Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
G3 (Bethesda)
2014 Nov 21;51:103-10. doi: 10.1534/g3.114.015735.
Show Gene links
Show Anatomy links
Developmental analysis of spliceosomal snRNA isoform expression.
Lu Z
,
Matera AG
.
???displayArticle.abstract???
Pre-mRNA splicing is a critical step in eukaryotic gene expression that contributes to proteomic, cellular, and developmental complexity. Small nuclear (sn)RNAs are core spliceosomal components; however, the extent to which differential expression of snRNA isoforms regulates splicing is completely unknown. This is partly due to difficulties in the accurate analysis of the spatial and temporal expression patterns of snRNAs. Here, we use high-throughput RNA-sequencing (RNA-seq) data to profile expression of four major snRNAs throughout Drosophila development. This analysis shows that individual isoforms of each snRNA have distinct expression patterns in the embryo, larva, and pharate adult stages. Expression of these isoforms is more heterogeneous during embryogenesis; as development progresses, a single isoform from each snRNA subtype gradually dominates expression. Despite the lack of stable snRNA orthologous groups during evolution, this developmental switching of snRNA isoforms also occurs in distantly related vertebrate species, such as Xenopus, mouse, and human. Our results indicate that expression of snRNA isoforms is regulated and lays the foundation for functional studies of individual snRNA isoforms.
Figure 1. Alignment of Drosophila snRNA paralogs. The secondary structure of each snRNA is presented on the top line of each alignment using the dot-bracket notation. The U1 and U2 paralogs have very few variable nucleotide positions (three for U1 and four for U2), and they are highlighted with the black background and white lettering. Sequence elements that are important for base-pairing with other RNAs or interaction with proteins are indicated. U1:21D, U1:95Ca, and U1:95Cb are identical. U2:34ABb and U2:34ABc are identical. 5′ ss recognition: sequence recognizing pre-mRNA 5′ splice site. BPRS: branch-point recognition sequence. SL1, SL2, SL2a, and SL4: stem loops. U4 and U5 paralogs have significant differences among them and U5 paralogs are the most diverse. The 3′ stem loop secondary structure of U5 isoforms is conserved, despite the divergence on the sequence level. Reads covering U4:25F (nucleotides 1–47), U4:38AB (1–46), and U4:39B (1–46) are unique among the three U4 paralogs. Reads covering U5:63BC (96–122) and the other six (97–end) are unique among all U5 paralogs. See Supplementary Methods for details of read mapping.
Figure 2. Alignment of mouse snRNA paralogs. Nucleotide variations are highlighted with the black background and white letters. See Figure 1 for abbreviated motif names. Sequence elements that are important for base-pairing with other RNA subtypes or interaction with proteins are indicated. Mouse (m), rat (r), chicken (c), and human (h) U4 snRNA paralogs are aligned together to show the two orthologous groups. Interestingly, even though the U4 snRNAs in several vertebrate species, human, mouse, rat, and chicken, have only three nucleotide variations, they clearly segregate into two groups, based on the two variants in the second stem-loop. Similar to fly U5 snRNAs, mouse U5 paralogs are also the most diverse, and the variable region is confined to the 3′ end. See Supplementary Methods for details of read mapping.
Figure 3. Differential expression of snRNA paralogs during development. (A and C) The fractional expression level for each snRNA paralog was calculated from reads mapping to the variable regions shown in Figure 1 and Figure 2. The fractions for the paralogs of each snRNA subtype add up to 1 in each stage. (A) U2:14B and U2:38ABa are not identical, but they are lumped together due to an insufficiency in read numbers for embryos. (B and D) The SD of the fractional expression values for each group of snRNA isoforms was calculated for each developmental stage. See Materials and Methods for the number of samples in each stage. (E) Summary of previous studies on snRNA isoform expression patterns in various species.
Alioto,
U12DB: a database of orthologous U12-type spliceosomal introns.
2007, Pubmed
Alioto,
U12DB: a database of orthologous U12-type spliceosomal introns.
2007,
Pubmed
Bach,
Structure-probing of U1 snRNPs gradually depleted of the U1-specific proteins A, C and 70k. Evidence that A interacts differentially with developmentally regulated mouse U1 snRNA variants.
1990,
Pubmed
Chen,
Identification and analysis of U5 snRNA variants in Drosophila.
2005,
Pubmed
Chen,
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.
2009,
Pubmed
Cheng,
Control of mouse U1 snRNA gene expression during in vitro differentiation of mouse embryonic stem cells.
1997,
Pubmed
Cui,
A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing.
2010,
Pubmed
Denison,
Abundant pseudogenes for small nuclear RNAs are dispersed in the human genome.
1981,
Pubmed
Domitrovich,
Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies.
2003,
Pubmed
Forbes,
Differential expression of multiple U1 small nuclear RNAs in oocytes and embryos of Xenopus laevis.
1984,
Pubmed
,
Xenbase
Garcia,
Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes.
