Identification and molecular structure analysis of a new noncoding RNA, a sbRNA homolog, in the silkworm Bombyx mori genome

Abstract

The small noncoding group of RNAs called stem-bulge RNAs (sbRNAs), first reported in Caenorhabditis elegans, is described as molecules homologous to the Y RNAs, a specific class of noncoding RNAs that is present in vertebrates. This homology indicates the possibility of the existence of sbRNAs in other invertebrate organisms. In this work, we used bioinformatic tools and conserved sequences of sbRNAs from C. Elegans and Y RNAs to search for homologous sbRNA sequences in the Bombyx mori genome. This analysis led to the discovery of one noncoding gene, which was translated into RNA segments and comparatively analysed with segments from human and hamster Y RNAs and C. elegans sbRNAs in molecular dynamic simulations. This gene represents the first evidence for a new sbRNA-like noncoding RNA, the BmsbRNA gene, in this Lepidoptera genome.

Functional roles of non-coding Y RNAs

“…Recently, a family of related small non-coding RNAs, termed stem-bulge RNAs (sbRNAs), was identified in nematode worms ( Aftab et al, 2008 , Boria et al, 2010 , Deng et al, 2006 ), and an sbRNA was also described for the silkworm, B. mori ( Duarte et al, 2015 ). The genome of C. elegans contains at least 18 sbRNA genes, in addition to the related aforementioned CeY RNA gene, each with a putative RNA polymerase III promoter, with many sbRNA genes also present in other nematode species ( Boria et al, 2010 ).…”

“…The family of small non-coding stem-bulge RNAs (sbRNAs) in nematodes has recently been shown to be homologous in structure and function to vertebrate Y RNAs ( Boria et al, 2010 , Kowalski et al, 2015 ). Small non-coding RNAs bearing similarities to vertebrate Y RNAs or nematode sbRNAs have also been reported in other eukaryotes, including the insects Anopheles gambiae ( Perreault et al, 2007 ) and Bombyx mori ( Duarte et al, 2015 ), and the lancet Branchiostoma floridae ( Mosig et al, 2007 ). Similar RNAs have also been described in some prokaryotes, including Deinococcus radiodurans ( Chen et al, 2000 ), Salmonella enterica serovar Typhimurium ( Chen et al, 2013 ), Mycobacterium smegmatis and possibly many more ( Chen et al, 2014 ).…”

Beyond DNA puffs: What can we learn from studying sciarids?

“…More recent studies have revealed that Y RNAs constitute essential initiation factors for chromosomal DNA replication in human cell nuclei and that this function is conserved in vertebrates and nematodes (Kowalski and Krude, ). Y RNAs have also been identified both in Anopheles gambie (Perreault et al ., ) and Bombyx mori (Duarte Junior et al ., ). Therefore it is important to verify if Y RNAs are conserved in sciarids, and if they have a role in DNA puff gene amplification.…”

Y RNA: An Overview of Their Role as Potential Biomarkers and Molecular Targets in Human Cancers

“…Y RNA are conserved molecules [11][12][13][14][15] ( Figure 1) and, in vertebrates, also their clustering is conserved [15][16][17]. A BLAST search shows that the sequence identity is higher than 90% in most vertebrates.…”