The evolution and expression of the snaR family of small non-coding RNAs

Abstract

We recently identified the snaR family of small non-coding RNAs that associate in vivo with the nuclear factor 90 (NF90/ILF3) protein. The major human species, snaR-A, is an RNA polymerase III transcript with restricted tissue distribution and orthologs in chimpanzee but not rhesus macaque or mouse. We report their expression in human tissues and their evolution in primates. snaR genes are exclusively in African Great Apes and some are unique to humans. Two novel families of snaR-related genetic elements were found in primates: CAS (catarrhine ancestor of snaR), limited to Old World Monkeys and apes; and ASR (Alu/snaR-related), present in all monkeys and apes. ASR and CAS appear to have spread by retrotransposition, whereas most snaR genes have spread by segmental duplication. snaR-A and snaR-G2 are differentially expressed in discrete regions of the human brain and other tissues, notably including testis. snaR-A is up-regulated in transformed and immortalized human cells, and is stably bound to ribosomes in HeLa cells. We infer that snaR evolved from the left monomer of the primate-specific Alu SINE family via ASR and CAS in conjunction with major primate speciation events, and suggest that snaRs participate in tissue- and species-specific regulation of cell growth and translation.

Analysis of the human immunodeficiency virus-1 RNA packageome

“…In addition to 7SL, we detected other host RNAs reported to be packaged, including 5S rRNA ), U1 snRNA (Khan et al 2007), U6 snRNA (Houzet et al 2007), and Y RNAs (Khan et al 2007;Tian et al 2007). We also detected RNAs not reported previously, including Alu RNAs, LINEs, the vtRNA1-1 RNA subunit of cytoplasmic vault RNPs (Kickhoefer et al 1998), and the primate-specific snaR-A RNA (Parrott et al 2011). All these RNAs appeared to be packaged in far lower amounts than 7SL RNA (Supplemental Table S1).…”

Expression of Type II Chorionic Gonadotropin Genes Supports a Role in the Male Reproductive System

“…Most of it (ϳ0.6 kb), including snaR-G and the unique first exon of hCG␤1/2, is orthologous to a chromosome 19 region located ϳ1.5 Mb downstream of the LH/CG␤ cluster. This region contains a homologous snaR gene, snaR-F, in the same position and orientation as in the insert (45,46). Abutting the 5Ј end of this region is a short sequence (80 bp) homologous to chromosome 18, embedded in Alu sequences.…”

“…The structure of the LH/CG␤ cluster has not yet been defined in gorilla, but this species appears to have distinct CG␤1 and CG␤2 genes (22). Correspondingly, gorilla has both snaR-G1 and snaR-G2, which have diverged considerably from each other, as in humans (45,46). Within the Pan genus the snaR-G genes are almost identical to one another and are more closely related to snaR-G1 than to snaR-G2 of humans (Fig.…”

“…In the evolution of type II CG␤ genes, an ϳ0.7-kb sequence (22) containing the snaR-G gene (44,46) replaced ancestral type I sequence encompassing its proximal promoter and nearly all of its 5Ј untranslated region (UTR) (Fig. 1B).…”

“…1A) (23). snaR-G1 and -G2 are located 86 bp upstream of the transcriptional start sites of hCG␤1 and -␤2, respectively, in the opposite orientation to the type II hCG␤ gene (44,46). The snaR genes are a family of ϳ30 genes in humans that are transcribed by polymerase III (Pol III) into small noncoding RNA (44).…”