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RNA 3′ processing functions of Arabidopsis FCA and FPA limit intergenic transcription

https://doi.org/10.1073/pnas.1105334108
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf00264213openalex-snapshot
A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana
inferredcites →https://doi.org/10.1016/0306-9877(95)90228-7openalex-snapshot
Mathematical formulae for the prediction of the residual beta cell function during the first two years of disease in children and adolescents with insulin-dependent diabetes mellitus
inferredcites →https://doi.org/10.1016/j.cell.2008.03.029openalex-snapshot
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
inferredcites →https://doi.org/10.1016/j.cell.2009.02.001openalex-snapshot
Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation
inferredcites →https://doi.org/10.1016/j.cell.2009.06.016openalex-snapshot
Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells
inferredcites →https://doi.org/10.1016/j.cell.2010.10.005openalex-snapshot
Upf1 Senses 3′UTR Length to Potentiate mRNA Decay
inferredcites →https://doi.org/10.1016/j.devcel.2009.12.009openalex-snapshot
The Spen Family Protein FPA Controls Alternative Cleavage and Polyadenylation of RNA
inferredcites →https://doi.org/10.1016/j.molcel.2005.10.004openalex-snapshot
From Transcription to mRNA: PAF Provides a New Path
inferredcites →https://doi.org/10.1016/j.molcel.2007.10.018openalex-snapshot
The Arabidopsis RNA-Binding Protein FCA Requires a Lysine-Specific Demethylase 1 Homolog to Downregulate FLC
inferredcites →https://doi.org/10.1016/j.molcel.2008.08.022openalex-snapshot
Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation
inferredcites →https://doi.org/10.1016/j.ygeno.2005.01.007openalex-snapshot
Sense and antisense Foxl2 transcripts in mouse
inferredcites →https://doi.org/10.1016/s0092-8674(00)80256-1openalex-snapshot
FCA, a Gene Controlling Flowering Time in Arabidopsis, Encodes a Protein Containing RNA-Binding Domains
inferredcites →https://doi.org/10.1016/s0092-8674(03)00425-2openalex-snapshot
FY Is an RNA 3′ End-Processing Factor that Interacts with FCA to Control the Arabidopsis Floral Transition
inferredcites →https://doi.org/10.1016/s1097-2765(04)00257-6openalex-snapshot
The Paf1 Complex Has Functions Independent of Actively Transcribing RNA Polymerase II
inferredcites →https://doi.org/10.1038/35012108openalex-snapshot
Disruption of the plant gene MOM releases transcriptional silencing of methylated genes
inferredcites →https://doi.org/10.1038/nature08618openalex-snapshot
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target
inferredcites →https://doi.org/10.1073/pnas.0606536103openalex-snapshot
Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis
inferredcites →https://doi.org/10.1073/pnas.0802493105openalex-snapshot
Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana
inferredcites →https://doi.org/10.1073/pnas.0900028106openalex-snapshot
Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
inferredcites →https://doi.org/10.1073/pnas.0903444106openalex-snapshot
Altered interactions within FY/AtCPSF complexes required for Arabidopsis FCA-mediated chromatin silencing
inferredcites →https://doi.org/10.1093/bioinformatics/btn025openalex-snapshot
SOAP: short oligonucleotide alignment program
inferredcites →https://doi.org/10.1093/emboj/cdg305openalex-snapshot
Autoregulation of FCA pre‐mRNA processing controls Arabidopsis flowering time
inferredcites →https://doi.org/10.1093/nar/gkm965openalex-snapshot
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
inferredcites →https://doi.org/10.1101/gad.522509openalex-snapshot
Trans -acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae
inferredcites →https://doi.org/10.1104/pp.108.118927openalex-snapshot
Functional Redundancy and New Roles for Genes of the Autonomous Floral-Promotion Pathway
