lack of translation of RPE65 mRNA in cell cultures.

References

Nov 5, 1997·Nature Genetics·F MarlhensC P Hamel
Apr 18, 1998·Proceedings of the National Academy of Sciences of the United States of America·H MorimuraT P Dryja
Jul 29, 1998·Journal of Theoretical Biology·G B GlazkoI B Rogozin
Dec 11, 1999·Mutation Research·N N Khromov-BorisovF J de Serres
Jan 15, 2004·Human Mutation·Alexey S Kondrashov, Igor B Rogozin
Jul 1, 2005·Physiological Reviews·Olaf Strauss
Aug 13, 2005·Cell·Minghao JinGabriel H Travis
Aug 24, 2005·Proceedings of the National Academy of Sciences of the United States of America·Gennadiy MoiseyevJian-Xing Ma
Sep 10, 2005·Proceedings of the National Academy of Sciences of the United States of America·T Michael RedmondSusan Gentleman
Nov 18, 2005·Trends in Genetics : TIG·Ken C PangJohn S Mattick
Oct 17, 2009·Briefings in Functional Genomics & Proteomics·Harm van Bakel, Timothy R Hughes
May 27, 2010·PLoS Biology·Richard Robinson
Jun 10, 2011·European Journal of Human Genetics : EJHG·Sara J BownePeter Humphries
Jul 6, 2013·Cell·Igor Ulitsky, David P Bartel
Apr 16, 2014·Experimental Eye Research·Lawrence J Rizzolo
Aug 26, 2014·Experimental Eye Research·Guillermo L LehmannEnrique Rodriguez-Boulan
Aug 26, 2014·Experimental Eye Research·Michael E Boulton
Nov 26, 2015·Nucleic Acids Research·Michael RyanJohn Weinstein
May 6, 2016·Cellular and Molecular Life Sciences : CMLS·Ismail OsmanJun Wei Pek
Jan 6, 2017·Cell Death & Disease·Nady GolestanehAlexander C Theos
Feb 10, 2018·Nucleic Acids Research·Natali Romero-BarriosMartin Crespi
Nov 6, 2018·Trends in Biochemical Sciences·Seow Neng Chan, Jun Wei Pek
Feb 20, 2019·Non-coding RNA·Juliane C R FernandesSandra M Muxel

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Methods Mentioned

BETA
transfection
RNA-seq
PCR

Software Mentioned

CLUSTERM
RepeatMasker
BLASTN
Ensembl
Fastq
EPI2ME
UCSC genome browser
COLLAPSE
minimap2
Geneious

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