#11642 TPV mRNA cleavage involved in gene silencing by miRNA

[David Osumi-Sutherland]

RNA processing: "Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules."
. % mRNA processing: "Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide."
. . % mRNA cleavage: "Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner." <- Note, requirement that a more mature product be produced dropped here.
. . . % mRNA cleavage involved in gene silencing by miRNA: "The process in which microRNAs (miRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically direct cleavage by base pairing with near-perfect complementarity to the target mRNA. Many plant miRNAs downregulate gene expression through this mechanism." <--- Clearly not resulting in production of a more mature product.

Potential solution: Need to distinguish cleavage of 3' end prior to polyadenylation, a process involved in maturation, from miRNA guided cleavage at internal site leading to silencing.

Question: should we have a general class for RNA cleavage that covers both cases, or just two specific cases? Need to check usage

[David Osumi-Sutherland]

ref for cleavage prior to polyadenylation: http://www.ncbi.nlm.nih.gov/books/NBK21563/#A2878

Refs for direct annotations to mRNA cleavage:

Processing:

PMID:10523662 = cleavage of 3' end prior to polyadenylation
PMID:10619842 = cleavage of 3' end prior to polyadenylation
PMID:10899131 = cleavage of 3' end prior to polyadenylation
PMID:11344258 = cleavage of 3' end prior to polyadenylation
PMID:11713271 = cleavage of 3' end prior to polyadenylation
PMID:12504017 = cleavage of 3' end prior to polyadenylation
PMID:18971324 = cleavage of 3' end prior to polyadenylation + involvement in snoRNA processing
PMID:7590244 = cleavage of 3' end prior to polyadenylation
PMID:9342333 = cleavage of 3' end prior to polyadenylation
PMID:21102410 = cleavage of 3' end prior to polyadenylation
PMID:12704082 = cleavage of 3' end prior to polyadenylation

PMID:21317875 = ribonuclease activity in regulated splicing (splices Xbp1 mRNA generating an active Xbp1s transcriptional activator) - fits under processing

PMID:9712888 = Earlier cleavage event - during transcription (involved in read through past block to elongation)
PMID:12692127 = Earlier cleavage event - during transcription ((involved in read through past block to elongation)

Leading to mRNA degredation:

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
PMID:15009896 = inhibition of translation in bacteria via mRNA cleavage
PMID:17158880 = 3' end cleavage -> degradation (controlling mRNA in cell cycle
PMID:18007599 = siRNA targeted mRNA cleavage
PMID:18454937 = siRNA pathway

Annotation error?

PMID:20424607 = Refers to miRNA process, possibly 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing

[rach_huntley]

Hi David,

Would the simplest solution be to broaden the definition of mRNA processing to include silencing events?
Or alternatively, would you expect "mRNA cleavage involved in gene silencing by miRNA" to be a child of "mRNA catabolic process”?
So, could you have…

mRNA catabolic process
— is_a mRNA cleavage involved in gene silencing by miRNA

mRNA cleavage
— has_part mRNA cleavage involved in gene silencing by miRNA

??

I don’t think you can say miRNA guided cleavage at internal site leading to silencing (in your potential solution) because miRNAs also direct deadenylation (does this count as cleavage?) of the polyA tail of mRNA, leading to degradation – which is represented by "deadenylation-dependent decapping of nuclear-transcribed mRNA” and "nuclear-transcribed mRNA poly(A) tail shortening” - but these terms also confuse me!

I did mention this in a previous email when we were discussing gene expression (see also the attached QuickGO comparison of these terms)…

Quote>>
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening (mRNA
deadenylation), and consequently its regulation terms, is under gene
expression
but GO:0000290 deadenylation-dependent decapping of nuclear-transcribed
mRNA (which happens if the poly(A) tail has reached a minimum length) is
under mRNA catabolic process.

I don¹t know enough about poly(A) tail shortening to know if the ontology
here is correct, but positive regulation of nuclear-transcribed mRNA
poly(A) tail shortening is a child of positive regulation of gene
expression - but if you get too much shortening, this is when the mRNA is
decapped and degraded = mRNA catabolism.
So I guess for gene silencing by miRNA, we would want to use positive
regulation of deadenylation-dependent decapping of nuclear-transcribed
mRNA because if we use positive regulation of nuclear-transcribed mRNA
poly(A) tail shortening, this would go up to positive regulation of gene
expression, which is not what is happening.

Maybe we should have new terms "positive regulation of nuclear-transcribed
mRNA poly(A) tail shortening involved in gene silencing by miRNA" and
"positive regulation of deadenylation-dependent decapping of
nuclear-transcribed mRNA involved in gene silencing by miRNA", that would
both come under gene silencing.
<<

I think we need to look at all these terms together rather than just fixing single problems. It doesn’t help that new mechanisms for miRNA action are being discovered all the time!

