Transcriptional analysis supports the expression of human snRNA variants and reveals U2 snRNA homeostasis by an abundant U2 variant

Kosmyna, Brian; Gupta, Varun; Query, Charles C.

doi:10.1101/2020.01.24.917260

Cited by 9 publications

(9 citation statements)

References 59 publications

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“…However, variants such as U2-2P, U4-2, and multiple U5 snRNAs exhibit prolonged stability and higher levels of expression as compared to the majority of snRNA variant genes. Together with a recent study indicating that snRNA genes exhibit varying levels of occupancy by transcription factors and RNA polymerase II (Kosmyna et al 2020), our data indicate that both transcription rates and snRNA stability determine variant snRNA abundances.…”

Section: Nearly All Snrna Variants Are Less Stable Than Their Canonic...supporting

confidence: 81%

“…Most snRNA genes have been identified using computational approaches and annotated as being pseudogenes due to sequence differences. However, only a small number have been manually evaluated or studied experimentally (Denison et al 1981;O'Reilly et al 2013;Vazquez-Arango et al 2016;Kosmyna et al 2020). Here, we refer to the most abundantly expressed and biochemically studied snRNA within each family as the "canonical" snRNA, and the remaining snRNAs as "variants."…”

Section: Resultsmentioning

confidence: 99%

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Human spliceosomal snRNA sequence variants generate variant spliceosomes

Mabin

Lewis

Brow

et al. 2021

RNA

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Human pre-mRNA splicing is primarily catalyzed by the major spliceosome, comprising five small nuclear ribonucleoprotein complexes, U1, U2, U4, U5, and U6 snRNPs, each of which contains the corresponding U-rich snRNA. These snRNAs are encoded by large gene families exhibiting significant sequence variation, but it remains unknown if most human snRNA genes are untranscribed pseudogenes or produce variant snRNAs with the potential to differentially influence splicing. Since gene duplication and variation are powerful mechanisms of evolutionary adaptation, we sought to address this knowledge gap by systematically profiling human U1, U2, U4, and U5 snRNA variant gene transcripts. We identified 55 transcripts that are detectably expressed in human cells, 38 of which incorporate into snRNPs and spliceosomes in 293T cells. All U1 snRNA variants are more than 1000-fold less abundant in spliceosomes than the canonical U1, whereas at least 1% of spliceosomes contain a variant of U2 or U4. In contrast, eight U5 snRNA sequence variants occupy spliceosomes at levels of 1% to 46%. Furthermore, snRNA variants display distinct expression patterns across five human cell lines and adult and fetal tissues. Different RNA degradation rates contribute to the diverse steady state levels of snRNA variants. Our findings suggest that variant spliceosomes containing noncanonical snRNAs may contribute to different tissue- and cell-type–specific alternative splicing patterns.

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Section: Nearly All Snrna Variants Are Less Stable Than Their Canonic...supporting

confidence: 81%

Section: Resultsmentioning

confidence: 99%

Human spliceosomal snRNA sequence variants generate variant spliceosomes

Mabin

Lewis

Brow

et al. 2021

RNA

View full text Add to dashboard Cite

show abstract

“…4C). Out of the two major isoforms of U2, U2-1 shows more efficient deposition of the Sm ring and incorporation into snRNP complexes than U2-2 (Kosmyna et al 2020), and we hypothesized that failure of assembly into an snRNP complex might be associated with U2:U2 dimerization. However, analysis of the exact sequences of U2:U2 overlapping chimeras showed that out of 223 reads that could be assigned to specific U2 isoforms, 162 were of the U2-1:U2-1 type, and 59 were U2-1:U2-2 chimeras, suggesting that both U2 isoforms may form homo-and heteromeric intermolecular interactions.…”

Section: Homodimerization Of Human and Yeast Rnasmentioning

confidence: 99%

Global mapping of RNA homodimers in living cells

et al. 2022

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RNA homodimerization is important for various physiological processes, including the assembly of membraneless organelles, RNA subcellular localization, and packaging of viral genomes. However, understanding RNA dimerization has been hampered by the lack of systematic in vivo detection methods. Here, we show that CLASH, PARIS, and other RNA proximity ligation methods detect RNA homodimers transcriptome-wide as “overlapping” chimeric reads that contain more than one copy of the same sequence. Analyzing published proximity ligation data sets, we show that RNA:RNA homodimers mediated by direct base-pairing are rare across the human transcriptome, but highly enriched in specific transcripts, including U8 snoRNA, U2 snRNA, and a subset of tRNAs. Mutations in the homodimerization domain of U8 snoRNA impede dimerization in vitro and disrupt zebrafish development in vivo, suggesting an evolutionarily conserved role of this domain. Analysis of virus-infected cells reveals homodimerization of SARS-CoV-2 and Zika genomes, mediated by specific palindromic sequences located within protein-coding regions of N gene in SARS-CoV-2 and NS2A gene in Zika. We speculate that regions of viral genomes involved in homodimerization may constitute effective targets for antiviral therapies.

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“…Most overlapping chimeras in U2 included the sequence of stem loop III, downstream of the Sm binding site, suggesting that in a fraction of U2 molecules found in the cell, stem loop III is unfolded and forms homomeric intermolecular interactions (Figure 4). Out of the two major isoforms of U2, U2-1 shows more efficient deposition of the Sm ring and incorporation into snRNP complexes than U2-2 (Kosmyna, et al 2020), and we hypothesized that failure of assembly into an snRNP complex might be associated with U2:U2 dimerization. However, analysis of the exact sequences of U2:U2 overlapping chimeras showed that out of 223 reads that could be assigned to specific U2 isoforms, 162 were of the U2-1:U2-1 type, and 59 were U2-1:U2-2 chimeras, suggesting that both U2 isoforms may form homo- and heteromeric intermolecular interactions.…”

Section: Resultsmentioning

confidence: 99%

Global mapping of RNA homodimers in living cells

Gabryelska

Kudla

2021

Preprint

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RNA homodimerization is important for various physiological processes, including the assembly of membraneless organelles, RNA subcellular localization, and packaging of viral genomes. However, understanding of RNA homodimerization has been hampered by the lack of systematic in vivo detection methods. Here we show that PARIS, COMRADES, and other RNA proximity ligation methods can detect RNA homodimers transcriptome-wide as "overlapping" chimeric reads that contain more than one copy of the same sequence. Analysing published proximity ligation datasets, we show that RNA:RNA homodimers mediated by direct base-pairing interactions are rare across the transcriptome, but highly enriched in specific transcripts, including U8 snoRNA, U2 snRNA and a subset of tRNAs. Analysis of data from virus-infected cells reveals homodimerization of SARS-CoV-2 and Zika genomes, mediated by specific palindromic sequences located within protein-coding regions of N protein in SARS-CoV-2 and NS2A gene in Zika. We speculate that regions of viral genomes involved in homodimerization may constitute effective targets for antiviral therapies.

show abstract

Transcriptional analysis supports the expression of human snRNA variants and reveals U2 snRNA homeostasis by an abundant U2 variant

Cited by 9 publications

References 59 publications

Human spliceosomal snRNA sequence variants generate variant spliceosomes

Human spliceosomal snRNA sequence variants generate variant spliceosomes

Global mapping of RNA homodimers in living cells

Global mapping of RNA homodimers in living cells

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