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Nucleic Acids Res. 2016 Jul 8;44(12):5773-84. doi: 10.1093/nar/gkw486. Epub 2016 May 27.

An atlas of gene expression and gene co-regulation in the human retina.

Author information

1
Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
2
Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy Dipartimento Studi Aziendali e Quantitativi (DISAQ), Università degli studi di Napoli 'Parthenope', Via Generale Parisi, 80132 Napoli, Italy.
3
Istituto per le Applicazioni del Calcolo, Consiglio Nazionale delle Ricerca, Via Pietro Castellino 111, 80131 Napoli, Italy.
4
Fondazione Banca degli Occhi del Veneto, Via Paccagnella 11, 30174 Zelarino (Venice), Italy.
5
Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, via Luigi De Crecchio 7, 80138 Naples (NA), Italy banfi@tigem.it.
6
Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy Dept. Of Chemical, Materials and Industrial Production Engineering, University of Naples 'Federico II', Piazzale Tecchio 80, 80125 Naples, Italy dibernardo@tigem.it.

Abstract

The human retina is a specialized tissue involved in light stimulus transduction. Despite its unique biology, an accurate reference transcriptome is still missing. Here, we performed gene expression analysis (RNA-seq) of 50 retinal samples from non-visually impaired post-mortem donors. We identified novel transcripts with high confidence (Observed Transcriptome (ObsT)) and quantified the expression level of known transcripts (Reference Transcriptome (RefT)). The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. The RefT included 13 792 genes across 94 521 known transcripts. Mitochondrial genes were among the most highly expressed, accounting for about 10% of the reads. Of all the protein-coding genes in Gencode, 65% are expressed in the retina. We exploited inter-individual variability in gene expression to infer a gene co-expression network and to identify genes specifically expressed in photoreceptor cells. We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. RNA-seq data and the gene co-expression network are available online (http://retina.tigem.it).

PMID:
27235414
PMCID:
PMC4937338
DOI:
10.1093/nar/gkw486
[Indexed for MEDLINE]
Free PMC Article
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