inferredcites →https://doi.org/10.1104/pp.110.162131openalex-snapshot
MORPHEUS’ MOLECULE1 Is Required to Prevent Aberrant RNA Transcriptional Read-Through in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.010017openalex-snapshot
FPA, a Gene Involved in Floral Induction in Arabidopsis, Encodes a Protein Containing RNA-Recognition Motifs
inferredcites →https://doi.org/10.1105/tpc.010456openalex-snapshot
Functional Significance of the Alternative Transcript Processing of the Arabidopsis Floral Promoter FCA
inferredcites →https://doi.org/10.1105/tpc.13.4.935openalex-snapshot
Loss of FLOWERING LOCUS C Activity Eliminates the Late-Flowering Phenotype of FRIGIDA and Autonomous Pathway Mutations but Not Responsiveness to Vernalization
inferredcites →https://doi.org/10.1105/tpc.13.6.1427openalex-snapshot
FPA, a Gene Involved in Floral Induction in Arabidopsis, Encodes a Protein Containing RNA-Recognition Motifs
inferredcites →https://doi.org/10.1126/science.1106910openalex-snapshot
RNA Polymerase IV Directs Silencing of Endogenous DNA
inferredcites →https://doi.org/10.1126/science.1112009openalex-snapshot
Antisense Transcription in the Mammalian Transcriptome
inferredcites →https://doi.org/10.1126/science.1146565openalex-snapshot
Widespread Role for the Flowering-Time Regulators FCA and FPA in RNA-Mediated Chromatin Silencing
inferredcites →https://doi.org/10.1126/science.1155390openalex-snapshot
Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites
inferredcites →https://doi.org/10.1126/science.1180278openalex-snapshot
Targeted 3′ Processing of Antisense Transcripts Triggers Arabidopsis FLC Chromatin Silencing
inferredcites →https://doi.org/10.1186/1471-2105-9-371openalex-snapshot
Kismeth: Analyzer of plant methylation states through bisulfite sequencing
inferredcites →https://doi.org/10.1186/gb-2008-9-7-r112openalex-snapshot
At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4512949openalex-extracted
The CPSF Phosphatase Module Links Transcription Termination to Chromatin Silencing
inferred← citeshttps://doi.org/10.1002/9780470015902.a0029557openalex-snapshot
Floral Meristems
inferred← citeshttps://doi.org/10.1002/9781118447093.ch2openalex-snapshot
The Complex Eukaryotic Transcriptome: Nonprotein‐Coding RNAs and Root Development
inferred← citeshttps://doi.org/10.1002/advs.202504562openalex-snapshot
Polyadenylation Complex CFII Recognizes Downstream Cis‐element for Pre‐mRNA Polyadenylation Through Interaction with an RNA‐Binding Protein in Arabidopsis
inferred← citeshttps://doi.org/10.1002/mco2.640openalex-snapshot
Liquid–liquid phase separation in diseases
inferred← citeshttps://doi.org/10.1002/pmic.202100143openalex-snapshot
Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation during soybean seed development
inferred← citeshttps://doi.org/10.1002/wrna.1575openalex-snapshot
mRNA 3′ end formation in plants: Novel connections to growth, development and environmental responses
inferred← citeshttps://doi.org/10.1007/s00299-024-03145-7openalex-snapshot
Integrated transcriptome and proteome analysis provides insights into CpFPA1 for floral induction in Chimonanthus praecox (Magnoliidae) without FLC in genome
inferred← citeshttps://doi.org/10.1007/s00412-017-0643-8openalex-snapshot
A proteomic portrait of dinoflagellate chromatin reveals abundant RNA-binding proteins
inferred← citeshttps://doi.org/10.1007/s00425-019-03309-wopenalex-snapshot
Alternative splicing is a Sorghum bicolor defense response to fungal infection
inferred← citeshttps://doi.org/10.1016/j.abiote.2025.100006openalex-snapshot
Co-transcriptional gene regulation in plants
inferred← citeshttps://doi.org/10.1016/j.cj.2025.09.010openalex-snapshot
Biomolecular condensates: Emerging regulatory mechanisms for crop improvement
inferred← citeshttps://doi.org/10.1016/j.cub.2021.09.074openalex-snapshot
