TY - JOUR

T1 - Capturing Auxin Response Factors Syntax Using DNA Binding Models

AU - Stigliani, Arnaud

AU - Martin-Arevalillo, Raquel

AU - Lucas, Jérémy

AU - Bessy, Adrien

AU - Vinos-Poyo, Thomas

AU - Mironova, Victoria

AU - Vernoux, Teva

AU - Dumas, Renaud

AU - Parcy, François

N1 - Publisher Copyright: © 2018 The Author

PY - 2019/6/3

Y1 - 2019/6/3

N2 - 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 of IAA19, 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.

AB - 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 of IAA19, 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.

KW - Auxin

KW - Auxin Response Factor

KW - DAP-seq

KW - DNA binding model

KW - ARF2

KW - SPECIFICITY

KW - IDENTIFICATION

KW - GENE

KW - STRUCTURAL BASIS

KW - BIOLOGY

KW - SITES

KW - PROTEINS

KW - EXPRESSION

UR - http://www.scopus.com/inward/record.url?scp=85060031038&partnerID=8YFLogxK

U2 - 10.1016/j.molp.2018.09.010

DO - 10.1016/j.molp.2018.09.010

M3 - Article

C2 - 30336329

AN - SCOPUS:85060031038

VL - 12

SP - 822

EP - 832

JO - Molecular Plant

JF - Molecular Plant

SN - 1674-2052

IS - 6

ER -