Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family

Abstract

Eukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre-mRNA) into mature messenger RNA. The mega-macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1-70K, are crucial for splice site recognition during early spliceosome assembly. The human U1-70K has been linked to several types of human autoimmune and neurodegenerative diseases. However, its phylogenetic relationship has been seldom reported. To this end, we carried out a systemic analysis of 95 animal U1-70K genes and compare these proteins to their yeast and plant counterparts. Analysis of their gene and protein structures, expression patterns and splicing conservation suggest that animal U1-70Ks are conserved in their molecular function, and may play essential role in cancers and juvenile development. In particular, animal U1-70Ks display unique characteristics of single copy number and a splicing isoform with truncated C-terminal, suggesting the specific role of these U1-70Ks in animal kingdom. In summary, our results provide phylogenetic overview of U1-70K gene family in vertebrates. In silico analyses conducted in this work will act as a reference for future functional studies of this crucial U1 splicing factor in animal kingdom.

QuantAS: a comprehensive pipeline to study alternative splicing by absolute quantification of splice isoforms

“…2f). U1-70K is the central component of U1 small nuclear ribonucleoprotein (U1 snRNP) responsible for the recognition of the 5 0 splice site during splicing, which is likely to function in response to osmotic stress in Arabidopsis thaliana (Fan et al, 2021). The change in AS2 was considerably higher than that in AS1 in response to lead(II) stress (P < 0.05) in roots, implying that AS2 may play a dominant role in coping with this stress.…”

“…By applying QuantAS to study all isoforms, a comprehensive understanding of their expression patterns and regulatory modes under different conditions can be achieved. In addition to facilitating gene function studies, QuantAS has potential applications in phylogenetic analysis and early screening of the disease by detection of abnormal AS events (K. L. Zhang et al, 2021;Y. Zhang et al, 2021).…”

Clinical significance of small nuclear ribonucleoprotein U1 subunit 70 in patients with hepatocellular carcinoma

“…SNRNP70 is a component of the spliceosome U1 snRNP, which is essential for recognizing the 5′ splice site of the mRNA precursor and subsequent assembly of the spliceosome ( Fan et al, 2021 ; Zahler et al, 2018 ). Current research reports chiefly pay attention to the spliceosome function of SNRNP70.…”