The BORDER family of negative transcription elongation factors regulates flowering time in Arabidopsis
inferred← citeshttps://doi.org/10.1016/j.jgg.2016.03.010openalex-snapshot
DNA methylation signature of intergenic region involves in nucleosome remodeler DDM1-mediated repression of aberrant gene transcriptional read-through
inferred← citeshttps://doi.org/10.1016/j.molcel.2014.03.026openalex-snapshot
Functional Consequences of Splicing of the Antisense Transcript COOLAIR on FLC Transcription
inferred← citeshttps://doi.org/10.1016/j.molcel.2024.05.014openalex-snapshot
Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing
inferred← citeshttps://doi.org/10.1016/j.molcel.2024.05.016openalex-snapshot
A CPF-like phosphatase module links transcription termination to chromatin silencing
inferred← citeshttps://doi.org/10.1016/j.pbi.2014.02.006openalex-snapshot
Interplay between chromatin and RNA processing
inferred← citeshttps://doi.org/10.1016/j.pbi.2016.11.003openalex-snapshot
Roles of pre-mRNA splicing and polyadenylation in plant development
inferred← citeshttps://doi.org/10.1016/j.plantsci.2016.09.015openalex-snapshot
APRF1 promotes flowering under long days in Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1016/j.plantsci.2022.111430openalex-snapshot
Review: Mechanisms underlying alternative polyadenylation in plants – looking in the right places
inferred← citeshttps://doi.org/10.1016/j.semcdb.2016.01.029openalex-snapshot
RNA binding proteins implicated in Xist-mediated chromosome silencing
inferred← citeshttps://doi.org/10.1016/j.tig.2012.06.002openalex-snapshot
Flowering time control: another window to the connection between antisense RNA and chromatin
inferred← citeshttps://doi.org/10.1016/j.tplants.2013.07.001openalex-snapshot
Emerging roles for RNA polymerase II CTD in Arabidopsis
inferred← citeshttps://doi.org/10.1016/j.xplc.2022.100307openalex-snapshot
Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis
inferred← citeshttps://doi.org/10.1038/emboj.2012.324openalex-snapshot
A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization
inferred← citeshttps://doi.org/10.1038/ncomms3301openalex-snapshot
Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin
inferred← citeshttps://doi.org/10.1038/s41467-021-22083-6openalex-snapshot
R-loop resolution promotes co-transcriptional chromatin silencing
inferred← citeshttps://doi.org/10.1038/s41467-021-27650-5openalex-snapshot
TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV
inferred← citeshttps://doi.org/10.1038/s41467-025-62555-7openalex-snapshot
Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination
inferred← citeshttps://doi.org/10.1038/s41576-026-00979-7openalex-snapshot
Molecular integration of seasonal temperature signals in flowering time control
inferred← citeshttps://doi.org/10.1038/s41586-019-1165-8openalex-snapshot
Arabidopsis FLL2 promotes liquid–liquid phase separation of polyadenylation complexes
inferred← citeshttps://doi.org/10.1038/srep02866openalex-snapshot
The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation
inferred← citeshttps://doi.org/10.1073/pnas.1406635111openalex-snapshot
Antisense-mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor
inferred← citeshttps://doi.org/10.1073/pnas.1604478113openalex-snapshot
Luminidependens (LD) is an Arabidopsis protein with prion behavior
inferred← citeshttps://doi.org/10.1073/pnas.2007268117openalex-snapshot
The 3′ processing of antisense RNAs physically links to chromatin-based transcriptional control
inferred← citeshttps://doi.org/10.1073/pnas.2102753118openalex-snapshot
Antagonistic activities of cotranscriptional regulators within an early developmental window set FLC expression level
inferred← citeshttps://doi.org/10.1074/jbc.m111.337485openalex-snapshot
Arabidopsis RNA-binding Protein FCA Regulates MicroRNA172 Processing in Thermosensory Flowering
inferred← citeshttps://doi.org/10.1080/07352689.2014.852920openalex-snapshot
