FPA

UniProt ID: Q8LPQ9
Organism: Arabidopsis thaliana
Review Status: COMPLETE
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Gene Description

FPA is a nuclear RNA-binding protein with RNA recognition motifs and a SPOC domain that regulates alternative cleavage and polyadenylation in Arabidopsis. It associates with chromatin near transcribed gene ends and controls termination and the production of read-through and chimeric RNAs. FPA promotes flowering by limiting FLC expression and also affects the processing of other transcripts, including immune-receptor genes. Its genetic overlap with FCA contributes to female gametophyte development, while their biochemical interactions are distinct.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0000785 chromatin
IDA
PMID:17916737
Widespread role for the flowering-time regulators FCA and FP... 		ACCEPT
Summary: FPA associates with chromatin at target loci (Baurle et al. 2007).
Reason: Experimental annotation made by the curator from the full text, which is not in the cache (abstract-only; the abstract does not describe the chromatin-association assay), so we defer to the curator. Chromatin association is independently corroborated by FPA ChIP-seq occupancy co-localising with Pol II Ser2 at gene 3' ends.
Supporting Evidence:
PMID:33904405
FPA co-localises with Pol II Ser2 at the 3′ end of genes.
GO:0000785 chromatin
IDA
PMID:20079695
The spen family protein FPA controls alternative cleavage an... 		ACCEPT
Summary: FPA chromatin association from Hornyik et al. 2010.
Reason: Experimental annotation made by the curator from the full text, which is not in the cache (abstract-only; the abstract does not describe the chromatin-association assay), so we defer to the curator. Consistent with co-transcriptional 3'-end processing control and with FPA ChIP-seq occupancy at gene 3' ends.
Supporting Evidence:
PMID:33904405
FPA co-localises with Pol II Ser2 at the 3′ end of genes.
GO:0003676 nucleic acid binding
IEA
GO_REF:0000002 		MODIFY
Summary: Nucleic acid binding from RRM superfamily signature.
Reason: Correct but uninformative; FPA is an RRM-containing RNA-binding protein.
Proposed replacements: RNA binding
Supporting Evidence:
PMID:11402170
Thus, FPA appears to be encoded by a putative RRM-containing protein.
GO:0003723 RNA binding
IBA
GO_REF:0000033 		ACCEPT
Summary: RNA binding propagated by PAINT from RRM/spen-family proteins.
Reason: FPA is an RRM-containing RNA-binding protein that regulates poly(A) site choice on target RNAs.
Supporting Evidence:
PMID:33904405
Here, we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, thereby controlling their functional expression and impacting immunity.
GO:0003723 RNA binding
IEA
GO_REF:0000002 		ACCEPT
Summary: RNA binding from RRM domain signature.
Reason: Consistent with the established RNA-binding role of FPA.
Supporting Evidence:
PMID:11402170
Thus, FPA appears to be encoded by a putative RRM-containing protein.
GO:0003723 RNA binding
ISS
PMID:11402170
FPA, a gene involved in floral induction in Arabidopsis, enc... 		ACCEPT
Summary: RNA binding by sequence similarity (RRMs) at cloning of FPA.
Reason: Consistent with later functional evidence.
Supporting Evidence:
PMID:11402170
Thus, FPA appears to be encoded by a putative RRM-containing protein.
GO:0005634 nucleus
IEA
GO_REF:0000044 		ACCEPT
Summary: Nuclear localization from UniProt subcellular location mapping.
Reason: FPA is a nuclear co-transcriptional regulator (UniProt cites experimental nuclear localization).
Supporting Evidence:
file:genes/ARATH/FPA/FPA-uniprot.txt
SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17916737}.
GO:0005634 nucleus
ISM
GO_REF:0000122 		ACCEPT
Summary: Nuclear localization predicted by AtSubP.
Reason: Consistent with experimental data.
Supporting Evidence:
file:genes/ARATH/FPA/FPA-uniprot.txt
SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17916737}.
GO:0009553 embryo sac development
IGI
PMID:17916737
Widespread role for the flowering-time regulators FCA and FP... 		KEEP AS NON CORE
Summary: fca fpa double mutants show female gametophyte defects.
Reason: Pleiotropic genetic requirement shared redundantly with FCA.
Supporting Evidence:
PMID:17916737
Female gametophytic development and early embryonic development are particularly susceptible to malfunctions in FCA and FPA.
GO:0009911 positive regulation of flower development
IMP
PMID:11402170
FPA, a gene involved in floral induction in Arabidopsis, enc... 		ACCEPT
Summary: fpa mutants are late flowering; FPA promotes flowering in the autonomous pathway.
Reason: Well-established genetic role in promotion of flowering.
Supporting Evidence:
PMID:11402170
FPA is a gene that regulates flowering time in Arabidopsis via a pathway that is independent of daylength (the autonomous pathway).
GO:0010228 vegetative to reproductive phase transition of meristem
IMP
PMID:11402170
FPA, a gene involved in floral induction in Arabidopsis, enc... 		ACCEPT
Summary: fpa mutants are delayed in the vegetative-to-reproductive transition.
Reason: Consistent with the late-flowering phenotype; FPA acts upstream (via FLC repression) of the meristem transition.
Supporting Evidence:
PMID:11402170
Mutations in FPA result in extremely delayed flowering.
GO:0031048 regulatory ncRNA-mediated heterochromatin formation
IMP
PMID:17916737
Widespread role for the flowering-time regulators FCA and FP... 		UNDECIDED
Summary: FPA silencing phenotypes include a demonstrated read-through explanation; the specific heterochromatin-forming contribution remains unresolved.
Reason: PMID:17916737 reports locus-dependent silencing and methylation effects, whereas PMID:20079695 identifies upstream read-through rather than loss of DNA methylation/siRNAs at AtSN1. Full PMID:24204292 finds no widespread RNA-mediated chromatin-silencing role and documents RNA termination defects. These results question the precise GO:0031048 mechanism without proving all original loci lack an FPA contribution. The original 2007 full locus-specific evidence was not accessible here; do not remove an experimental annotation or assert universal absence.
Supporting Evidence:
PMID:17916737
At some target loci, FCA and FPA promote asymmetric DNA methylation, whereas at others they function in parallel to DNA methylation.
PMID:24204292
do not detect evidence of a widespread role for FPA in RNA-mediated chromatin silencing
GO:0110104 mRNA alternative polyadenylation
IMP
PMID:20079695
The spen family protein FPA controls alternative cleavage an... 		NEW
Summary: NEW. FPA controls alternative cleavage and polyadenylation genome-wide, including proximal COOLAIR poly(A) site use (redundantly with FCA), intronic poly(A) sites and premature termination of NLR transcripts.
Reason: Directly demonstrated core activity of FPA (trans-acting regulator of poly(A) site choice), supported by direct RNA sequencing and Nanopore studies.
Supporting Evidence:
PMID:20079695
We show that FPA functions redundantly with FCA, another RNA binding protein that controls flowering and RNA silencing, to control the expression of alternatively polyadenylated antisense RNAs at the locus encoding the floral repressor FLC.
PMID:24204292
The Arabidopsis thaliana protein FPA is a rare example of a trans-acting regulator of poly(A) site choice.
PMID:24204292
We identify alternative polyadenylation within introns that is sensitive to FPA and show FPA-dependent shifts in IBM1 poly(A) site selection

