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Capturing Auxin Response Factors Syntax Using DNA Binding Models

Molecular Plant 2019年第6期12卷 822-832页

作者： Amaud Stigliani Raquel Martin-Arevalillo Jeremy Lucas Adrien Bessy Thomas Vinos-Poyo Victoria Mironova Teva Vernoux renaud dumas Francois Parcy Univ. Grenoble Alpes CNRS CEA INRA BIG-LPCV 38000 Grenoble France Laboratoire de Reproduction et Developpement des Plantes Univ. Lyon ENS de Lyon UCB Lyonl CNRS INRA 46 allee dMtalie 69364 Lyon France Novosibirsk State University Pirogova Street 2 Novosibirsk Russia Institute of Cytology and Genetics SB RAS Lavrentyeva Avenue 10 Novosibirsk Russia

Auxin is a key hormone performing a wealth of functions throughout the life cycle of plants. It acts largely by regulating genes at the transcriptional level through a family of transcription factors called auxin response factors (ARFs). Even though all ARF monomers analyzed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here, we report the use of position weight matrices (PWMs) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We found that the genome binding of two ARFs (ARF2 and ARF5/ Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrated why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrated their power with biochemical experiments in the identification of the regulatory regions o1IAA19, an well-characterized auxin-responsive gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin-upregulated genes, thus deciphering the ARFbs syntax functional for regulation. Our study provides a general method to exploit the potential of genome-wide DNA binding assays and to decode gene regulation.

关键词： Auxin Auxin Response Factor DAP-seq DNA binding model

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The LEAFY floral regulator displays pioneer transcription factor properties

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Molecular Plant 2021年第5期14卷 829-837页

作者： Xuelei Lai Romain Blanc-Mathieu Loïc GrandVuillemin Ying Huang Arnaud Stigliani Jeremy Lucas Emmanuel Thevenon Jeanne Loue-Manifel Laura Turchi Hussein Daher Eugenia Brun-Hernandez Gilles Vachon David Latrasse Moussa Benhamed renaud dumas Chloe Zubieta François Parcy Laboratoire Physiologie Cellulaire et Vegetale Universite Grenoble AlpesCNRSCEAINRAEIRIG-DBSCI-LPCV17 avenue des martyrs38054GrenobleFrance Universite Paris-Saclay CNRSINRAEUniversite d'EvryInstitute of Plant Sciences Paris-Saclay(IPS2)91405OrsayFrance The Bioinformatics Centre Department of Biology and Biotech and Research Innovation CentreUniversity of CopenhagenOle Maalces Vej 5DK2200 Copenhagen NDenmark Laboratoire Reproduction et Developpement des Plantes Universite de LyonENS de LyonUCB Lyon 1CNRSINRA69342 LyonFrance Institut de Biologie Structurale Universite Grenoble AlpesCEACNRSGrenobleFrance Universite de Paris Institute of Plant Sciences Paris-Saclay(IPS2)75006 ParisFrance

Pioneer transcription factors(TFs)are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and may be highly ***,pioneer TFs are able to modify the chromatin state to initiate gene *** plants,LEAFY(LFY)is a master floral regulator and has been suggested to act as a pioneer TF in ***,we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genomewide binding experiments and structural *** between regions bound by LFY in vivo and chromatin accessibility data suggest that a subset of LFY bound regions is occupied by *** confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted ***,we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes APETALA1 and *** together,our study suggests that LFY possesses key pioneer TF features that contribute to launching the floral gene expression program.

关键词： flower development pioneer transcription factor gene regulation chromatin remodeling

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