U6 snRNA variants isolated from the posterior silk gland of the silk moth Bombyx mori

Smail, Shamayra S.; Ayesh, Karima; Sierra-Montes, Julie M.; Herrera, René J.

doi:10.1016/j.ibmb.2006.03.004

Cited by 8 publications

(17 citation statements)

References 36 publications

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“…Distinguishable snRNA paralogs that are often differentially expressed have previously been reported for a diverse collection of major spliceosmal snRNAs including U1 snRNAs in insects [43,64,77], Xenopus [12], and human [39], U2 snRNAs in Dictyostelium [29], sea urchin [80] and silk moth [77], U5 snRNAs in human [79], sea urchin [52], and Drosophilids [8], U6 snRNAs in silk moth [78] and human [85,14].…”

Section: Phylogenetic Analysis and Paralogsmentioning

confidence: 99%

“…Very recently, however, some of these variants have been studied in more details, see e.g. [64,8,39,77,29,78] and the references therein. The only systematic study that we are aware of is the recent comprehensive analysis of 11 insect genomes [53] which reported that phylogenetic gene trees of insect snRNAs do not provide clear support for discernible paralog groups of U1 and/or U5 snRNAs that would correspond to the variants with tissue-specific expression patterns.…”

Section: Introductionmentioning

confidence: 99%

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Evolution of Spliceosomal snRNA Genes in Metazoan Animals

2008

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While studies of the evolutionary histories of protein families are common place, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the 9 spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs was detected in Nematodes and in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralog groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit in particular U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.

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Section: Phylogenetic Analysis and Paralogsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

2008

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“…Interestingly, expressed snRNA variants have been described in a number of organisms, including Dictyostelium discoideum (Hinas, Larsson et al 2006), Drosophila melanogaster (Chen, Lullo et al 2005), the silk moth, Bombyx mori (Sierra-Montes, Freund et al 2002; Sierra-Montes, Pereira-Simon et al 2003; Sierra-Montes, Pereira-Simon et al 2005; Smail, Ayesh et al 2006) and humans (Kyriakopoulou, Larsson et al 2006). In the case of human U1-like sequences, Kyriakopoulou et al 2006 identified four expressed variants, U1A4, U1A5, U1A6, and U1A7, which were hypermethylated, bound Sm proteins in varying degrees and formed high molecular weight complexes.…”

Section: Introductionmentioning

confidence: 99%

U1 small nuclear RNA variants differentially form ribonucleoprotein particles in vitro

Somarelli

Mesa

Rodriguez

et al. 2014

Gene

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The U1 small nuclear (sn)RNA participates in splicing of pre-mRNAs by recognizing and binding to 5′ splice sites at exon/intron boundaries. U1 snRNAs associate with 5′ splice sites in the form of ribonucleoprotein particles (snRNPs) that are comprised of the U1 snRNA and 10 core components, including U1A, U1-70K, U1C and the ‘Smith antigen’, or Sm, heptamer. The U1 snRNA is highly conserved across a wide range of taxa; however, a number of reports have identified the presence of expressed U1-like snRNAs in multiple species, including humans. While numerous U1-like molecules have been shown to be expressed, it is unclear whether these variant snRNAs have the capacity to form snRNPs and participate in splicing. The purpose of the present study was to further characterize biochemically the ability of previously identified human U1-like variants to form snRNPs and bind to U1 snRNP proteins. A bioinformatics analysis provided support for the existence of multiple expressed variants. In vitro gel shift assays, competition assays, and (IPs) precipitations revealed that the variants formed high molecular weight assemblies to varying degrees and associated with core U1 snRNP proteins to a lesser extent than the canonical U1 snRNA. Together, these data suggest that the hU1 snRNA variants analyzed here are unable to efficiently bind U1 snRNP proteins. The current work provides additional biochemical insights into the ability of the variants to assemble into snRNPs.

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“…Shamayra et al (2006) investigated the posterior silk gland of the B. mori Nistari strain and obtained five U6 small nuclear RNA (snRNA) isoforms. Their sequences were identical to the 35 full-length U6 variants recently released in the Whole Genome Shotgun (WGS; Mita et al 2004 ) database of the p50T strain.…”

Section: Introductionmentioning

confidence: 99%

“…Their sequences were identical to the 35 full-length U6 variants recently released in the Whole Genome Shotgun (WGS; Mita et al 2004 ) database of the p50T strain. The main function of U6 snRNA is in pre-mRNA processing, in which variants can modulate the assemblage of the catalytic core as well as affect the splicing rate ( Shamayra et al 2006 ). U6 snRNA is commonly employed as the universal reference gene in identifying gene expression ( Liu et al 2008 ; Yu et al 2008a ; Yu et al 2009 ; Huang et al 2011b ).…”

Section: Introductionmentioning

confidence: 99%

Overview of research on Bombyx mori microRNA

Wang

Tang

Shen

2014

Journal of Insect Science

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MicroRNAs (miRNAs) constitute some of the most significant regulatory factors involved at the post-transcriptional level after gene expression, contributing to the modulation of a large number of physiological processes such as development, metabolism, and disease occurrence. This review comprehensively and retrospectively explores the literature investigating silkworm, Bombyx mori L. (Lepidoptera: Bombicidae), miRNAs published to date, including discovery, identification, expression profiling analysis, target gene prediction, and the functional analysis of both miRNAs and their targets. It may provide experimental considerations and approaches for future study of miRNAs and benefit elucidation of the mechanisms of miRNAs involved in silkworm developmental processes and intracellular activities of other unknown non-coding RNAs.

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U6 snRNA variants isolated from the posterior silk gland of the silk moth Bombyx mori

Cited by 8 publications

References 36 publications

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

U1 small nuclear RNA variants differentially form ribonucleoprotein particles in vitro

Overview of research on Bombyx mori microRNA

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