RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants

Area of Science:

• Plant molecular biology
• Genomics
• Gene regulation

Background:

• Gene expression control is crucial for cellular function.
• Promoter-proximal pausing and divergent transcription are well-studied in animals but less so in plants.
• Understanding these mechanisms in plants is vital for agricultural applications.

Purpose of the Study:

• To investigate promoter-proximal pausing and divergent transcription in plants.
• To identify and characterize novel intergenic regulatory elements (IREs) in plants.
• To assess the functional significance of IREs for gene regulation and crop traits.

Main Methods:

• PRO-Seq and GRO-Seq analyses were used to map RNA polymerase activity in cassava and maize.
• A mammalian enhancer detection algorithm (dREG) was adapted for genome-wide identification of bi-directional transcription sites.
• Genomic evolutionary rate profiling (GERP) and single nucleotide polymorphism (SNP) analysis were employed to assess IREs' functional importance.
• Overlap analysis with open chromatin, histone marks, methylation, and eQTL data was performed in maize.

Main Results:

• PRO-Seq in cassava revealed RNA polymerase peaks consistent with pausing and identified divergent transcription at intergenic sites.
• Genome-wide analysis using dREG identified numerous intergenic regulatory element (IRE) candidates in cassava.
• IREs exhibited distinct methylation and nucleotide conservation patterns (GERP) and SNPs within them explained significant trait variation.
• Maize data confirmed RNA polymerase occupancy at IREs and showed significant overlap with regulatory marks and eQTLs.

Conclusions:

• Bidirectional transcription is a valuable marker for identifying functional intergenic regulatory regions in plants.
• These identified IREs play a significant role in transcription regulation.
• The identification of IREs holds potential for improving crop traits through genetic manipulation.