Biology subjects

Tichtinsky, G.

Publications and source records attributed to Tichtinsky, G..

4 recordsLinked to original sources

bioRxiv2025

Beyond binding motif: genomic context predicts transcription factor dependent regulation in Arabidopsis

Transcription Factors (TFs) play a crucial role in the spatiotemporal control of gene expression. Despite the presence of many potential TF binding sites (TFBS) across the genome, TFs do not interact with all of them, and, among those, only a subset leads to actual regulation. In this work, we investigate how the genomic context of a putative TFBS, including the occurrence of binding motifs for other TFs, can be used to predict effective transcriptional regulation by a TF of interest. We focus on LEAFY (LFY), a plant-specific TF and master regulator of flower development. Using available transcriptomes and TF-DNA binding experiments, we identify 1164 LFY binding sites associated with a regulatory response in Arabidopsis thaliana. We then apply a machine learning approach based on properties of the surrounding genomic region, to discriminate these regulatory LFY binding sites from non-regulatory ones. Detailed analysis of the models components reveals that, for LFY, the density and quality of binding sites constitute the most important features but were not sufficient on their own to predict regulatory activity. The presence of binding sites for other transcription factors and the overall richness in TFBS were also essential. These results clarify the nature of the regulatory code by which LFY operates and could serve as a basis for the study of the regulatory elements of other transcription factors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/655699v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1a1a80org.highwire.dtl.DTLVardef@1c1fee5org.highwire.dtl.DTLVardef@1457164org.highwire.dtl.DTLVardef@176c46_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2022

The F-box cofactor UFO redirects the LEAFY floral regulator to novel cis-elements

In angiosperms, flower patterning requires the localized expression of the APETALA3 (AP3) floral homeotic gene involved in petal and stamen development. AP3 is synergistically induced by the master transcription factor (TF) LEAFY (LFY) and the F-box protein UNUSUAL FLORAL ORGANS (UFO), but the molecular mechanism underlying this synergy has remained unknown. Here we show that the connection to ubiquitination pathways suggested by the F-box domain of UFO is mostly dispensable for its function and that UFO instead acts by forming a transcriptional complex with LFY and binds to newly discovered regulatory elements. Cryo-electron microscopy explains how a LFY-UFO complex forms on these novel DNA sites due to direct interaction of UFO with LFY and DNA. Finally, we show that this complex has a deep evolutionary origin, largely predating flowering plants. This work reveals a novel mechanism of an F-box protein in directly modulating the DNA-binding specificity of a master TF.

plant biology↗

bioRxiv2021

The making of cauliflowers: the story of unsuccessful flowers

The arrangement of plant organs, called phyllotaxis, produce remarkable spiral or whorled patterns. Cauliflowers present a unique phyllotaxis with a multitude of spirals over a wide range of scales. How such a self-similar fractal organization emerges from developmental mechanisms has remained elusive. Combining experimental assays with modeling, we found that cauliflowers arise due to the hysteresis of the bistable floral network that generates inflorescences imprinted by a transient floral state. We further show how additional mutations affecting meristem growth dynamics can induce the production of conical phyllotactic structures reminiscent of the conspicuous fractal Romanesco shape. This study reveals how the spectacular morphological modification of the inflorescences in cauliflower and Romanesco shape arises from the hysteresis of the genetic programs controlling inflorescence development. One Sentence SummaryThe molecular making of cauliflowers

plant biology↗

bioRxiv2018

Control of stem-cell niche establishment in Arabidopsis flowers by REVOLUTA and the LEAFY-RAX1 module

Plants retain the ability to produce organs throughout their life by maintaining active stem cell niches called meristems. The shoot apical meristem (SAM) is responsible for the growth of aerial plant structures. In Arabidopsis thaliana, the SAM initially produces leaves during the vegetative phase and later flowers during reproductive development. In the early stages of floral initiation, a group of cells first emerges from the SAM to form a stereotypically organized meristematic structure on its flank. However, the molecular mechanisms underlying the acquisition of this specific meristematic organization remain elusive. We show here that the transcription factors LEAFY (LFY) and REVOLUTA (REV) control two partially redundant pathways controlling meristematic organization in early flower primordia. We found that LFY acts through the transcription factor REGULATOR OF AXILLARY MERISTEM1 (RAX1) and we provide mechanistic insights in how RAX1 allows meristem identity establishment in young flowers. Our work provides a molecular link between the processes of meristem formation and floral identity acquisition in the nascent flower.

plant biology↗