Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate.
- Resource Type
- Academic Journal
- Authors
- Contreras-López O; Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation, 8370415 Santiago, Chile.; Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile.; Vidal EA; Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565 Santiago, Chile.; Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, 8580745 Santiago, Chile.; Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, 8580745 Santiago, Chile.; Riveras E; Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation, 8370415 Santiago, Chile.; Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile.; Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565 Santiago, Chile.; Alvarez JM; Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565 Santiago, Chile.; Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, 8580745 Santiago, Chile.; Moyano TC; Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation, 8370415 Santiago, Chile.; Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile.; Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565 Santiago, Chile.; Sparks EE; Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19713.; Medina J; Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, 28040 Madrid, Spain.; Pasquino A; Center for Genomics and Systems Biology, New York University, New York, NY 10003.; Benfey PN; Department of Biology, Duke University, Durham, NC 27708.; HHMI, Duke University, Durham, NC 27708.; Coruzzi GM; Center for Genomics and Systems Biology, New York University, New York, NY 10003.; Gutiérrez RA; Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation, 8370415 Santiago, Chile; rgutierrez@bio.puc.cl.; Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile.; Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565 Santiago, Chile.
- Source
- Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc Natl Acad Sci U S A Subsets: MEDLINE
- Subject
- Language
- English
Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type-specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.
Competing Interests: The authors declare no competing interest.
(Copyright © 2022 the Author(s). Published by PNAS.)