DOI: 10.5061/dryad.fttdz090f
title: Two modes of gene regulation by TFL1 mediate its dual function in flowering time and shoot determinacy of Arabidopsis

description: Plant organ primordia develop successively at the shoot apical meristem
 (SAM). In Arabidopsis, primordia formed early in development differentiate
 into vegetative leaves, whereas those formed later generate inflorescence
 branches and flowers. TERMINAL FLOWER 1 (TFL1), a negative regulator of
 transcription, acts in the SAM to delay flowering and to maintain
 inflorescence meristem indeterminacy. We used confocal microscopy,
 time-resolved transcript profiling, and reverse genetics to elucidate this
 dual role of TFL1. We find that TFL1 accumulates dynamically in the SAM
 reflecting its dual function. Moreover, TFL1 represses two major sets of
 genes. One set includes genes that promote flowering and whose expression
 increases earlier in tfl1. The other set is spatially misexpressed in tfl1
 inflorescence meristems. The misexpression of these two gene sets in tfl1
 mutants depends upon FD transcription factor with which TFL1 interacts.
 Furthermore, the MADS-box gene SEPALLATA4, which is upregulated in tfl1,
 contributes both to the floral transition and shoot determinacy defects of
 tfl1 mutants. Thus, we delineate the dual function of TFL1 in shoot
 development in terms of its dynamic spatial distribution and different
 modes of gene repression.
description: # Two modes of gene regulation by TFL1 mediate its dual function in
 flowering time and shoot determinacy of Arabidopsis
 Give a brief summary of
 dataset contents, contextualized in experimental procedures and results.
 ## Description of the data and file structure ``` To make the RNA-seq as
 accessible as possible we inserted a special folder called
 "RNA-seq_navigator" in this folder is present the R app and the
 analysed data file to extract the RNA expression from the RNA-seq. Inside
 the folder is present a READ ME file with detailed instruction to use the
 R app. The RNA-seq app was developed by Edouard Severin. In the dataset
 you will find folders for each Main Figure and Supplementary Figure of the
 manuscript. Inside these folder divided by Pannel there will be the data
 used to create any single figure of the paper. The data files include
 confocal acquisitions (.lif and .tif; open with Fiji), in situ images
 (.tif; open with Fiji), MorphographX analysis (.mgxm open with
 MorphographX software), raw data of flowering time, real time and the
 statistical analysis (.xlsx; open with excel. .pzfx open with Prism
 GraphPad), sequencing results (.abi open with ApE - Aplasmid Editor).
 Figure_1 -Panels A and B: Confocal acquisition of meristems of Col-0,
 tfl1-18, fd-3 and fd-3 tfl1-18 at different stages of floral transition.
 Every .lif file contains multiple images. .lif files could be open with
 the software Fiji. Inside the folder: ----Height and width statistic.xlsx:
 meristem measurements of height and width and statistical test. Excel file
 +--- Replica 1: all the files can be open with Fiji | | RNA seq REP1 10
 DAS .lif | | RNA seq REP1 13 DAS .lif | | RNA seq REP1 16 DAS.lif | | RNA
 seq REP1 19 DAS .lif | | RNA seq REP1 22 DAS .lif | | RNA seq REP1 7
 DAS.lif +--- Replica 2: all the files can be open with Fiji | | RNA seq 10
