Systematic Identification Of Intergenic Long-Noncoding RNAs In Mouse Retinas Using Full-Length Isoform Sequencing

A great mass of long noncoding RNAs(lncRNAs)have been identified in mou-se genome and increasing evidence in the last decades has revealed their cruci-al roles in diverse biological processes.Nevertheless,biological roles of lncRN-As in mouse retina remains largely unknown,which is largely ascribed to the lack of a comprehensive annotation of lncRNAs expressed in the retina tissue.In this work,by using long-read sequencing method,we identified a total of 940 intergenic lncRNAs(lincRNAs)that transcribed from 690 locus in the retinas of embryotic and neonatal mice,with about 16% of them were potentially retina specific.Function analyses of their neighboring genes revealed these ret-inal lincRNA genes were closely associated with retinal neuron cell differentiat-ion and development,including 90 lincRNAs that were differentially expressed after function loss of the key regulators of retinal ganglion cell(RGC)differe-ntiation.Several lincRNAs were potentially RGC specific,including three adjacent to POU domain transcription factors(Pou4f1,Pou4f2 and Pou4f3)that we are validated by in situ hybridization.In summary,this work provided a more comprehensive annotation of mouse retinal lincRNAs that would assist the furth-er exploration of their importance in retina development.