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Archana D Siddam, Deepti Anand, Luc Paillard, Salil Anil Lachke; RNA sequencing analysis of Celf1 mouse mutants identifies a cohort of abnormally expressed lens development regulators. Invest. Ophthalmol. Vis. Sci. 201657(12):.
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© 2017 Association for Research in Vision and Ophthalmology.
RNA binding proteins (RBPs) such as Tdrd7 and Caprin2 have recently been recognized as important regulators of post-transcriptional gene expression associated with lens development and disease. We have identified another conserved RBP, Celf1 (CUGBP1), to be essential for lens development and find its deficiency to disrupt this process and cause cataracts. To comprehensively identify the molecular changes associated with Celf1 deficiency, we have analyzed mouse Celf1 conditional (cKO) lenses by deep RNA sequencing (RNA-seq).
Total RNA was extracted from Post-natal day 0 (P0) lenses of Celf1 cKO mutants. 100bp paired-end libraries were prepared and RNA-seq was performed using the Illumina HiSeq platform. Data processing was performed and short reads were aligned against the Mus musculus reference genome (mm10). Differentially expressed genes (DEGs) were analyzed using an established RNA-seq pipeline.
We obtained ~380 million read pairs for control and Celf1 cKO lens samples together. Using a filtering criteria of 2 or greater fold-change and a p-value <0.05, we have identified 310 DEGs in Celf1 cKO lens. Several of the identified DEGs have known key function in the lens. For example, among the DEGs are genes encoding proteins with a structural function, such as Lgsn, Col4a3, Col4a4, Bfsp1, Gja3, Sorbin and Crybb2. Celf1 cKO DEGs also include genes encoding hydrolases (e.g. Dnase2b, Casp3, Trex1), cell cycle related genes (e.g. Cdkna1, Ccnd2, Ccng1, Ddit3), heat shock proteins (e.g. Hspb1, Hspb8), transcription factors (e.g. Prdm16, Zbtb8b) and RNA binding proteins (e.g. Tdrd7). Interestingly, we have also identified differential expression of isoforms of a new cytoskeletal remodeling gene, Asap1. In other cell types, Celf1 is documented to mediate distinct post-transcriptional controls such as RNA decay or splicing to regulate gene expression. These data provides an essential platform to investigate the basis of Celf1-facilitated molecular mechanism in controlling the developing lens.
We have identified many DEGs in the Celf1 cKO lens with established relationship to lens defects as well as several new genes that potentially function in the lens. These findings support the hypothesis that Celf1 participates in mediating multiple and distinct regulatory events in the lens to control its structural organization and fiber cell differentiation.
This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.
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