 DAS rep 2.lif | | RNA seq 13 DAS rep 2.lif | | RNA seq 16 DAS rep 2.lif |
 | RNA seq 19 DAS rep2.lif | | RNA seq 22 DAS rep2.lif | | RNA seq 7 DAS
 rep2 .lif +--- Replica 3: all the files can be open with Fiji | RNA sea 7
 DAS rep3.lif | RNA seq 10 DAS rep 3.lif | RNA seq 13 DAS rep 3.lif | RNA
 seq 16 DAS rep 3.lif | RNA seq 19 DAS rep 3.lif | RNA seq 22 DAS rep 3.lif
 -Panel C:MorphographX pannel data. Confocal acquisition (in .lif file) of
 Col and tfl1-18 during floral transition and MorphographX analysis file
 (in .mgxm). .lif files could be open with the software Fiji and .mgxm
 could be open with MorphographX software. +---Confocal acquisition: all
 the files can be open with Fiji | | | | Col_0 10 DAS.lif | | | | Col_0 13
 DAS.lif | | | | Col_0 16 DAS.lif | | | | Col_0 8 DAS August.lif | | | |
 Col_0 8 DAS.lif | | | | Col_0 9 DAS.lif | | | | tfl1-18 10 DAS .lif | | |
 | tfl1-18 13 DAS .lif | | | | tfl1-18 8 DAS.lif | | | | tfl1-18 9 DAS .lif
 | | | +---MorphographX analysis: the folder contains all the files for
 MorphographX analysis. Both final mesh and in process one. | | ----All
 choosen Meristem morphographX.xlsx (Excel file) | | | | | +---Col0
 MERISTEM: the foder contains all the MorphographX analysis of Col-0
 meristems with 3 replica for time point. Inside every subfolder all the
 steps of morphographX analysis are present. .tif files could be open with
 the software Fiji and .mgxm could be open with MorphographX software. | |
 | +---Col0 10 DAS | | | | +---Col0 SAM2.2 | | | | +---Col0 SAM4.2 | | | |
 +---Col0 SAM6.1 | | | +---Col0 16 DAS | | | | +---SAM1 | | | | +---SAM2 |
 | | | ---SAM5 | | | +---Col0 8 DAS | | | | +---SAM2 | | | | +---SAM2
 August 2021 | | | | ---SAM3 | | | +---Col0 9 DAS | | | | +---SAM2 | | | |
 +---SAM3 | | | | ---SAM4 | | | ---Col013 DAS | | | +---Col0 SAM7.1 | | |
 +---SAM4 | | | ---SAM5 | | ---tfl1-18 MERISTEM: the foder contains all the
 MorphographX analysis of tfl1-18 meristems with 3 replica for time point.
 Inside every subfolder all the steps of morphographX analysis are present.
 .tif files could be open with the software Fiji and .mgxm could be open
 with MorphographX software. | | +---tfl1 10 DAS | | | +---SAM10.1 | | |
 +---SAM6.2 | | | ---SAM8 | | +---tfl1 13 DAS | | | +---SAM1 | | | +---SAM2
 | | | +---SAM3 | | +---tfl1 8 DAS | | | +---SAM3 | | | +---SAM5 | | |
 ---SAM6.1 | | ---tfl1 9 DAS | | +---SAM2 | | +---SAM3 | | +---SAM6 |
 +---Figure_2 | +---Panel A: Confocal acquisition of meristems of Col-0 at
 different stages of floral transition. Every .lif file contains multiple
 images. All the files can be open with Fiji | | | 10 LDs pFD_mC_FD
 gTFL1_Venus.lif | | | 13 LDs pFD_mC_FD gTFL1_Venus.lif | | | 16 LDs
 pFD_mC_FD gTFL1_Venus.lif | | | 19 LDs pFD_mC_FD gTFL1_Venus.lif | | | 22
 LDs pFD_mC_FD gTFL1_Venus.lif | | | 25 LDs pFD_mC_FD gTFL1_Venus.lif | | |
 7 LDs pFD_mC_FD gTFL1_Venus.lif | +---Panel B and C: Raw data of the
 signal quantification analysis. | Raw_data_Fig2_BC.csv |
 Raw_data_Fig2_BC.ods | Raw_data_Fig2_BC.xlsx | +---Figure_3 | Read me.txt
 | Supplemental_Table_S4.xlsx | +---Figure_4 | ---Panels A-E: Confocal
 acquisition of meristems of Col-0, tfl1-18 at different stages of floral
 transition expressing AP1:GFP, FD:VENUS, FUL:VENUS, SEP3:GFP, SOC1:GFP.
