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#1317 Review annotations to mRNA cleavage
mRNA cleavage (GO:0006379) was, until recently, under mRNA processing. But this is incorrect, as mRNA processing only covers processes leading to production of mature mRNA, whereas only some mRNA cleavage processes do.
Reviewing direct annotations to this term (see below) shows they are a mixed bag - some processing some not. So, I've generalised the meaning and classification of mRNA cleavage.
The new structure is.
mRNA cleavage (GO:0006379)
. % mRNA cleavage involved in gene silencing
. % mRNA cleavage involved in mRNA processing
. . % pre-mRNA cleavage required for polyadenylation
Ref for cleavage prior to polyadenylation: http://www.ncbi.nlm.nih.gov/books/NBK21563/#A2878
A review of annotations shows As the definition is now more general, current annotations are correct, but could be made more specific.
Review of refs for direct annotations to mRNA cleavage (manual experimental evidence only)
mRNA cleavage involved in mRNA processing:
UniProtKB PMID:10523662 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:10619842 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:10899131 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:11344258 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:11713271 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:12504017 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:18971324 = pre-mRNA cleavage required for polyadenylation + involvement in snoRNA processing
UniProtKB PMID:7590244 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:9342333 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:21102410 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:12704082 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:21317875 = ribonuclease activity in regulated splicing (splices Xbp1 mRNA generating an active Xbp1s transcriptional activator) - fits under processing
UniProtKB PMID:9712888 = Earlier cleavage event - during transcription (involved in read through past block to elongation). Fits under processing?
PMID:12692127 = Earlier cleavage event - during transcription ((involved in read through past block to elongation). Fits under processing?
Leading to mRNA degredation / gene silencing / negative reg of translation
UniProtKB PMID:14729943 = novel method of mRNA degradation: RNase MRP specifically cleaves the CLB2 mRNA in its 5'-UTR to allow rapid 5' to 3' degradation by the Xrn1 nuclease
UniProtKB PMID:15009896 = inhibition of translation in bacteria via mRNA cleavage
UniProtKB PMID:17158880 = 3' end cleavage -> degradation (controlling mRNA in cell cycle
UniProtKB PMID:18007599 = siRNA targeted mRNA cleavage
UniProtKB PMID:18454937 = siRNA pathway
Annotation error?
UniProtKB PMID:20424607 = Refers to miRNA processing, possibly 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing
Above list of annotations with curation groups identified;
mRNA cleavage involved in mRNA processing:
SGD PMID:10523662 = pre-mRNA cleavage required for polyadenylation
SGD PMID:10619842 = pre-mRNA cleavage required for polyadenylation
SGD PMID:10899131 = pre-mRNA cleavage required for polyadenylation
SGD PMID:11344258 = pre-mRNA cleavage required for polyadenylation
SGD PMID:11713271 = pre-mRNA cleavage required for polyadenylation
SGD PMID:12504017 = pre-mRNA cleavage required for polyadenylation
SGD PMID:18971324 = pre-mRNA cleavage required for polyadenylation + involvement in snoRNA processing
SGD PMID:12704082 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:7590244 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:9342333 = pre-mRNA cleavage required for polyadenylation
UniProtKB PMID:21102410 = pre-mRNA cleavage required for polyadenylation
PARL PMID:21317875 = ribonuclease activity in regulated splicing (splices Xbp1 mRNA generating an active Xbp1s transcriptional activator) - fits under processing
SGD PMID:9712888 = Earlier cleavage event - during transcription (involved in read through past block to elongation). Fits under processing?
SGD PMID:12692127 = Earlier cleavage event - during transcription ((involved in read through past block to elongation). Fits under processing?
Leading to mRNA degradation / gene silencing / negative reg of translation:
SGD PMID:14729943 = novel method of mRNA degradation: RNase MRP specifically cleaves the CLB2 mRNA in its 5'-UTR to allow rapid 5' to 3' degradation by the Xrn1 nuclease
SGD PMID:17158880 = 3' end cleavage -> degradation (controlling mRNA in cell cycle
UniProtKB PMID:15009896 = inhibition of translation in bacteria via mRNA cleavage
WB PMID:18007599 = siRNA targeted mRNA cleavage
FB PMID:18454937 = siRNA pathway
Annotation error?
MGI PMID:20424607 = Refers to miRNA processing, possibly 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing