Two modes of gene regulation by TFL1 mediate its dual function in flowering time and shoot determinacy of Arabidopsis
Data files
Dec 01, 2023 version files 115.75 GB
-
Figure_1.tar.gz
-
Figure_2.tar.gz
-
Figure_3.tar.gz
-
Figure_4.tar.gz
-
Figure_5.tar.gz
-
Figure_6.tar.gz
-
README.md
-
RNA-seq_navigator.tar.gz
-
Suppl_Fig_1.tar.gz
-
Suppl_Fig_2.tar.gz
-
Suppl_Fig_3.tar.gz
-
Suppl_Fig_4.tar.gz
-
Suppl_Fig_5.tar.gz
-
Suppl_Fig_6.tar.gz
Abstract
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.
README: Two modes of gene regulation by TFL1 mediate its dual function in flowering time and shoot determinacy of Arabidopsis
https://doi.org/10.5061/dryad.fttdz090f
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
https://gitlab.com/slcu/teamHJ/pau/RegionsAnalysis/-/releases/TFL1\\_FD\\_code
This code was developed by Gabriel Rodriguez Maroto