 Every .lif file contains multiple images. All the files can be open with
 Fiji | +---gAP1_GFP | | AP1 tfl1 11 DAS.lif | | AP1 tfl1 13 das.lif | |
 AP1 tfl1 15 DAS.lif | | AP1 tfl1 5 DAS.lif | | AP1 tfl1 7 DAS.lif | | AP1
 tfl1 9 DAS.lif | | AP1 WT 11 DAS.lif | | AP1 WT 13 DAS.lif | | AP1 WT 15
 DAS.lif | | AP1 WT 5 DAS.lif | | AP1 WT 7 DAS.lif | | AP1 WT 9 DAS.lif | |
 | +---gFD_Venus | | FD_Venus tfl1 10 DAS.lif | | FD_Venus tfl1 13 DAS.lif
 | | FD_Venus tfl1 7das.lif | | FD_venus wt 10 DAS.lif | | FD_Venus wt 13
 DAS.lif | | FD_Venus wt 16 DAS.lif | | FD_Venus wt 7das.lif | | FD__Venus
 tfl1 16 DAS.lif | | | +---gFUL_Venus | | FUL_Venus tfl1-18 10 LDs.lif | |
 FUL_Venus tfl1-18 13 LDs.lif | | FUL_Venus tfl1-18 16 LDs.lif | |
 FUL_Venus tfl1-18 7 LDs.lif | | FUL_Venus wild type 10 LDs.lif | |
 FUL_Venus wild type 13 LDs.lif | | FUL_Venus wild type 16 LDs.lif | |
 FUL_Venus wild type 7 LDs.lif | | | +---gSEP3-GFP | | 10 LDs SEP3_GFP
 Col.lif | | 10 LDs SEP3_GFP tfl1-18.lif | | 13 LDs SEP3_GFP Col.lif | | 13
 LDs SEP3_GFP tfl1-18.lif | | 16 LDs SEP3_GFP Col-0.lif | | 16 LDs SEP3_GFP
 tfl1-18.lif | | 7 LDs SEP3_GFP Col.lif | | 7 LDs SEP3_GFP tfl1-18.lif | |
 | ---gSOC1_GFP | Soc1 tfl1 10 DAS.lif | SOC1 tfl1 13 DAS.lif | SOC1 tfl1 7
 DAS.lif | SOC1 tl1 16 DAS.lif | Soc1 WT 10 DAS.lif | Soc1 WT 13 DAS.lif |
 Soc1 WT 16 DAS.lif | Soc1 WT 7 DAS.lif | +---Figure_5 | +---Panels B and
 C: in situ hybridization of SEP3 and SEP4 during floral transition in
 Col-0 and tfl1-18. .tif files can be open with Fiji. | | ST3483 2x2
 i-Stitching-48-Image Export-63.tif | | ST3484 2x2 i-Stitching-49-Image
 Export-62.tif | | ST3485 2x2 i-Stitching-50-Image Export-61.tif | | ST3486
 2x2 i-Stitching-52-Image Export-59.tif | | ST3487 2x2
 iiii-Stitching-56-Image Export-55.tif | | ST3489 2x2 i-Stitching-63-Image
 Export-48.tif | | ST3490 2x2 i-Stitching-64-Image Export-47.tif | | ST3491
 2x2 i-Stitching-66-Image Export-45.tif | | ST3492 2x2
 ii-Stitching-70-Image Export-41.tif | | ST3493 2x2 iii-Stitching-73-Image
 Export-38.tif | | ST3495 2x2 ii-Stitching-77-Image Export-34.tif | |
 ST3496 2x2 i-Stitching-78-Image Export-33.tif | | ST3497 2x2
 i-Stitching-79-Image Export-32.tif | | ST3498 2x2 ii-Stitching-83-Image
 Export-28.tif | | ST3499 2x2 iii-Stitching-88-Image Export-23.tif | |
 ST3501 2x2 ii-Stitching-95-Image Export-16.tif | | ST3502 2x2
 i-Stitching-97-Image Export-14.tif | | ST3503 2x2 ii-Stitching-101-Image
 Export-10.tif | | ST3504 2x2 ii-Stitching-104-Image Export-07.tif | |
 ST3505 2x2 ii-Stitching-108-Image Export-03.tif | | Thumbs.db | | |
 ---Panels D and E: flowering time data of sep3 tfl1-18 and sep4 tfl1-18.
