Using iRNA-seq analysis to predict gene expression regulatory level and activity in Zea mays tissues

Area of Science:

• Plant molecular biology
• Genomics
• Gene expression regulation

Background:

• Plants utilize transcriptional and post-transcriptional regulation for diverse cell and tissue development.
• Tissue-specific gene expression is crucial for plant growth and environmental responses.
• Current RNA-sequencing methods cannot distinguish active transcription from mRNA degradation.

Purpose of the Study:

• To adapt intron RNA-sequencing for genome-wide transcriptional activity analysis in maize.
• To investigate tissue-specific transcriptional regulation in maize husk and V2-inner stem tissues.

Main Methods:

• Intron RNA-sequencing analysis was adapted to quantify transcriptional activity.
• Genome-wide transcriptional activity was assessed in two distinct maize tissues.
• Gene regulatory network analysis was employed to model transcription factor activity.

Main Results:

• Over 5,300 genes were predicted to be transcriptionally differentially expressed between maize husk and V2-inner stem tissues.
• Identified genes are relevant to the specific functions and development of each tissue.
• Correlations with transcriptional enhancers and transcription factors validated the intron RNA-sequencing predictions.

Conclusions:

• Intron RNA-sequencing is a viable method for assessing genome-wide transcriptional activity in plants.
• The study provides a foundational dataset for understanding maize tissue-specific transcriptional regulation.
• Predicted gene regulatory networks offer insights into the control of tissue identity in maize.