The silk moth Bombyx mori U1 and U2 snRNA variants are differentially expressed

Sierra-Montes, Julie M.; Pereira-Simon, Simone; Smail, Shamayra S.; Herrera, René J.

doi:10.1016/j.gene.2005.02.013

Cited by 19 publications

(39 citation statements)

References 30 publications

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“…For Drosophilids, on the other hand, our analysis is almost identical to the results of [53,Tab.1] and the data reported in [77]. Furthermore, we come close the results of a comparative genomics screen for non-coding RNAs in C. elegans [49], which reported 12 U1, 19 U2, 5 U4, 13 U5, and 23 U6, i.e., only a few more candidates than our present purely homology-based approach.…”

Section: Homology Searchsupporting

confidence: 89%

“…They were manually compared with previously published sequence elements. We visually compared the MEME -patterns with the upstream elements in related species from the following literature sources: [26] (general motifs), [14,82,2,38] (human), [36,5] (chicken), [53] (insects), [77] (Bombyx mori), [81] (Strongylocentrotus purpuratus), [84] (Caenorhabditis elegans).…”

Section: Upstream Region Analysismentioning

confidence: 99%

“…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: Homology Searchsupporting

confidence: 89%

Section: Upstream Region Analysismentioning

confidence: 99%

Section: Phylogenetic Analysis and Paralogsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evolution of Spliceosomal snRNA Genes in Metazoan Animals

2008

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“…In each case, individual variants with distinct sequences showed unique patterns of developmental and tissue-specific expression. Similar observations have been made in pea (Hanley and Schuler 1991) and silk moth (Sierra-Montes et al 2005). The differential expression of snRNA variants could be due to functional differences.…”

Section: Snrnas and Snrna Variantssupporting

confidence: 82%

Spliceosomal small nuclear RNA genes in 11 insect genomes

Mount¹,

Gotea²,

Lin³

et al. 2006

RNA

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The removal of introns from the primary transcripts of protein-coding genes is accomplished by the spliceosome, a large macromolecular complex of which small nuclear RNAs (snRNAs) are crucial components. Following the recent sequencing of the honeybee (Apis mellifera) genome, we used various computational methods, ranging from sequence similarity search to RNA secondary structure prediction, to search for putative snRNA genes (including their promoters) and to examine their pattern of conservation among 11 available insect genomes (A. mellifera, Tribolium castaneum, Bombyx mori, Anopheles gambiae, Aedes aegypti, and six Drosophila species). We identified candidates for all nine spliceosomal snRNA genes in all the analyzed genomes. All the species contain a similar number of snRNA genes, with the exception of A. aegypti, whose genome contains more U1, U2, and U5 genes, and A. mellifera, whose genome contains fewer U2 and U5 genes. We found that snRNA genes are generally more closely related to homologs within the same genus than to those in other genera. Promoter regions for all spliceosomal snRNA genes within each insect species share similar sequence motifs that are likely to correspond to the PSEA (proximal sequence element A), the binding site for snRNA activating protein complex, but these promoter elements vary in sequence among the five insect families surveyed here. In contrast to the other insect species investigated, Dipteran genomes are characterized by a rapid evolution (or loss) of components of the U12 spliceosome and a striking loss of U12-type introns.

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Spliceosomal snRNAs, the Essential Players in pre‐mRNA Processing in Eukaryotic Nucleus: From Biogenesis to Functions and Spatiotemporal Characteristics

Su,

Wu,

Chen

et al. 2024

Advanced Biology

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Spliceosomal small nuclear RNAs (snRNAs) are a fundamental class of non‐coding small RNAs abundant in the nucleoplasm of eukaryotic cells, playing a crucial role in splicing precursor messenger RNAs (pre‐mRNAs). They are transcribed by DNA‐dependent RNA polymerase II (Pol II) or III (Pol III), and undergo subsequent processing and 3′ end cleavage to become mature snRNAs. Numerous protein factors are involved in the transcription initiation, elongation, termination, splicing, cellular localization, and terminal modification processes of snRNAs. The transcription and processing of snRNAs are regulated spatiotemporally by various mechanisms, and the homeostatic balance of snRNAs within cells is of great significance for the growth and development of organisms. snRNAs assemble with specific accessory proteins to form small nuclear ribonucleoprotein particles (snRNPs) that are the basal components of spliceosomes responsible for pre‐mRNA maturation. This article provides an overview of the biological functions, biosynthesis, terminal structure, and tissue‐specific regulation of snRNAs.

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The silk moth Bombyx mori U1 and U2 snRNA variants are differentially expressed

Cited by 19 publications

References 30 publications

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Spliceosomal small nuclear RNA genes in 11 insect genomes

Spliceosomal snRNAs, the Essential Players in pre‐mRNA Processing in Eukaryotic Nucleus: From Biogenesis to Functions and Spatiotemporal Characteristics

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