| Summary: | Defects in the development of the ocular lens can cause congenital cataracts. To understand the various etiologies of congenital cataracts, it is important to characterize the genes linked to this developmental defect and to define their downstream pathways that are relevant to lens biology and pathology. Deficiency or alteration of several RNA-binding proteins, including the conserved RBP Celf1 (CUGBP Elav-like family member 1), has been described to cause lens defects and early onset cataracts in animal models and/or humans. Celf1 is involved in various aspects of post-transcriptional gene expression control, including regulation of mRNA stability/decay, alternative splicing and translation. <i>Celf1</i> germline knockout mice and lens conditional knockout (<i>Celf1</i><sup>cKO</sup>) mice develop fully penetrant cataracts in early postnatal stages. To define the genome-level changes in RNA transcripts that result from <i>Celf1</i> deficiency, we performed high-throughput RNA-sequencing of <i>Celf1</i><sup>cKO</sup> mouse lenses at postnatal day (P) 0. <i>Celf1</i><sup>cKO</sup> lenses exhibit 987 differentially expressed genes (DEGs) at cut-offs of >1.0 log2 counts per million (CPM), ≥±0.58 log2 fold-change and <0.05 false discovery rate (FDR). Of these, 327 RNAs were reduced while 660 were elevated in <i>Celf1</i><sup>cKO</sup> lenses. The DEGs were subjected to various downstream analyses including iSyTE lens enriched-expression, presence in Cat-map, and gene ontology (GO) and representation of regulatory pathways. Further, a comparative analysis was done with previously generated microarray datasets on <i>Celf1</i><sup>cKO</sup> lenses P0 and P6. Together, these analyses validated and prioritized several key genes mis-expressed in <i>Celf1</i><sup>cKO</sup> lenses that are relevant to lens biology, including known cataract-linked genes (e.g., <i>Cryab</i>, <i>Cryba2</i>, <i>Cryba4</i>, <i>Crybb1</i>, <i>Crybb2</i>, <i>Cryga</i>, <i>Crygb</i>, <i>Crygc</i>, <i>Crygd</i>, <i>Cryge</i>, <i>Crygf</i>, <i>Dnase2b</i>, <i>Bfsp1</i>, <i>Gja3</i>, <i>Pxdn</i>, <i>Sparc</i>, <i>Tdrd7</i>, etc.) as well as novel candidates (e.g., <i>Ell2</i> and <i>Prdm16</i>). Together, these data have defined the alterations in lens transcriptome caused by Celf1 deficiency, in turn uncovering downstream genes and pathways (e.g., structural constituents of eye lenses, lens fiber cell differentiation, etc.) associated with lens development and early-onset cataracts.
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