Identification and Characterization of a Class of MALAT1-like Genomic Loci

The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a noncoding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using an RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3′ end triple-helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a co-occurrence of components of the 3′ end module. MALAT1-like genes in Anolis carolinensis are highly expressed in adult testis, thus we named them testis-abundant long noncoding RNAs (tancRNAs). MALAT1-like loci also produce multiple small RNA species, including PIWI-interacting RNAs (piRNAs), from the antisense strand. The 3′ ends of tancRNAs serve as potential targets for the PIWI-piRNA complex. Thus, we have identified an evolutionarily conserved class of long noncoding RNAs (lncRNAs) with similar structural constraints, post-transcriptional processing, and subcellular localization and a distinct function in spermatocytes. [Display omitted] •The 3′ end of MALAT1-like RNAs contains triple-helix and tRNA-like structures•A secondary structure-based covariance model identifies 132 MALAT1-like genomic loci•These genomic loci in lizard express MALAT1-like noncoding RNAs and piRNAs•Lizard long noncoding RNAs recruit the PIWI/piRNA complex to meiotic chromatin Zhang et al. find that vertebrate genomes have more than 130 genomic loci with a unique 3′ end structure similar to that of MALAT1. This class of MALAT1-like noncoding RNAs in green lizard is expressed in testis, and it recruits piRNAs derived from the opposite strands to meiotic chromatin in spermatocytes.