Establishing the Architecture of Plant Gene Regulatory Networks

Fan, Yun; Ouma, Wilberforce Zachary; Li, Shirley Weishi; Doseff, Andrea I.; Grotewold, Erich

doi:10.1016/bs.mie.2016.03.003

Cited by 12 publications

(12 citation statements)

References 315 publications

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“…Functional characterization of CRMs includes the identification of TFs binding to individual CREs within CRMs and the interplay between CRM-bound TFs. Methods applied can be divided into TF- and DNA-centered approaches ( Yang et al, 2016 ; Springer et al, 2019 ). ChIP-seq is the gold standard to map genome-wide TF binding in vivo ( Johnson et al, 2007 ; Kaufmann et al, 2009 ).…”

Section: Identifying and Verifying Crms Individually And Genome-widementioning

confidence: 99%

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

2021

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The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.

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Section: Identifying and Verifying Crms Individually And Genome-widementioning

confidence: 99%

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

2021

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“…HIS3 selectable marker, resulting in the collection of Promoter-pMW#2 plasmids (see Methods). These plasmids were then used for individual integration into the genome of yeast strain YM4271 (Liu et al, 1993), which was verified by PCR, giving rise to 54 different bait strains, each harboring one maize promoter::HIS3 construct (Yang et al, 2016). Because a low level of HIS3 expression is often sufficient for yeast growth in synthetic medium without histidine and uracil (SD-His-Ura), we tested each yeast bait strain for growth in SD-His-Ura medium containing increasing concentrations (0-100 mM) of 3-amino-1,2,4-triazole (3-AT), establishing an ideal 3-AT concentration for each bait yeast strain (Supplemental Table 1).…”

Section: Generation Of Yeast Strains For Y1h Assaysmentioning

confidence: 99%

“…Each yeast strain was tested for autoactivation by growth in SD-His-Ura medium containing increasing concentrations (5,10,20,40,60,80,100, and 120 mM) of 3-amino-1,2,4-triazole (3-AT; Sigma Life Sciences, St. Louis, MO), as previously described (Deplancke et al, 2006b). Y1H screens were performed using 54 different promoter bait strains corresponding to genes encoding enzymes involved in the phenolic biosynthetic pathway, as described previously (Yang et al, 2016) using the maize transcription factor (TFome) library we generated (Burdo et al, 2014). The coding DNA sequences of 1901 TFs were cloned downstream of the GAL4 activation domain in the pAD-GAL4-GW-C1 vector (Machemer et al, 2011) by LR Clonase (Life Technologies).…”

Section: Generation Of Yeast Strains and Y1h Screeningsmentioning

confidence: 99%

A Maize Gene Regulatory Network for Phenolic Metabolism

Fan

Jiang

et al. 2017

Molecular Plant

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The translation of the genotype into phenotype, represented for example by the expression of genes encoding enzymes required for the biosynthesis of phytochemicals that are important for interaction of plants with the environment, is largely carried out by transcription factors (TFs) that recognize specific cis-regulatory elements in the genes that they control. TFs and their target genes are organized in gene regulatory networks (GRNs), and thus uncovering GRN architecture presents an important biological challenge necessary to explain gene regulation. Linking TFs to the genes they control, central to understanding GRNs, can be carried out using gene- or TF-centered approaches. In this study, we employed a gene-centered approach utilizing the yeast one-hybrid assay to generate a network of protein-DNA interactions that participate in the transcriptional control of genes involved in the biosynthesis of maize phenolic compounds including general phenylpropanoids, lignins, and flavonoids. We identified 1100 protein-DNA interactions involving 54 phenolic gene promoters and 568 TFs. A set of 11 TFs recognized 10 or more promoters, suggesting a role in coordinating pathway gene expression. The integration of the gene-centered network with information derived from TF-centered approaches provides a foundation for a phenolics GRN characterized by interlaced feed-forward loops that link developmental regulators with biosynthetic genes.

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“…This approach serves as an iterative screening process that selects nucleic acid molecules from a large pool of oligonucleotides of variant sequences, followed by multiple rounds of enrichment of bound oligonucleotides. 74 Via the selecting assay, aptamers are then optimized for higher affinity and selectivity with specific target molecules, which can cover an extensive range, from tiny molecules such as drugs and ions to whole cells such as cancer cells and bacteria. 75…”

Section: Advancements In Biomarker Detection In Saliva By Ecbssmentioning

confidence: 99%