Human spliceosomal snRNA sequence variants generate variant spliceosomes.

Area of Science:

• Molecular Biology
• Genetics
• RNA Biology

Background:

• Human pre-mRNA splicing is mainly performed by the major spliceosome, composed of U1, U2, U4, U5, and U6 snRNPs, each containing a U-rich snRNA.
• Human snRNA genes form large families with sequence variations, but their transcriptional activity and functional relevance remain largely uncharacterized.

Purpose of the Study:

• To systematically profile human U1, U2, U4, and U5 snRNA variant gene transcripts.
• To determine if variant snRNAs are transcribed, incorporated into spliceosomes, and if they exhibit differential expression patterns.

Main Methods:

• Systematic profiling of human U1, U2, U4, and U5 snRNA variant gene transcripts.
• Quantification of variant snRNA incorporation into snRNPs and spliceosomes in 293T cells.
• Analysis of snRNA variant expression across multiple human cell lines and tissues.
• Investigation of RNA degradation rates influencing steady-state levels.

Main Results:

• Identified 55 detectable human snRNA variant transcripts, with 38 incorporating into snRNPs and spliceosomes.
• U1 snRNA variants were significantly less abundant (<0.1%) in spliceosomes compared to canonical U1.
• Variant U2 and U4 snRNAs were found in at least 1% of spliceosomes.
• Eight U5 snRNA variants were present in spliceosomes at levels ranging from 1% to 46%.

Conclusions:

• Variant spliceosomes containing noncanonical snRNAs are present in human cells.
• Distinct expression patterns and varying incorporation levels suggest functional roles for snRNA variants.
• These variant spliceosomes may contribute to tissue- and cell-type-specific alternative splicing patterns.