 Discrete data | sep tfl1 flowering.xlsx | Statistics tfl1 sep3 sep4.xlsx |
 +---Figure_6 | +---Panels A-D: flowering time data of Col-0, tfl1-18, fd-3
 and fd-3 tfl1-18. Discrete data | | Col, tfl1-18, fd-3 and tfl1-18 fd-3
 under LDs.xlsx | | Col, tfl1-18, fd-3 and tfl1-18 fd-3 under SD .xlsx | |
 | ---Pannel E: RNA-seq comparisons used for the heat map. | Allgenotypes
 10 and 13 LDs.csv | fd_3_vs_Col-0_10DAS.csv | fd_3_vs_Col-0_13DAS.csv |
 tfl1-18_vs_Col-0_10DAS.csv | tfl1-18_vs_Col-0_13DAS.csv |
 tfl1_18_fd_3_vs_Col-0_10DAS.csv | tfl1_18_fd_3_vs_Col-0_13DAS.csv |
 +---RNA-seq_navigator: To make the RNA-seq as accessible as possible we
 inserted a special folder called "RNA-seq_navigator" in this
 folder is present the R app and the analysed data file to extract the RNA
 expression from the RNA-seq. Inside the folder is present a "READ
 ME" file with detailed instruction to use the R app. The RNA-seq app
 was developed by Edouard Severin | .RData | .Rhistory | finalGeneList.txt
 | officialmeta.txt | qfpkms.txt | READ ME.txt | RNA-seq navigator app.R |
 +---Suppl_Fig_1 | Read me.txt | +---Suppl_Fig_2 | +---Suppl. Fig. 2.1 | |
 +---Pannel A: in situ hybridization of TFL1 during floral transition in
 Col-0. .tif files can be open with Fiji. | | | TFL1 probe Col-0 10 LDs.tif
 | | | TFL1 probe Col-0 13 LDs.tif | | | TFL1 probe Col-0 16 LDs.tif | | |
 TFL1 probe Col-0 7 LDs.tif | | | Thumbs.db | | | | | +---Pannel B:
 Confocal acquisition of meristems of gTFL1_Venus 3.3 tfl1-18
 complementation line at different stages of floral transition under long
 day. Every .lif file contains multiple images. All the files can be open
 with Fiji. | | | gTFL1 Venus 11 DAS.lif | | | gTFL1 Venus 14 DAS.lif | | |
 gTFL1 Venus 17 DAS.lif | | | gTFL1 Venus 8 DAS.lif | | | | | ---Pannel C:
 Confocal acquisition of meristems of gFD:mCherry #6 gTFL1_Venus 5.3 fd-3
 tfl1-18 complementation line at different stages of floral transition
 under Short day. Every .lif file contains multiple images. All the files
 can be open with Fiji. | | | 2 w SD pFD_mC_FD gTFL1_V.lif | | | 3 w SD
 pFD_mC_FD gTFL1_V.lif | | | 4 w SD pFD_mC_FD gTFL1_V.lif | | | 5 w SD
 pFD_mC_FD gTFL1_V.lif | | | 6 w SD pFD_mC_FD gTFL1_V.lif | | | 7 w SD
 pFD_mC_FD gTFL1_V.lif | | | 8 w SD pFD_mC_FD gTFL1_V.lif | | | Bolting SD
 pFD_mC_FD gTFL1_V.lif | | | +---Suppl. Fig. 2.2 | | +---Pannel A-B:
 flowering time data of Col-0, tfl1-18, gTFL1_Venus 3.3 tfl1-18,
 gTFL1_Venus 5.3 tfl1-18. Discrete data | | | Flowering time data.xlsx | |
 | Statistic flowering.xlsx | | | | | ---Pannel C-D: Meristem morphology
 data of Col-0, tfl1-18, gTFL1_Venus 3.3 tfl1-18, gTFL1_Venus 5.3 tfl1-18.
