Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Aug 1;23(15):4001-14.
doi: 10.1093/hmg/ddu114. Epub 2014 Mar 14.

Comprehensive analysis of gene expression in human retina and supporting tissues

Mingyao Li  1 , Cheng Jia  1 , Krista L Kazmierkiewicz  2 , Anita S Bowman  2 , Lifeng Tian  3 , Yichuan Liu  1 , Neel A Gupta  4 , Harini V Gudiseva  2 , Stephanie S Yee  2 , Mijin Kim  2 , Tzvete Dentchev  5 , James A Kimble  6 , John S Parker  7 , Jeffrey D Messinger  7 , Hakon Hakonarson  8 , Christine A Curcio  7 , Dwight Stambolian  9
Affiliations

Comprehensive analysis of gene expression in human retina and supporting tissues

Mingyao Li et al. Hum Mol Genet. .

Abstract

Understanding the influence of gene expression on the molecular mechanisms underpinning human phenotypic diversity is fundamental to being able to predict health outcomes and treat disease. We have carried out whole transcriptome expression analysis on a series of eight normal human postmortem eyes by RNA sequencing. Here we present data showing that ∼80% of the transcriptome is expressed in the posterior layers of the eye and that there is significant differential expression not only between the layers of the posterior part of the eye but also between locations of a tissue layer. These differences in expression also extend to alternative splicing and splicing factors. Differentially expressed genes are enriched for genes associated with psychiatric, immune and cardiovascular disorders. Enrichment categories for gene ontology included ion transport, synaptic transmission and visual and sensory perception. Lastly, allele-specific expression was found to be significant for CFH, C3 and CFB, which are known risk genes for age-related macular degeneration. These expression differences should be useful in determining the underlying biology of associations with common diseases of the human retina, retinal pigment epithelium and choroid and in guiding the analysis of the genomic regions involved in the control of normal gene expression.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Gene expression. (A) Hierarchical clustering analysis of top 1000 most divergent genes. For each gene, we calculated its coefficient of variation (CV) based on its log-transformed FPKM values across all RNA-Seq samples. The genes were then ranked based on their CV values. The heatmap was generated by hierarchical clustering of the top 1000 genes with the largest CV values. (B) Number of differentially expressed (DE) genes identified from each comparison. Analysis was completed using Cuffdiff v2.1.1. A gene was considered DE if FDR-adjustedP-value was <0.05. (C) Comparison of gene expression profiles between different tissues within the same location. The Venn diagram shows the numbers of DE genes that were unique to each comparison as well as the number of DE genes that were common between the two comparisons. (D) Comparison of gene expression profiles between different locations within the same tissue.
Figure 2.
Figure 2.
Alternative splicing (AS). (A) Numbers of AS events. An exon was considered alternatively spliced if its exon-inclusion level was >0 but <1. The minimum, maximum and mean numbers of AS events were calculated based on the eight samples in each eye part. (B) Hierarchical clustering analysis of top 150 most divergent alternative splicing events. For each AS event, we calculated its CV based on its exon-inclusion levels across all RNA-Seq samples. The AS events were then ranked based on their CV values. The heatmap was generated by hierarchical clustering of the top 150 AS events with the largest CV values. (C) Number of DAS genes identified from each comparison. Analysis was completed using MATS. An exon was considered DAS if FDR-adjustedP-value was <0.05. (D) Comparison of exon-inclusion levels between different tissues within the same location. The Venn diagram shows the numbers of DAS events that were unique to each comparison as well as the number of DE genes that were common between the two comparisons. (E) Comparison of exon-inclusion levels between different locations within the same tissue. (F) Classification of DAS events by degree of confidence. Tier 1 includes high-confidence events that have been annotated by RefSeq; tier 2 includes moderate-confidence events for each the corresponding genes are alternatively spliced according to uniProt; tier 3 includes the remaining events.
Figure 3.
Figure 3.
RT-PCR biological replication of differential alternative splicing (DAS) events. (A) Replication ofTIMM8B1 DAS event from PR versus PRCS comparison. (B) Replication ofSTXBP1 DAS event from PR versus PRCS comparison. (C) Replication ofCSDA (YBX3) DAS event from PR versus PRCS comparison. (D) Replication ofPKP4 DAS event from PR versus PRCS comparison. (E) Replication ofFMNL1 DAS event from MR versus MRCS comparison.
Figure 4.
Figure 4.
Ex vivo imaging and histology of eye contralateral to that used for RNA-Seq. (A andB) Color image of excised preserved macula (A) and fovea (B) from a 79-year-old Caucasian male. Optic nerve is at the left edge of the punch. (C)Ex vivo spectral domain optical coherence tomography of excised preserved macula, with neurosensory retina at the top and RPE–choroid–sclera at the bottom. The optic nerve is at the left, and the fovea is the dip in the middle. This fovea has postmortem cystic change (arrowheads). The macula is otherwise unremarkable. (D) 0.8-µm-thick epoxy section of tissue post-fixed with the OTAP method, stained with toluidine blue and scanned. Detachment of the neurosensory retina from the RPE is common in postmortem specimens, even if microscopically well-preserved like this one. Green frame indicates area shown at higher magnification inE. (E) Chorioretinal layers on the foveal slope. This area of the retina is cone-dominated, as evidence by the few darkly stained rod nuclei that contrast with numerous cone nuclei in the ONL. Layers: GCL, ganglion cell layer; IPL, inner plexiform layer; INL, inner nuclear layer; OPL, outer plexiform layer; HFL, Henle fiber layer; IS, inner segments of photoreceptors; OS, outer segments of photoreceptors; RPE, retinal pigment epithelium; Ch, choroid; Sc, sclera. Detached retina was digitally reapposed to RPE for illustrative purposes (Eye 2011001R is shown as a left eye by UAB lab convention. As AEB 11-1515-P, it is contralateral to 11-1516-P analyzed by RNA-Seq.).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Freedman M.L., Monteiro A.N., Gayther S.A., Coetzee G.A., Risch A., Plass C., Casey G., De Biasi M., Carlson C., Duggan D., et al. Principles for the post-GWAS functional characterization of cancer risk loci. Nat. Genet. 2011;43:513–518. - PMC - PubMed
    1. Stambolian D. Genetic susceptibility and mechanisms for refractive error. Clin. Genet. 2013;84:102–108. - PMC - PubMed
    1. Cooke Bailey J.N., Sobrin L., Pericak-Vance M.A., Haines J.L., Hammond C.J., Wiggs J.L. Advances in the genomics of common eye diseases. Hum. Mol. Genet. 2013;22:R59–R65. - PMC - PubMed
    1. Klein R.J., Zeiss C., Chew E.Y., Tsai J.Y., Sackler R.S., Haynes C., Henning A.K., SanGiovanni J.P., Mane S.M., Mayne S.T., et al. Complement factor H polymorphism in age-related macular degeneration. Science. 2005;308:385–389. - PMC - PubMed
    1. Nicolae D.L., Gamazon E., Zhang W., Duan S., Dolan M.E., Cox N.J. Trait associated SNPs are more likely to be eQTLS: Annotation to enhance discovery from GWAS. PLoS Genet. 2010;6:e1000888. - PMC - PubMed

Publication types

-