ReviewThe Plant cell2022
Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.
Review in The Plant cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers.
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Who cites it
191 citing papers in PubMed, 345 citations in OpenAlex.
- Predicting transcriptional regulators in plants in the era of artificial intelligence.Current opinion in plant biology · 2026Review
- Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.Plant communications · 2026Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Accelerating iron biofortification in millets: progress, challenges, and future prospects.Planta · 2026Review
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- Article
- Genome-wide identification of HCT gene family in sugarcane (Saccharum spp. hybrid) and characterization of putative cis-elements in gene regulation.BMC genomics · 2026Article
- Genome-wide modelling of plant transcription factor binding captures regulatory variants associated with phenotypic traits.Nature communications · 2026Article
- A synthetic expression system for orthogonal gene expression in Nicotiana benthamiana.Plant molecular biology · 2026Article
- Systematic identification, characterization, and expression analysis of rice strubbelig-receptor family genes associated with fluroxypyr-meptyl and oxyfluorfen metabolism.Journal, genetic engineering & biotechnology · 2026Article
- Single-cell chromatin accessibility and cis-regulatory element analyses in plants using the scPlantReg platform.Nature plants · 2026Article
- Pan-genome analysis reveals hidden diversity and selection signatures of auxin response factors (ARFs) associated with breeding in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Article
- Cis-regulatory architecture downstream of FLOWERING LOCUS T underlies quantitative control of flowering in Arabidopsis thaliana.Genome biology · 2026Article
- Construction of a flavonoid transcriptional-metabolic network and analysis of auxin signaling activation in Leymus chinensis in response to animal feeding.Plant cell reports · 2026Article
- The landscape of regulatory element evolution in a C4 perennial grass.BMC genomics · 2026Article
- Comprehensive genomic and haplotype analysis of the phytocyanin gene family reveals evolutionary expansion and functional diversification in Setaria italica.Plant cell reports · 2026Article
- Novel Molecular Markers and Immune-Related Candidate Genes for Blackleg Resistance in Rapeseed: A Genome-Wide Analysis.International journal of molecular sciences · 2026Article
131 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.