 Discrete data | | Meristem morphology data.xlsx | | Statistic
 morphology.xlsx | | | ---Suppl. Fig. 2.3 | +---Pannel A | | Read me.txt |
 | | ---Pannel B-C: Raw data of total intensity and Concentration of
 TFL1_Venus quantification. | Raw_data_SuppFig2.3_BC.csv |
 Raw_data_SuppFig2.3_BC.ods | Raw_data_SuppFig2.3_BC.xlsx | +---Suppl_Fig_3
 | +---Suppl. Fig. 3.1 | | ---Pannel A: Confocal acquisition of meristems
 of Col-0 and tfl1-18 at different stages of floral transition under long
 day. Every .lif file contains multiple images. All the files can be open
 with Fiji. | | | Read me.txt | | | | | +---Rep1 | | | RNA seq 10 DAS .lif
 | | | RNA seq 13 DAS .lif | | | RNA seq 16 DAS.lif | | | RNA seq 19 DAS
 .lif | | | RNA seq 22 DAS .lif | | | RNA seq 7 DAS.lif | | | | | +---Rep2
 | | | RNA seq 10 DAS rep 2.lif | | | RNA seq 13 DAS rep 2.lif | | | RNA
 seq 16 DAS rep 2.lif | | | RNA seq 19 DAS rep2.lif | | | RNA seq 22 DAS
 rep2.lif | | | RNA seq 7 DAS rep2 .lif | | | Thumbs.db | | | | | ---Rep3 |
 | RNA sea 7 DAS rep3.lif | | RNA seq 10 DAS rep 3.lif | | RNA seq 13 DAS
 rep 3.lif | | RNA seq 16 DAS rep 3.lif | | RNA seq 19 DAS rep 3.lif | |
 RNA seq 22 DAS rep 3.lif | | | +---Suppl. Fig. 3.2 | | +---Pannel A-B:
 RNA-seq Cluster analysis. .R script can be read using R studio software. |
 | | Clusters tfl1 vs Col.pdf | | | Heatmap tfl1-18 vs Col-0 Martina and
 Vitor version.R | | | Summary.xlsx | | | tf1-18_vs_Col-0_10DAS.csv | | |
 tf1-18_vs_Col-0_13DAS.csv | | | Unique for tfl1 10 13 only class 2 and
 3.csv | | | Unique for tfl1 10 13 without unique clustered genes.csv | | |
 Unique for tfl1 10 13.csv | | | Unique for tfl1 complete lists without
 unique clustered genes.pdf | | | Unique for tfl1 complete lists.pdf | | |
 | | ---Pannel C: RNA-seq Go analysis. | | Full GO analysis.xlsx | | go
 order.pptx | | Thumbs.db | | | +---Suppl. Fig. 3.3 | | +---Pannel A: Real
 time data. .pzfx can be read using Prism-GraphPad software | | | Graphs
 meristems.pzfx | | | real time data.xlsx | | | | | ---Pannel B-C | | Read
 me.txt | | | ---Suppl. Fig. 3.5 | +---Pannel A and B: Real time data.
 .pzfx can be read using Prism-GraphPad software | | Graphs.pzfx | | Real
 time data.xlsx | | | ---Pannel C: Confocal acquisition of meristems of
 Col-0 and tfl1-18 at different stages of floral transition under short
 day. Every .lif file contains multiple images. All the files can be open
 with Fiji. | Col 10w SD zoom1.5 .lif | Col 2w SD zoom2 .lif | Col 4w SD
 zoom1.25 .lif | Col 6w SD zoom1.5 .lif | Col 8w SD zoom1.5 .lif | tfl1 10w
 SD zoom1.5 .lif | tfl1 2w SD zoom2 .lif | tfl1 4w SD zoom1.25 .lif | tfl1
 6w SD zoom1.5 .lif | tfl1 8w SD zoom1.5 .lif | +---Suppl_Fig_4 | ---Suppl.
