Widespread long-range cis-regulatory elements in the maize genome

Area of Science:

• Plant genetics and genomics
• Molecular biology
• Epigenetics

Background:

• Agronomic traits in crops can be influenced by gene-distant intergenic regions.
• These gene-distal loci are largely uncharacterized despite their biological significance and potential for crop improvement.

Purpose of the Study:

• To investigate the existence and function of gene-distal loci as long-range transcriptional cis-regulatory elements (CREs) in the maize genome.
• To provide genetic, epigenomic, and functional evidence for these regulatory elements.

Main Methods:

• Analysis of genetic mapping data in crops.
• Epigenomic profiling to identify euchromatic features.
• Chromatin conformation capture to identify DNA loops.
• Self-transcribing active regulatory region sequencing (STARR-seq) to measure enhancer activity.

Main Results:

• Gene-distal loci in maize are enriched for features indicative of regulatory function.
• Chromatin looping connects putative CREs with target genes, consistent with genetic interactions.
• Putative CREs exhibit significant transcriptional enhancer activity.

Conclusions:

• The study provides strong evidence for the widespread presence and function of gene-distal cis-regulatory elements in maize.
• These elements regulate gene expression over long genomic distances, offering new targets for crop improvement.