{"doi":"10.7554/elife.102529","title":"Companion cells with high florigen production express other small proteins and reveal a nitrogen-sensitive FT repressor","abstract":"The precise onset of flowering is crucial for successful reproduction. In longer days, the florigen gene FLOWERING LOCUS T ( FT ) is induced in specific leaf phloem companion cells in Arabidopsis . However, the molecular nature of these cells remains elusive. Here, we utilized bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate transcription in FT -expressing cells and other companion cells. Our bulk nuclei RNA-seq demonstrated that FT -expressing cells in cotyledons and true leaves showed differences in FT repressor gene expression. Within true leaves, our snRNA-seq analysis revealed that companion cells with high FT expression form a unique cluster. The cluster expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). We also found that the promoters of FT and the genes co-expressed with FT in the cluster were enriched for the binding motif of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of NIGT1.2 and NIGT1.4 repressed FT and delayed flowering under nitrogen-rich conditions, implying the roles of NIGT1s as nitrogen-dependent FT repressors. Taken together, our results indicate that unique FT -expressing phloem cells may produce multiple systemic signals to regulate plant growth and development.","journal":"eLife","year":2025,"id":555832,"datarank":0.174037590284057,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.009245746983840526,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.009245746983840526,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":2,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9598,"is_data_producer":true,"deposit_databanks":{"GEO":["GSE273032"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1329572,"name":"Shogo Ito","orcid":"0000-0002-8434-6652","position":1,"is_corresponding":false},{"id":1351675,"name":"Jae Sung Shim","orcid":"0000-0002-7352-437X","position":2,"is_corresponding":false},{"id":1088687,"name":"Akane Kubota","orcid":"0000-0003-1347-3950","position":3,"is_corresponding":false},{"id":560166,"name":"Andrew K Hempton","orcid":"0000-0002-3018-6091","position":4,"is_corresponding":false},{"id":292375,"name":"Nayoung Lee","orcid":"0000-0002-0353-6455","position":5,"is_corresponding":false},{"id":685277,"name":"Takamasa Suzuki","orcid":"0000-0002-1977-0510","position":6,"is_corresponding":false},{"id":1455206,"name":"Jared S Wong","orcid":null,"position":7,"is_corresponding":false},{"id":1351676,"name":"Chansie Yang","orcid":"0000-0002-8118-2883","position":8,"is_corresponding":false},{"id":393208,"name":"Christine T Nolan","orcid":"0009-0001-9257-9595","position":9,"is_corresponding":false},{"id":931859,"name":"Kerry L. Bubb","orcid":"0000-0002-1117-2591","position":10,"is_corresponding":false},{"id":554717,"name":"Cristina M Alexandre","orcid":"0000-0003-0047-0312","position":11,"is_corresponding":false},{"id":1329575,"name":"Daisuke Kurihara","orcid":"0000-0003-2703-0405","position":12,"is_corresponding":false},{"id":1329577,"name":"Yoshikatsu Sato","orcid":"0000-0002-4967-2698","position":13,"is_corresponding":false},{"id":1329579,"name":"Yasuomi Tada","orcid":"0000-0001-9900-069X","position":14,"is_corresponding":false},{"id":1351677,"name":"Takatoshi Kiba","orcid":"0000-0001-8651-0404","position":15,"is_corresponding":false},{"id":583671,"name":"José L. Pruneda-Paz","orcid":"0000-0002-0054-0918","position":16,"is_corresponding":false},{"id":239744,"name":"Christine Queitsch","orcid":"0000-0002-0905-4705","position":17,"is_corresponding":false},{"id":554720,"name":"Josh T. Cuperus","orcid":"0000-0002-8019-7733","position":18,"is_corresponding":false},{"id":292377,"name":"Takato Imaizumi","orcid":"0000-0001-9396-4412","position":19,"is_corresponding":false},{"id":1016350,"name":"Hiroshi Takagi","orcid":"0000-0003-0321-0284","position":0,"is_corresponding":true}],"reference_count":67,"raw_metadata":null,"created_at":"2026-07-19T02:55:03.976486Z","pmid":"41165729","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}