The Role of the Epigenome in Gene Expression Control and the Epimark Changes in Response to the Environment
inferred← citeshttps://doi.org/10.1080/07388551.2020.1751059openalex-snapshot
Insights into the N6-methyladenosine mechanism and its functionality: progress and questions
inferred← citeshttps://doi.org/10.1093/jxb/erae054openalex-snapshot
Epigenetics and plant hormone dynamics: a functional and methodological perspective
inferred← citeshttps://doi.org/10.1093/jxb/ert439openalex-snapshot
Message ends: RNA 3′ processing and flowering time control
inferred← citeshttps://doi.org/10.1093/jxb/eru085openalex-snapshot
Regulation of the circadian clock through pre-mRNA splicing in Arabidopsis
inferred← citeshttps://doi.org/10.1093/jxb/ery393openalex-snapshot
Alternative splicing and translation play important roles in hypoxic germination in rice
inferred← citeshttps://doi.org/10.1093/plcell/koab310openalex-snapshot
Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes
inferred← citeshttps://doi.org/10.1101/371583openalex-snapshot
Alternative splicing and translation play important roles in parallel with transcriptional regulation during rice hypoxic germination
inferred← citeshttps://doi.org/10.1101/818187openalex-snapshot
PLETHORA-WOX5 interaction and subnuclear localisation control Arabidopsis root stem cell maintenance
inferred← citeshttps://doi.org/10.1101/gad.350314.122openalex-snapshot
SPOC domain proteins in health and disease
inferred← citeshttps://doi.org/10.1101/gr.218669.116openalex-snapshot
Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
inferred← citeshttps://doi.org/10.1101/gr.277473.122openalex-snapshot
SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
inferred← citeshttps://doi.org/10.1104/pp.111.191700openalex-snapshot
Phosphoproteomic Analysis of Seed Maturation in Arabidopsis, Rapeseed, and Soybean
inferred← citeshttps://doi.org/10.1104/pp.18.01106openalex-snapshot
Antagonistic Actions of FPA and IBM2 Regulate Transcript Processing from Genes Containing Heterochromatin
inferred← citeshttps://doi.org/10.1104/pp.19.00374openalex-snapshot
Epigenetic Regulation of mRNA Polyadenylation Site Selection
inferred← citeshttps://doi.org/10.1104/pp.19.01009openalex-snapshot
Autonomous Pathway: FLOWERING LOCUS C Repression through an Antisense-Mediated Chromatin-Silencing Mechanism
inferred← citeshttps://doi.org/10.1105/tpc.113.110296openalex-snapshot
The Cyclophilin CYP20-2 Modulates the Conformation of BRASSINAZOLE-RESISTANT1, Which Binds the Promoter of FLOWERING LOCUS D to Regulate Flowering in Arabidopsis
inferred← citeshttps://doi.org/10.1111/jipb.13152openalex-snapshot
Phase separation in plants: New insights into cellular compartmentalization
inferred← citeshttps://doi.org/10.1111/jipb.13583openalex-snapshot
Post‐transcriptional regulation of grain weight and shape by the RBP‐A‐J‐K complex in rice
inferred← citeshttps://doi.org/10.1111/nph.12787openalex-snapshot
Widespread anti‐sense transcription in apple is correlated with si RNA production and indicates a large potential for transcriptional and/or post‐transcriptional control
inferred← citeshttps://doi.org/10.1111/pbi.12336openalex-snapshot
Long noncoding RNA transcriptome of plants
inferred← citeshttps://doi.org/10.1111/tpj.13571openalex-snapshot
Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings
inferred← citeshttps://doi.org/10.1111/tpj.13611openalex-snapshot
Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination
inferred← citeshttps://doi.org/10.1111/tpj.13826openalex-snapshot
Defective XRN 3‐mediated transcription termination in Arabidopsis affects the expression of protein‐coding genes
inferred← citeshttps://doi.org/10.1126/sciadv.aau7246openalex-snapshot
PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR
inferred← citeshttps://doi.org/10.1186/s12864-015-1446-zopenalex-snapshot
Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer
inferred← citeshttps://doi.org/10.1186/s13059-023-03050-4openalex-snapshot
Coupling of co-transcriptional splicing and 3’ end Pol II pausing during termination in Arabidopsis
inferred← citeshttps://doi.org/10.1371/journal.pbio.1002571openalex-snapshot
snRNA 3′ End Processing by a CPSF73-Containing Complex Essential for Development in Arabidopsis
inferred← citeshttps://doi.org/10.1371/journal.pgen.1003867openalex-snapshot
Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA
inferred← citeshttps://doi.org/10.1371/journal.pgen.1005924openalex-snapshot
BRR2a Affects Flowering Time via FLC Splicing
inferred← citeshttps://doi.org/10.1371/journal.pone.0030715openalex-snapshot
Antagonistic Roles of SEPALLATA3, FT and FLC Genes as Targets of the Polycomb Group Gene CURLY LEAF
inferred← citeshttps://doi.org/10.1371/journal.pone.0115779openalex-snapshot
Integration of Developmental and Environmental Signals via a Polyadenylation Factor in Arabidopsis
inferred← citeshttps://doi.org/10.1371/journal.pone.0127699openalex-snapshot
Investigating the Association between Flowering Time and Defense in the Arabidopsis thaliana-Fusarium oxysporum Interaction
inferred← citeshttps://doi.org/10.15252/embr.202154105openalex-snapshot
PLETHORA‐WOX5 interaction and subnuclear localization control Arabidopsis root stem cell maintenance
inferred← citeshttps://doi.org/10.1534/g3.111.001362openalex-snapshot
Surveillance of 3′ Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis
inferred← citeshttps://doi.org/10.26508/lsa.201900393openalex-snapshot
The m6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants
inferred← citeshttps://doi.org/10.3389/fpls.2021.702303openalex-snapshot
Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea (Camellia sinensis) Leaves During Withering Process
inferred← citeshttps://doi.org/10.3389/fpls.2022.1052107openalex-snapshot
Come together now: Dynamic body-formation of key regulators integrates environmental cues in plant development
inferred← citeshttps://doi.org/10.3390/ijms22062845openalex-snapshot
The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status
inferred← citeshttps://doi.org/10.3390/plants12234020openalex-snapshot
Unlocking Nature’s Clock: CRISPR Technology in Flowering Time Engineering
inferred← citeshttps://doi.org/10.4103/2395-3977.151483openalex-snapshot
Split End Family RNA Binding Proteins: Novel Tumor Suppressors Coupling Transcriptional Regulation with RNA Processing
inferred← citeshttps://doi.org/10.4161/rna.18668openalex-snapshot
Transcription beyond borders has downstream consequences
inferred← citeshttps://doi.org/10.6084/m9.figshare.24123741openalex-snapshot
Additional file 1 of Coupling of co-transcriptional splicing and 3’ end Pol II pausing during termination in Arabidopsis
inferred← citeshttps://doi.org/10.6084/m9.figshare.24123747openalex-snapshot
Additional file 2 of Coupling of co-transcriptional splicing and 3’ end Pol II pausing during termination in Arabidopsis
inferred← citeshttps://doi.org/10.6084/m9.figshare.24123750openalex-snapshot
Additional file 3 of Coupling of co-transcriptional splicing and 3’ end Pol II pausing during termination in Arabidopsis
inferred← citeshttps://doi.org/10.70675/299aa774z2e73z48acz89fcz20db55683507openalex-snapshot
Functional involvement of two histone-methyltransferases in response to stress and in regulation of flowering time in Arabidopsis thaliana
inferred← citeshttps://doi.org/10.70675/44dfd2d8za3f1z4d2azb17az7b325385be3bopenalex-snapshot
Epigenetic regulation of transcription from genes-containing heterochromatin
inferred← citeshttps://doi.org/10.70675/fc16267dzad68z4beczb28bz9a828aba2035openalex-snapshot
Conflit moléculaire entre les protéines Vpr et Vpx des virus HIV/SIV et les facteurs HUSH et SAMHD1
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