Core Functions

Spen-family RRM RNA-binding protein that acts as a trans-acting regulator of poly(A) site choice, promoting proximal/premature cleavage and polyadenylation (including COOLAIR at FLC, redundantly with FCA), thereby limiting read-through transcription. Through COOLAIR 3'-end formation it acts upstream of FLC repression in the autonomous pathway; loss of FPA strongly delays flowering and overexpression accelerates flowering.

Molecular Function:
RNA binding
Directly Involved In:
mRNA alternative polyadenylation positive regulation of flower development
Cellular Locations:
nucleus
Supporting Evidence:
  • PMID:24204292
    The Arabidopsis thaliana protein FPA is a rare example of a trans-acting regulator of poly(A) site choice.
  • PMID:20079695
    We show that FPA functions redundantly with FCA, another RNA binding protein that controls flowering and RNA silencing, to control the expression of alternatively polyadenylated antisense RNAs at the locus encoding the floral repressor FLC.
  • PMID:11402170
    FPA is a gene that regulates flowering time in Arabidopsis via a pathway that is independent of daylength (the autonomous pathway).
  • PMID:11402170
    Overexpression of FPA in Arabidopsis causes early flowering in noninductive short days and creates plants that exhibit a more day-neutral flowering behavior.
  • PMID:20079695
    The spen family protein FPA is required for flowering time control and has been implicated in RNA silencing.

References

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Suggested Questions for Experts

Q: How does FPA, which is not a stable component of CPSF/CstF, recruit or activate the cleavage and polyadenylation machinery at proximal sites, and is its SPOC domain the key interaction module (e.g. with RNA Pol II CTD or 3'-end factors)?

Suggested Experiments

Experiment: Proximity labelling (TurboID-FPA) and SPOC-domain mutants combined with Nanopore direct RNA sequencing to identify the partners required for FPA-dependent proximal polyadenylation.

Hypothesis: The FPA SPOC domain recruits 3'-end processing/termination factors to nascent transcripts.

Type: Proximity proteomics / direct RNA sequencing

📚 Additional Documentation

Notes

(FPA-notes.md)

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