Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq

Abstract

Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmentosa, preferentially affect distinct topographic regions of the retina. While much is known about the distribution of cell-types in the retina, the distribution of molecular components across the posterior pole of the eye has not been well-studied. To investigate regional difference in molecular composition of ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq. RNA from temporal, macular, and nasal retina and RPE/choroid from four human donor eyes was extracted, poly-A selected, fragmented, and sequenced as 100 bp read pairs. Digital read files were mapped to the human genome and analyzed for differential expression using the Tuxedo software suite. Retina and RPE/choroid samples were clearly distinguishable at the transcriptome level. Numerous transcription factors were differentially expressed between regions of the retina and RPE/choroid. Photoreceptor-specific genes were enriched in the peripheral samples, while ganglion cell and amacrine cell genes were enriched in the macula. Within the RPE/choroid, RPE-specific genes were upregulated at the periphery while endothelium associated genes were upregulated in the macula. Consistent with previous studies, BEST1 expression was lower in macular than extramacular regions. The MAK gene was expressed at lower levels in macula than in extramacular regions, but did not exhibit a significant difference between nasal and temporal retina. The regional molecular distinction is greatest between macula and periphery and decreases between different peripheral regions within a tissue. Datasets such as these can be used to prioritize candidate genes for possible involvement in retinal diseases with regional phenotypes.

North Carolina Macular Dystrophy Is Caused by Dysregulation of the Retinal Transcription Factor PRDM13

“…This variant lies in a 255 bp region of DNase I hypersensitivity that is upstream of a gene encoding a retinal transcription factor, PRDM13 . It is noteworthy that PRDM13 is the only gene in the MCDR1 critical region that is solely expressed in the neural retina 48,49 . DNAse I hypersensitivity is an indicator of chromatin accessibility that is often associated with transcription factor binding sites 50 .…”

Transcriptome of the human retina, retinal pigmented epithelium and choroid

“…reported that 1) no genes were differentially expressed between temporal and nasal retina; 2) 30 genes showed increased expression in nasal retina and 128 genes showed decreased expression when comparing nasal retina vs. macular retina; and 3) 37 genes showed increased expression in temporal retina and 323 genes showed decreased expression when comparing temporal retina vs. macular retina [32]. Li et al .…”

Characterization of Cav1.4 Complexes (α11.4, β2, and α2δ4) in HEK293T Cells and in the Retina

“…1C). Further evidence for the predominance of ␤ 2X13 in the human retina was obtained in a retinal RNA-seq data set (35), which was specifically evaluated for the inclusion rates of exons 7A, 7B, and 7C. A Cloning of the ␤ 2X13 cDNAs is described in the "Experimental Procedures."…”

“…A retinal RNA-seq experiment using samples from donor eyes (35) was used to determine the expression of human retinal ␤ 2 splice variants. These sequences were aligned to the human genome (release GRCh 37) using the Tuxedo pipeline (36).…”