Abstract：
:Post-transcriptional regulation and the formation of mRNA 3' ends are crucial for gene expression in eukaryotes. Interspecies conservation of many sequences within 3'UTRs reveals selective constraint due to similar function. To study the pattern of conservation within 3'UTRs, we compiled and aligned 50 sets of complete orthologous 3'UTRs from four orders of mammals. We observed a mosaic pattern of conservation, with alternating regions of high (phylogenetic footprints) and low similarity. Conservation in 3'UTRs correlates with their base composition and also with the synonymous substitution rate in corresponding coding regions. The non-uniform distribution of conservation is more pronounced for 3'UTRs with a moderate or low level of overall conservation, where invariant nucleotides are more numerous, and their runs of lengths 4-7 occur more frequently than if conservation were random. Many runs of invariant nucleotides are AU-rich or pyrimidine-rich. Some of these runs coincide with known functional cis- elements of eukaryotic mRNAs, such as the U-rich upstream element, polyadenylation signal and DICE regulatory signal. More divergent regions of multiple alignments of 3'UTRs are often more G- and/or C-rich. Our results provide evidence on the importance of moderately conserved regions in 3'UTRs and suggest that regulatory functions of 3'UTRs might utilize gene-specific information in these regions.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Shabalina SA,Ogurtsov AY,Lipman DJ,Kondrashov ASdoi
10.1093/nar/gkg751keywords:
subject
Has Abstractpub_date
2003-09-15 00:00:00pages
5433-9issue
18eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract：:Proteomic and RNomic approaches have identified many components of different ribonucleoprotein particles (RNPs), yet still little is known about the organization and protein proximities within these heterogeneous and highly dynamic complexes. Here we describe a targeted cross-linking approach, which combines cross-lin...
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