Developmental Analysis of Spliceosomal snRNA Isoform Expression

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.

[1]  Zhipeng Lu,et al.  Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments , 2014, Nucleic acids research.

[2]  A. Gregory Matera,et al.  A day in the life of the spliceosome , 2014, Nature Reviews Molecular Cell Biology.

[3]  A. Matera,et al.  RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins , 2014, Genome Biology.

[4]  Michael P. Meers,et al.  Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes , 2013, RNA.

[5]  Marek Drozdz,et al.  Differentially expressed, variant U1 snRNAs regulate gene expression in human cells , 2013, Genome research.

[6]  K. Praveen,et al.  A Drosophila model of spinal muscular atrophy uncouples snRNP biogenesis functions of survival motor neuron from locomotion and viability defects. , 2012, Cell reports.

[7]  R. Xu,et al.  Structure and assembly of the SF3a splicing factor complex of U2 snRNP , 2012, The EMBO journal.

[8]  S. Ackerman,et al.  Mutation of a U2 snRNA Gene Causes Global Disruption of Alternative Splicing and Neurodegeneration , 2012, Cell.

[9]  Wanfei Liu,et al.  Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing , 2011, Front. Gene..

[10]  A. Shilatifard,et al.  The little elongation complex regulates small nuclear RNA transcription. , 2011, Molecular cell.

[11]  F. Pauler,et al.  An RNA-Seq Strategy to Detect the Complete Coding and Non-Coding Transcriptome Including Full-Length Imprinted Macro ncRNAs , 2011, PloS one.

[12]  C. Will,et al.  Spliceosome structure and function. , 2011, Cold Spring Harbor perspectives in biology.

[13]  Li Yang,et al.  Genomewide characterization of non-polyadenylated RNAs , 2011, Genome Biology.

[14]  Peter J. Bickel,et al.  The Developmental Transcriptome of Drosophila melanogaster , 2010, Nature.

[15]  Songnian Hu,et al.  A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. , 2010, Genomics.

[16]  B. Graveley.  The developmental transcriptome of Drosophila melanogaster , 2010, Nature.

[17]  J. Manley,et al.  Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches , 2009, Nature Reviews Molecular Cell Biology.

[18]  Toralf Kirsten,et al.  Evolution of Spliceosomal snRNA Genes in Metazoan Animals , 2008, Journal of Molecular Evolution.

[19]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[20]  Tyler S. Alioto,et al.  U12DB: a database of orthologous U12-type spliceosomal introns , 2006, Nucleic Acids Res..

[21]  Valer Gotea,et al.  Spliceosomal small nuclear RNA genes in 11 insect genomes. , 2006, RNA.

[22]  Pontus Larsson,et al.  Identification of the Major Spliceosomal RNAs in Dictyostelium discoideum Reveals Developmentally Regulated U2 Variants and Polyadenylated snRNAs , 2006, Eukaryotic Cell.

[23]  R. J. Herrera,et al.  U6 snRNA variants isolated from the posterior silk gland of the silk moth Bombyx mori. , 2006, Insect biochemistry and molecular biology.

[24]  S. Celniker,et al.  Identification and analysis of U5 snRNA variants in Drosophila. , 2005, RNA.

[25]  R. J. Herrera,et al.  The silk moth Bombyx mori U1 and U2 snRNA variants are differentially expressed. , 2005, Gene.

[26]  J. M. Sierra-Montes,et al.  Variants of U1 small nuclear RNA assemble into spliceosomal complexes , 2004, Insect molecular biology.

[27]  G. Kunkel,et al.  Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies. , 2003, Nucleic acids research.

[28]  R. J. Herrera,et al.  Multiple forms of U2 snRNA coexist in the silk moth Bombyx mori , 2002, Insect molecular biology.

[29]  D. P. Pomeranz Krummel,et al.  Structure and assembly of the spliceosomal snRNPs. Novartis Medal Lecture. , 2001, Biochemical Society transactions.

[30]  Yutaka Muto,et al.  Structure and Assembly of the Spliceosomal snRNPs , 2001 .

[31]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[32]  A. Weiner,et al.  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, The EMBO journal.

[33]  E. Lund,et al.  Control of mouse U1 snRNA gene expression during in vitro differentiation of mouse embryonic stem cells. , 1997, Nucleic acids research.

[34]  A. Weiner,et al.  Concerted evolution of the tandem array encoding primate U2 snRNA occurs in situ, without changing the cytological context of the RNU2 locus. , 1995, The EMBO journal.

[35]  Hiten D. Madhani,et al.  A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome , 1992, Cell.

[36]  J. Steitz,et al.  Three novel functional variants of human U5 small nuclear RNA , 1992, Molecular and cellular biology.

[37]  M. Schuler,et al.  Developmental expression of plant snRNAs. , 1991, Nucleic acids research.

[38]  B. Stefanovic,et al.  Isolation and characterization of developmentally regulated sea urchin U2 snRNA genes. , 1991, Developmental biology.

[39]  A. Weiner,et al.  Structure and evolution of the U2 small nuclear RNA multigene family in primates: gene amplification under natural selection? , 1990, Molecular and cellular biology.

[40]  R. Lührmann,et al.  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, Nucleic acids research.

[41]  W. Marzluff,et al.  A developmental switch in sea urchin U1 RNA. , 1989, Developmental biology.

[42]  W. Marzluff,et al.  Expression of the U1 RNA gene repeat during early sea urchin development: evidence for a switch in U1 RNA genes during development. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[43]  I. Mattaj,et al.  Regulated splicing in early development and stage-specific U snRNPs. , 1989, Development.

[44]  I. Botros,et al.  Developmental and tissue-specific expression of U4 small nuclear RNA genes , 1988, Molecular and cellular biology.

[45]  E. Lund,et al.  Heterogeneity of human U1 snRNAs , 1988, Nucleic Acids Res..

[46]  G. Schatten,et al.  Localization and expression of U1 RNA in early mouse embryo development. , 1988, Developmental biology.

[47]  G. Zieve,et al.  Cytoplasmic assembly of snRNP particles from stored proteins and newly transcribed snRNA's in L929 mouse fibroblasts. , 1988, Experimental cell research.

[48]  E. Lund,et al.  Differential accumulation of U1 and U4 small nuclear RNAs during Xenopus development. , 1987, Genes & development.

[49]  E. Lund,et al.  The transcription of Xenopus laevis embryonic U1 snRNA genes changes when oocytes mature into eggs. , 1987, Genes & development.

[50]  E. Lund,et al.  Differential control of U1 small nuclear RNA expression during mouse development. , 1985, Science.

[51]  M. Kirschner,et al.  Differential expression of multiple U1 small nuclear RNAs in oocytes and embryos of Xenopus laevis , 1984, Cell.

[52]  A. Weiner,et al.  Abundant pseudogenes for small nuclear RNAs are dispersed in the human genome. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[53]  I. Schneider,et al.  Cell lines derived from late embryonic stages of Drosophila melanogaster. , 1972, Journal of embryology and experimental morphology.

[54]  R. J. Herrera,et al.  A diversity of U1 small nuclear RNAs in the silk moth Bombyx mori. , 2003, Insect biochemistry and molecular biology.

[55]  Stephen M. Mount,et al.  Drosophila melanogaster genes for U1 snRNA variants and their expression during development. , 1990, Nucleic acids research.