TY - JOUR
T1 - Mapping Regulatory Determinants in Plants
AU - Galli, Mary
AU - Feng, Fan
AU - Gallavotti, Andrea
N1 - Funding Information: MG, FF, and AG are supported by a grant from the National Science Foundation (TRTech-PGR IOS1916804). Publisher Copyright: © Copyright © 2020 Galli, Feng and Gallavotti.
PY - 2020/10/28
Y1 - 2020/10/28
N2 - The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.
AB - The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.
KW - chromatin
KW - cis-regulatory regions
KW - plant genomics
KW - transcription factor binding
KW - transcriptional regulation
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U2 - https://doi.org/10.3389/fgene.2020.591194
DO - https://doi.org/10.3389/fgene.2020.591194
M3 - Review article
VL - 11
JO - Frontiers in Genetics
JF - Frontiers in Genetics
SN - 1664-8021
M1 - 591194
ER -