ArticleBMC genomics2006
A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 49 citations in OpenAlex.
- A comprehensive analysis of 3'UTRs in Caenorhabditis elegans.Nucleic acids research · 2024Article
- Slight Variations in the Sequence Downstream of the Polyadenylation Signal Significantly Increase Transgene Expression in HEK293T and CHO Cells.International journal of molecular sciences · 2022Article
- CSTF2 Acts as a Prognostic Marker Correlated with Immune Infiltration in Hepatocellular Carcinoma.Cancer management and research · 2022Article
- Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence.Nature communications · 2021Article
- Fine gene expression regulation by minor sequence variations downstream of the polyadenylation signal.Molecular biology reports · 2021Article
- Modeling of Genome-Wide Polyadenylation Signals inFrontiers in genetics · 2019Article
- Reconstitution of the CstF complex unveils a regulatory role for CstF-50 in recognition of 3'-end processing signals.Nucleic acids research · 2018Article
- Localization of RNAPII and 3' end formation factor CstF subunits on C. elegans genes and operons.Transcription · 2016Article
- CstF-64 is necessary for endoderm differentiation resulting in cardiomyocyte defects.Stem cell research · 2014Article
- Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals.BMC evolutionary biology · 2014Article
- A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression.Genes & development · 2014Review
- Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.Nature structural & molecular biology · 2013Article
- A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.BMC bioinformatics · 2013Article
- A viral genome landscape of RNA polyadenylation from KSHV latent to lytic infection.PLoS pathogens · 2013Article
- A multispecies polyadenylation site model.BMC bioinformatics · 2013Article
- Dynamic transitions in RNA polymerase II density profiles during transcription termination.Genome research · 2012Article
- Article
- Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination.Molecular cell · 2011Article
- Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives.Frontiers in plant science · 2011Article
- Long conserved fragments upstream of Mammalian polyadenylation sites.Genome biology and evolution · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe Cleavage Stimulation Factor (CstF) is a required protein complex for eukaryotic mRNA 3'-processing. CstF interacts with 3'-processing downstream elements (DSEs) through its 64-kDa subunit, CstF-64; however, the exact nature of this interaction has remained unclear. We used EST-to-genome alignments to identify and extract large sets of putative 3'-processing sites for mRNA from ten metazoan species, including Homo sapiens, Canis familiaris, Rattus norvegicus, Mus musculus, Gallus gallus, Danio rerio, Takifugu rubripes, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans. In order to further delineate the details of the mRNA-protein interaction, we obtained and multiply aligned CstF-64 protein sequences from the same species.
resultsWe characterized the sequence content and specific positioning of putative DSEs across the range of organisms studied. Our analysis characterized the downstream element (DSE) as two distinct parts - a proximal UG-rich element and a distal U-rich element. We find that while the U-rich element is largely conserved in all of the organisms studied, the UG-rich element is not. Multiple alignment of the CstF-64 RNA recognition motif revealed that, while it is highly conserved throughout metazoans, we can identify amino acid changes that correlate with observed variation in the sequence content and positioning of the DSEs.
conclusionOur analysis confirms the early reports of separate U- and UG-rich DSEs. The correlated variations in protein sequence and mRNA binding sequences provide novel insights into the interactions between the precursor mRNA and the 3'-processing machinery.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.