[David Osumi-Sutherland]

Would the simplest solution be to broaden the definition of mRNA processing to include silencing events?

But everything else currently under gene expression is a process involved in generating a mature gene product. Cleavage involved in silencing is the opposite.

Or alternatively, would you expect "mRNA cleavage involved in gene silencing by miRNA" to be a child of "mRNA catabolic process”?

It can (and probably should) be that as well.

So, could you have…

mRNA catabolic process
— is_a mRNA cleavage involved in gene silencing by miRNA

mRNA cleavage
— has_part mRNA cleavage involved in gene silencing by miRNA

??

I don’t think you can say miRNA guided cleavage at internal site leading to silencing (in your potential solution) because miRNAs also direct deadenylation (does this count as cleavage?) of the polyA tail of mRNA, leading to degradation – which is represented by "deadenylation-dependent decapping of nuclear-transcribed mRNA” and "nuclear-transcribed mRNA poly(A) tail shortening” - but these terms also confuse me!

I've been assuming cleavage corresponds to endonuclease activity in this case, rather than exonuclease. This fits with the dictionary definition of the verb.

Deadenylation leading to degredation seems to be a distinct mechanism from silencing by cleavage. See http://cshperspectives.cshlp.org/content/4/12/a012328.full.pdf.

Cleavage at internal site (common in plants):
"In instances when the complementarity between the target and the miRNA is extensive and the AGO protein is catalytically active, the target is cleaved by AGO within the base-paired region (between nucleotides 10 and 11, opposite the miRNA strand) (Fig. 1) (Bartel 2009; Jı´nek and Doudna 2009; Voinnet 2009). This mechanism appears to be most prominent in plants where miRNAs recognize fully or nearly complementary binding sites, which are gen- erally located in the mRNA open reading frames (ORFs) (Voinnet 2009)"

"In animals, miRNAs recognize partially complementary binding sites, which are generally located in the mRNA 30 untranslated region (UTR) (Bartel 2009)." This results in blocking of translation and, in some cases also in deadenylation leading to degredation.

From : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890232/
"Deadenylation is followed by one of two alternate degradation pathways: 3′→5′ degradation by the cytoplasmic exosome, or removal of the 5′ cap (decapping) by Dcp1p/Dcp2p and 5′→3′ degradation by the Xrn1p exonuclease."

Don't think either of these processes are cleavage.

I think we need to look at all these terms together rather than just fixing single problems.

Agreed. Reviewing related function terms now.

[David Osumi-Sutherland]

Proposed Solution:

Given that 'mRNA cleavage' has been used for a range of cases, some of which are not processing (see above), we should redefine mRNA cleavage as a more general term, add new specific child terms and submit a re-annotation ticket to get annotations moved to the appropriate specific term.

mRNA cleavage
. is_a mRNA cleavage involved in mRNA processing
. is_a mRNA cleavage involved in gene silencing (or perhaps, mRNA cleavage involved in negative regulation of gene expression?)
. . is_a mRNA cleavage involved in gene silencing my miRNA

gene silencing by miRNA
. part_of 'deadenylation involved in gene silencing by miRNA' (EquivalentTo: 'nuclear-transcribed mRNA poly(A) tail shortening' that part_of some 'gene silencing by miRNA')
. part_of mRNA cleavage involved in gene silencing (or perhaps, mRNA cleavage involved in negative regulation of gene expression?)
. . part_of mRNA cleavage involved in gene silencing my miRNA

[Tanya Berardini]

Cross-referencing to

https://sourceforge.net/p/geneontology/ontology-requests/11638/

for the broader issue of definition of 'gene silencing'.

[rach_huntley]

I think the proposed solution looks OK. You would then have the major mechanisms of gene silencing grouped, i.e. cleavage, deadenylation and negative regulation of translation - GO:0035278 negative regulation of translation involved in gene silencing by miRNA is already a child of gene silencing by miRNA.

Rachael.

[rach_huntley]

Hi David,

Is the above proposed solution agreed now?
I would like to update my guidelines with the new terms.

Thanks,
Rachael.

[David Osumi-Sutherland]

Fixed pretty much as outlined above see:

Also added comments to 'regulation of gene expression' and 'negative regulation of gene expression' to make it clear that reg of mRNA levels covered:

• comment: This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availabiliy of mRNA for translation and thereby regulates the rate of production of the encoded protein via translation.
• comment: This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availabiliy of mRNA for translation and thereby reduces the rate of production of the encoded protein via translation.

[David Osumi-Sutherland]

Annotation issues moved to new annotation ticket: https://sourceforge.net/p/geneontology/annotation-issues/1317/

Closing as fixed.