2013,
Pubmed
Graveley,
The developmental transcriptome of Drosophila melanogaster.
2011,
Pubmed
Hanley,
Developmental expression of plant snRNAs.
1991,
Pubmed
Hinas,
Identification of the major spliceosomal RNAs in Dictyostelium discoideum reveals developmentally regulated U2 variants and polyadenylated snRNAs.
2006,
Pubmed
Huang,
An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.
2011,
Pubmed
Jia,
Mutation of a U2 snRNA gene causes global disruption of alternative splicing and neurodegeneration.
2012,
Pubmed
Korf,
Developmental and tissue-specific expression of U4 small nuclear RNA genes.
1988,
Pubmed
Li,
Mapping short DNA sequencing reads and calling variants using mapping quality scores.
2008,
Pubmed
Lin,
Structure and assembly of the SF3a splicing factor complex of U2 snRNP.
2012,
Pubmed
Liu,
Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing.
2011,
Pubmed
Lo,
Drosophila melanogaster genes for U1 snRNA variants and their expression during development.
1990,
Pubmed
,
Xenbase
Lobo,
Localization and expression of U1 RNA in early mouse embryo development.
1988,
Pubmed
Lu,
RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins.
2014,
Pubmed
Lu,
Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments.
2014,
Pubmed
Lund,
Differential accumulation of U1 and U4 small nuclear RNAs during Xenopus development.
1987,
Pubmed
,
Xenbase
Lund,
Heterogeneity of human U1 snRNAs.
1988,
Pubmed
Lund,
The transcription of Xenopus laevis embryonic U1 snRNA genes changes when oocytes mature into eggs.
1987,
Pubmed
,
Xenbase
Lund,
Differential control of U1 small nuclear RNA expression during mouse development.
1985,
Pubmed
Madhani,
A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome.
1992,
Pubmed
Marz,
Evolution of spliceosomal snRNA genes in metazoan animals.
2008,
Pubmed
Matera,
Structure and evolution of the U2 small nuclear RNA multigene family in primates: gene amplification under natural selection?
1990,
Pubmed
Matera,
A day in the life of the spliceosome.
2014,
Pubmed
Mattaj,
Regulated splicing in early development and stage-specific U snRNPs.
1989,
Pubmed
Mount,
Spliceosomal small nuclear RNA genes in 11 insect genomes.
2007,
Pubmed
Nagai,
Structure and assembly of the spliceosomal snRNPs. Novartis Medal Lecture.
2001,
Pubmed
Nash,
A developmental switch in sea urchin U1 RNA.
1989,
Pubmed
O'Reilly,
Differentially expressed, variant U1 snRNAs regulate gene expression in human cells.
2013,
Pubmed
Pavelitz,
Concerted evolution of the tandem array encoding primate U2 snRNA occurs in situ, without changing the cytological context of the RNU2 locus.
1995,
Pubmed
Pavelitz,
Concerted evolution of the tandem array encoding primate U2 snRNA (the RNU2 locus) is accompanied by dramatic remodeling of the junctions with flanking chromosomal sequences.
1999,
Pubmed
Pereira-Simon,
Variants of U1 small nuclear RNA assemble into spliceosomal complexes.
2004,
Pubmed
Praveen,
A Drosophila model of spinal muscular atrophy uncouples snRNP biogenesis functions of survival motor neuron from locomotion and viability defects.
2012,
Pubmed
Rice,
EMBOSS: the European Molecular Biology Open Software Suite.
2000,
Pubmed
Santiago,
Expression of the U1 RNA gene repeat during early sea urchin development: evidence for a switch in U1 RNA genes during development.
1989,
Pubmed
Sauterer,
Cytoplasmic assembly of snRNP particles from stored proteins and newly transcribed snRNA's in L929 mouse fibroblasts.
1988,
Pubmed
Schneider,
Cell lines derived from late embryonic stages of Drosophila melanogaster.
1972,
Pubmed
Sierra-Montes,
The silk moth Bombyx mori U1 and U2 snRNA variants are differentially expressed.
2005,
Pubmed
Sierra-Montes,
Multiple forms of U2 snRNA coexist in the silk moth Bombyx mori.
2002,
Pubmed
Sierra-Montes,
A diversity of U1 small nuclear RNAs in the silk moth Bombyx mori.
2003,
Pubmed
Smail,
U6 snRNA variants isolated from the posterior silk gland of the silk moth Bombyx mori.
2006,
Pubmed
Smith,
The little elongation complex regulates small nuclear RNA transcription.
2011,
Pubmed
Sontheimer,
Three novel functional variants of human U5 small nuclear RNA.
1992,
Pubmed
Stefanovic,
Isolation and characterization of developmentally regulated sea urchin U2 snRNA genes.
1991,
Pubmed
Will,
Spliceosome structure and function.
2011,
Pubmed
Yang,
Genomewide characterization of non-polyadenylated RNAs.
2011,
Pubmed
