Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants

Proceedings of the National Academy of Sciences of the United States of America
Kranthi VaralaGloria M Coruzzi

Abstract

This study exploits time, the relatively unexplored fourth dimension of gene regulatory networks (GRNs), to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. Our "just-in-time" analysis of time-series transcriptome data uncovered a temporal cascade of cis elements underlying dynamic N signaling. To infer transcription factor (TF)-target edges in a GRN, we applied a time-based machine learning method to 2,174 dynamic N-responsive genes. We experimentally determined a network precision cutoff, using TF-regulated genome-wide targets of three TF hubs (CRF4, SNZ, and CDF1), used to "prune" the network to 155 TFs and 608 targets. This network precision was reconfirmed using genome-wide TF-target regulation data for four additional TFs (TGA1, HHO5/6, and PHL1) not used in network pruning. These higher-confidence edges in the GRN were further filtered by independent TF-target binding data, used to calculate a TF "N-specificity" index. This refined GRN identifies the temporal relationship of known/validated regulators of N signaling (NLP7/8, TGA1/4, NAC4, HRS1, and LBD37/38/39) and 146 additional regulators. Six TFs-CRF4, SNZ, CDF1, HHO5/6, and PHL1-validated herein regulate a significant numb...Continue Reading

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Citations

Jun 5, 2019·Cellular and Molecular Life Sciences : CMLS·Xiaohuan Mu, Jie Luo
Apr 25, 2020·Nucleic Acids Research·Qi SongSong Li
Jul 28, 2020·The Plant Journal : for Cell and Molecular Biology·Dae Kwan Ko, Federica Brandizzi
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Jan 28, 2020·Journal of Experimental Botany·Kun-Hsiang LiuJen Sheen
Apr 24, 2020·Scientific Reports·Jacopo CirroneDennis E Shasha
Jun 7, 2018·Proceedings of the National Academy of Sciences of the United States of America·Kathleen Greenham, C Robertson McClung
Feb 14, 2020·The Plant Journal : for Cell and Molecular Biology·Bedrich BenesMatthew J Turk
May 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Joseph SwiftGloria M Coruzzi
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Sep 2, 2020·Journal of Experimental Botany·Amel MaghiaouiLiên Bach
Dec 18, 2020·Frontiers in Plant Science·José Domínguez-FigueroaJoaquín Medina
Dec 29, 2020·IScience·Aalt Dirk Jan van DijkDick de Ridder
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May 28, 2021·Frontiers in Plant Science·Suresh KumarTrilochan Mohapatra
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Mar 17, 2020·Computers in Biology and Medicine·Turki Turki, Y-H Taguchi
Aug 6, 2021·Annual Review of Cell and Developmental Biology·Lei LiJen Sheen

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Methods Mentioned

BETA
Assay
DAP-Seq
ChIP-Seq

Software Mentioned

SEq
Elefinder
NxTime
TARGET
DESeq2
AUPR
DAP
JIT

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