Considering pre-mRNA splicing is highly conserved across species 4, we hypothesized that the computational prediction of branch point sequences is also possible in cattle, for which experimentally validated branch point sequences are not yet available. Computational methods leveraging the features of a high confidence set of few experimentally detected branch point sequences enable systematic assessment of this intronic motif at a genome-wide scale 18, 19, 20. Intronic branch point sequences have been identified experimentally in humans and model organisms 16, 17. Thus, widely used tools to predict functional consequences of genetic variants such as Ensembl’s Variant Effect Predictor 15 are largely blind to branch point sequences. Despite their functional importance, branch point sequences are not systematically studied because they are not annotated in gene transfer files. Mutations affecting the branch point sequence may compromise the assembly of the spliceosome, leading to dramatic changes in splicing and gene expression with disease consequences 10, 13, 14. Subsequently, the free 5′ exon attacks the 3′ splice site resulting in exon ligation, and release and degradation of the intron lariat 5. An attack of the unpaired branch point nucleotide to the 5′ splice site, frees the 5’ exon, and forms a lariat intermediate. The unpaired branch point, usually adenine, bulges out of the U2 snRNA-pre-mRNA duplex. All residues of the heptamer except the branch point undergo base-pairing 12. During pre-mRNA splicing, the branch point sequence undergoes base-pairing with a conserved 6-bp motif (GUAGUA) of the U2 snRNA. In the vast majority of introns, this motif resides between 18 and 37 bases upstream of the 3′ splice site 9, 10, 11. The branch point is contained within a degenerate intronic heptamer called the branch point sequence 8. Cis-acting intronic elements include the highly conserved splice acceptor and donor sites at the exon-intron boundaries, the branch point sequence and a polypyrimidine tract between the branch point and the 3′ splice acceptor site 7. Motifs necessary for recruitment and assembly of the spliceosome are contained in both intronic and exonic sequences 6. These subunits of the spliceosome are sequentially recruited and assembled anew 5 at the intron-exon boundary to remove noncoding sequences (introns) and ligate coding sequences (exons) together. The spliceosome complex consists of five small ribonucleic protein particles (snRNP), namely U1, U2, U4, U5, and U6 and a multitude of other proteins. Pre-mRNA splicing by the spliceosome is evolutionarily conserved across eukaryotes 4. Such regulatory elements, in particular expression and splicing QTL, contribute disproportionately to the heritability of complex traits and diseases 3. Transcriptome analyses in large cohorts of humans, model organisms, and livestock have revealed regulatory elements in noncoding sequences that modulate gene expression and alternative splicing 1, 2. Noncoding sequences of the genome are an important source of genetic variation.
0 Comments
Leave a Reply. |
Details
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |