Christophe Liseron-Monfils

Cold Spring Harbor Laboratory

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Doreen Ware

Cornell University

Andrew Olson

Cold Spring Harbor Laboratory

Lewis Lukens

University of Guelph

Manish N. Raizada

University of Guelph

Gregory S. Downs

Weatherford College

Sarah Hake

Plant Gene Expression Center

Susumu Hiraga

Institute of Crop Science

Erica Unger‐Wallace

Iowa State University

Allison Gaudinier

University of California, Davis

Lotte Pollaris

VIB-UGent Center for Inflammation Research

Cooperative Institutions

University of Guelph

Ghent University

University of California, Davis

Cold Spring Harbor Laboratory

VIB-UGent Center for Plant Systems Biology

Pioneer Hi-Bred

Vlaams Instituut voor Biotechnologie

University of California, Berkeley

United States Department of Agriculture

Agricultural Research Service

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Regulatory modules controlling maize inflorescence architecture

Genome Research (2013)

Andrea L. Eveland Alexander Goldshmidt Michael Pautler Kengo Morohashi Christophe Liseron-Monfils

Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize ( Zea mays ) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. Developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, revealed potential mechanisms for repressing branches in distinct stem cell populations, including interactions with KNOTTED1, a master regulator of stem cell maintenance. Our results uncover discrete developmental modules that function in determining grass-specific morphology and provide a basis for targeted crop improvement and translation to other cereal crops with comparable inflorescence architectures.

10.1101/gr.166397.113

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Citations (154)

Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas

BMC Plant Biology (2013)

Christophe Liseron-Monfils Tim Lewis Daniel Ashlock Paul D. McNicholas François Fauteux

Abstract Background The discovery of genetic networks and cis -acting DNA motifs underlying their regulation is a major objective of transcriptome studies. The recent release of the maize genome ( Zea mays L.) has facilitated in silico searches for regulatory motifs. Several algorithms exist to predict cis -acting elements, but none have been adapted for maize. Results A benchmark data set was used to evaluate the accuracy of three motif discovery programs: BioProspector, Weeder and MEME. Analysis showed that each motif discovery tool had limited accuracy and appeared to retrieve a distinct set of motifs. Therefore, using the benchmark, statistical filters were optimized to reduce the false discovery ratio, and then remaining motifs from all programs were combined to improve motif prediction. These principles were integrated into a user-friendly pipeline for motif discovery in maize called Promzea, available at http://www.promzea.org and on the Discovery Environment of the iPlant Collaborative website. Promzea was subsequently expanded to include rice and Arabidopsis. Within Promzea, a user enters cDNA sequences or gene IDs; corresponding upstream sequences are retrieved from the maize genome. Predicted motifs are filtered, combined and ranked. Promzea searches the chosen plant genome for genes containing each candidate motif, providing the user with the gene list and corresponding gene annotations. Promzea was validated in silico using a benchmark data set: the Promzea pipeline showed a 22% increase in nucleotide sensitivity compared to the best standalone program tool, Weeder, with equivalent nucleotide specificity. Promzea was also validated by its ability to retrieve the experimentally defined binding sites of transcription factors that regulate the maize anthocyanin and phlobaphene biosynthetic pathways. Promzea predicted additional promoter motifs, and genome-wide motif searches by Promzea identified 127 non-anthocyanin/phlobaphene genes that each contained all five predicted promoter motifs in their promoters, perhaps uncovering a broader co-regulated gene network. Promzea was also tested against tissue-specific microarray data from maize. Conclusions An online tool customized for promoter motif discovery in plants has been generated called Promzea. Promzea was validated in silico by its ability to retrieve benchmark motifs and experimentally defined motifs and was tested using tissue-specific microarray data. Promzea predicted broader networks of gene regulation associated with the historic anthocyanin and phlobaphene biosynthetic pathways. Promzea is a new bioinformatics tool for understanding transcriptional gene regulation in maize and has been expanded to include rice and Arabidopsis.

Motif (music)

Cis-regulatory module

10.1186/1471-2229-13-42

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Citations (22)

Regulatory motifs identified from a maize developmental coexpression network

Genome (2014)

Gregory S. Downs Christophe Liseron-Monfils Lewis Lukens

Transcriptional control is an important determinant of plant development, and distinct modules of coordinated genes characterize the maize developmental transcriptome. Upstream regulatory sequences are often the primary factors that control gene expression pattern and abundance. Here, we identify 244 regulatory motifs that are significantly enriched within 24 gene expression modules previously constructed from transcript abundances of 34,876 Zea mays (maize) gene models from embryogenesis to senescence. Within modules, we identify motifs that have not been characterized. In addition, we identify motifs similar to experimentally verified motifs, and the functions of these motifs overlap with predicted module functions. This work demonstrates the power of transcript-level coexpression modules to identify both variants of known regulatory motifs and novel motifs that control a species' developmental transcriptome.

Gene regulatory network

Sequence motif

Cis-regulatory module

10.1139/gen-2013-0177

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Citations (3)

Revealing gene regulation and associations through biological networks

Current Plant Biology (2015)

Christophe Liseron-Monfils Doreen Ware

Traditionally, over the last 10,000 years, agriculture has relied on natural biological evolution and careful selection of plant varieties by farmers that was used as the founder material by plant breeders in the last 150 years for further genetic improvement. Plant breeders played an important role mainly by introgression of a trait of interest, through the transfer of genetic loci, into an elite crop line that exhibits high-yield performance across a wide range of conditions. Modern agriculture has relied on the use of biotechnologies and molecular biology to improve marker development and aid in the discovery of candidate loci or genes associated with desirable traits, thereby reducing the time required for selective breeding. In this review, we briefly describe the evolution of the methods used to identify candidate leads (gene, loci or regulatory regions) for crop improvement, starting by quantitative genetic methods. The development of co-expression and molecular networks will be described. It will be shown how network analysis can reinforced the discovery of candidate genes/loci more rapidly and with higher confidence. These improvements will serve to accelerate genetic engineering and molecular breeding as modern agriculture confronts the challenging times ahead, with the increase of abiotic stresses for crops as drought, heat, soil high salinity or waterlogging. Without taking in account possible losses due these growing stresses, the increase in crop yields needs to be significantly accelerated to feed the growing world population, following the FAO previsions.

Candidate gene

Introgression

Trait

Plant Breeding

Molecular breeding

10.1016/j.cpb.2015.11.001

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Citations (39)

GENETIC NETWORKS of PLANT DEVELOPMENT and NUTRIENT-TREATED ROOT HAIRS

Christophe Liseron-Monfils

Root (linguistics)

Root hair

Plant roots

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NECorr, a Tool to Rank Gene Importance in Biological Processes using Molecular Networks and Transcriptome Data

bioRxiv (Cold Spring Harbor Laboratory) (2018)

Christophe Liseron-Monfils Andrew Olson Doreen Ware

Abstract The challenge of increasing crop yield while decreasing plants’ susceptibility to various stresses can be lessened by understanding plant regulatory processes in a tissue-specific manner. Molecular network analysis techniques were developed to aid in understanding gene inter-regulation. However, few tools for molecular network mining are designed to extract the most relevant genes to act upon. In order to find and to rank these putative regulator genes, we generated NECorr, a computational pipeline based on multiple-criteria decision-making algorithms. With the objective of ranking genes and their interactions in a selected condition or tissue, NECorr uses the molecular network topology as well as global gene expression analysis to find hub genes and their condition-specific regulators. NECorr was applied to Arabidopsis thaliana flower tissue and identifies known regulators in the developmental processes of this tissue as well as new putative regulators. NECorr will accelerate translational research by ranking candidate genes within a molecular network of interest.

Gene regulatory network

Rank (graph theory)

10.1101/326868

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Citations (9)

Transcriptional regulation of nitrogen-associated metabolism and growth

Nature (2018)

Allison Gaudinier Joel Rodríguez-Medina Lifang Zhang Andrew Olson Christophe Liseron-Monfils

Nitrogen Cycle

10.1038/s41586-018-0656-3

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Citations (281)

Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea maysL.) associated with distinctcis-acting promoter motifs

Plant Signaling & Behavior (2013)

Christophe Liseron-Monfils Yong‐Mei Bi Gregory S. Downs Wenqing Wu Tara Signorelli

Nitrogen is considered the most limiting nutrient for maize (Zea mays L.), but there is limited understanding of the regulation of nitrogen-related genes during maize development. An Affymetrix 82K maize array was used to analyze the expression of ≤ 46 unique nitrogen uptake and assimilation probes in 50 maize tissues from seedling emergence to 31 d after pollination. Four nitrogen-related expression clusters were identified in roots and shoots corresponding to, or overlapping, juvenile, adult, and reproductive phases of development. Quantitative real time PCR data was consistent with the existence of these distinct expression clusters. Promoters corresponding to each cluster were screened for over-represented cis-acting elements. The 8-bp distal motif of the Arabidopsis 43-bp nitrogen response element (NRE) was over-represented in nitrogen-related maize gene promoters. This conserved motif, referred to here as NRE43-d8, was previously shown to be critical for nitrate-activated transcription of nitrate reductase (NIA1) and nitrite reductase (NIR1) by the NIN-LIKE PROTEIN 6 (NLP6) in Arabidopsis. Here, NRE43-d8 was over-represented in the promoters of maize nitrate and ammonium transporter genes, specifically those that showed peak expression during early-stage vegetative development. This result predicts an expansion of the NRE-NLP6 regulon and suggests that it may have a developmental component in maize. We also report leaf expression of putative orthologs of nitrite transporters (NiTR1), a transporter not previously reported in maize. We conclude by discussing how each of the four transcriptional modules may be responsible for the different nitrogen uptake and assimilation requirements of leaves and roots at different stages of maize development.

Nitrogen Assimilation

Regulon

Nitrogen deficiency

10.4161/psb.26056

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Citations (22)

A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

Cell Reports (2025)

Yuji Ke Vincent Pujol Jasper Staut Lotte Pollaris Ruth Seurinck

Despite the broad use of single-cell/nucleus RNA sequencing in plant research, accurate cluster annotation in less-studied plant species remains a major challenge due to the lack of validated marker genes. Here, we generated a single-cell RNA sequencing atlas of soil-grown wheat roots and annotated cluster identities by transferring annotations from publicly available datasets in wheat, rice, maize, and Arabidopsis. The predictions from our orthology-based annotation approach were next validated using untargeted spatial transcriptomics. These results allowed us to predict evolutionarily conserved tissue-specific markers and generate cell type-specific gene regulatory networks for root tissues of wheat and the other species used in our analysis. In summary, we generated a single-cell and spatial transcriptomics resource for wheat root apical meristems, including numerous known and uncharacterized cell type-specific marker genes and developmental regulators. These data and analyses will facilitate future cell type annotation in non-model plant species.

10.1016/j.celrep.2025.115240

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