Profiling of testis-specific long noncoding RNAs in mice

Abstract

Background: Spermatogenesis, which is the complex and highly regulated process of producing haploid spermatozoa, involves testis-specific transcripts. Recent studies have discovered that long noncoding RNAs (IncRNAs) are novel regulatory molecules that play important roles in various biological processes. However, there has been no report on the comprehensive identification of testis-specific IncRNAs in mice. Results: We performed microarray analysis of transcripts from mouse brain, heart, kidney, liver and testis. We found that testis harbored the highest proportion of tissue-specific IncRNAs (11%; 1607 of 14,256). Testis also harbored the largest number of tissue-specific mRNAs among the examined tissues, but the proportion was lower than that of IncRNAs (7%; 1090 of 16,587). We categorized the testis-specific IncRNAs and found that a large portion corresponded to long intergenic ncRNAs (IincRNAs). Genomic analysis identified 250 protein-coding genes located near (<= 10kb) 194 of the loci encoding testis-specific IincRNAs. Gene ontology (GO) analysis showed that these protein-coding genes were enriched for transcriptional regulation-related terms. Analysis of male germ cell-related cell lines (F9, GC-1 and GC-2) revealed that some of the testis-specific IncRNAs were expressed in each of these cell lines. Finally, we arbitrarily selected 26 testis-specific IncRNAs and performed in vitro expression analysis. Our results revealed that all of them were expressed exclusively in the testis, and 23 of the 26 showed germ cell-specific expression. Conclusion: This study provides a catalog of testis-specific IncRNAs and a basis for future investigation of the IncRNAs involved in spermatogenesis and testicular functions.