 Fig. 4.1 | +---Pannel A-B | | Read me.txt | | | ---Pannel C: in situ
 hybridization of AP1 during floral transition in Col-0 and tfl1-18. .tif
 files can be open with Fiji. | AP1 probe Col-0 11 LDs.tif | AP1 probe
 Col-0 13 LDs.tif | AP1 probe Col-0 15 LDs.tif | AP1 probe Col-0 17 LDs.tif
 | AP1 probe Col-0 7 LDs.tif | AP1 probe Col-0 9 LDs.tif | AP1 probe
 tfl1-18 11 LDs.tif | AP1 probe tfl1-18 13 LDs.tif | AP1 probe tfl1-18 15
 LDs.tif | AP1 probe tfl1-18 17 LDs.tif | AP1 probe tfl1-18 7 LDs.tif | AP1
 probe tfl1-18 9 LDs.tif | Thumbs.db | +---Suppl_Fig_5 | +---Suppl. Fig.
 5.1 | | +---Pannel B: in situ hybridization of SEP1 during floral
 transition in Col-0 and tfl1-18. .tif files can be open with Fiji. | | |
 SEP1 probe Col-0 11 LDs.tif | | | SEP1 probe Col-0 13 LDs.tif | | | SEP1
 probe Col-0 15 LDs.tif | | | SEP1 probe Col-0 7 LDs.tif | | | SEP1 probe
 Col-0 9 LDs.tif | | | SEP1 probe tfl1-18 11 LDs.tif | | | SEP1 probe
 tfl1-18 13 LDs.tif | | | SEP1 probe tfl1-18 15 LDs.tif | | | SEP1 probe
 tfl1-18 7 LDs.tif | | | SEP1 probe tfl1-18 9 LDs.tif | | | | | ---Pannel
 D: in situ hybridization of SEP2 during floral transition in Col-0 and
 tfl1-18. .tif files can be open with Fiji. | | SEP2 probe Col-0 11 LDs.tif
 | | SEP2 probe Col-0 13 LDs.tif | | SEP2 probe Col-0 15 LDs.tif | | SEP2
 probe Col-0 7 LDs.tif | | SEP2 probe Col-0 9 LDs.tif | | SEP2 probe
 tfl1-18 11 LDs.tif | | SEP2 probe tfl1-18 13 LDs.tif | | SEP2 probe
 tfl1-18 15 LDs.tif | | SEP2 probe tfl1-18 7 LDs.tif | | SEP2 probe tfl1-18
 9 LDs.tif | | | +---Suppl. Fig. 5.2 | | ---Pannel A: flowering time data
 of Col-0, tfl1-18, soc1-2, tfl1-18 soc1-6, ful-2, tfl1-18 ful-2, fd-3,
 tfl1-18 fd-3. Discrete data. .pzfx can be read using Prism-GraphPad
 software | | Statistics tfl1 ful and tfl1 soc1.xlsx | | tfl1 ful and tfl1
 soc1.pzfx | | | ---Suppl. Fig. 5.3 | ---Pannel C: sequencing data of the
 different sep3 and sep4 mutant. alleles. The .abi and .ape files can be
 read by any software for sequence analysis. ApE is an online free tool to
 read these file and can be downloaded here
 https://jorgensen.biology.utah.edu/wayned/ape/ | sep3-3.ab1 | sep3-4.ab1 |
 sep3-5.ab1 | sep3-6.ab1 | sep3-7.ab1 | sep3-8.ab1 | sep4-3.ab1 |
 sep4-4.ab1 | WT SEP3.ape | WT SEP4.ape | ---Suppl_Fig_6 ---Suppl. Fig.
 6.1: Real time data. .pzfx can be read using Prism-GraphPad software
 Graphs.pzfx real time data.xlsx ``` ## Sharing/Access information RNA-seq
 raw data are deposit in BioProjectID: PRJNA942265. The seeds will be
 deposit in the NASC. ## Code
 This code was developed by Gabriel Rodriguez Maroto