title: An atlas of gene expression and gene co-regulation in the human retina.
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).
authors.affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Pinelli
authors.affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
authors.forename: Annamaria
authors.initials: A
authors.lastname: Carissimo
authors.affiliation: 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.
authors.forename: Luisa
authors.initials: L
authors.lastname: Cutillo
authors.affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
authors.forename: Ching-Hung
authors.initials: CH
authors.lastname: Lai
authors.affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
authors.forename: Margherita
authors.initials: M
authors.lastname: Mutarelli
authors.affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
authors.forename: Maria Nicoletta
authors.initials: MN
authors.lastname: Moretti
authors.affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
authors.forename: Marwah Veer
authors.initials: MV
authors.lastname: Singh
authors.affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
authors.forename: Marianthi
authors.initials: M
authors.lastname: Karali
authors.affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
authors.forename: Diego
authors.initials: D
authors.lastname: Carrella
authors.affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
authors.forename: Mariateresa
authors.initials: M
authors.lastname: Pizzo
authors.affiliation: Istituto per le Applicazioni del Calcolo, Consiglio Nazionale delle Ricerca, Via Pietro Castellino 111, 80131 Napoli, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Russo
authors.affiliation: Fondazione Banca degli Occhi del Veneto, Via Paccagnella 11, 30174 Zelarino (Venice), Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Ferrari
authors.affiliation: Fondazione Banca degli Occhi del Veneto, Via Paccagnella 11, 30174 Zelarino (Venice), Italy.
authors.forename: Diego
authors.initials: D
authors.lastname: Ponzin
authors.affiliation: Istituto per le Applicazioni del Calcolo, Consiglio Nazionale delle Ricerca, Via Pietro Castellino 111, 80131 Napoli, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Angelini
authors.affiliation: 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.
authors.forename: Sandro
authors.initials: S
authors.lastname: Banfi
authors.affiliation: 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.
authors.forename: Diego
authors.initials: D
authors.lastname: di Bernardo
mesh_terms: D000328:Adult; D000368:Aged; D017398:Alternative Splicing; D001271:Atlases as Topic; D002874:Chromosome Mapping; D005091:Exons; D005136:Eye Proteins / Q000235:genetics* / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D024101:Mitochondrial Proteins / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D012160:Retina / Q000166:cytology / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D005136:Eye Proteins; D024101:Mitochondrial Proteins; D020033:Protein Isoforms