Genome imbalance modulates the expression of long non-coding RNAs in maize

Area of Science:

• Genomics
• Molecular Biology
• Plant Science

Background:

• Aneuploidy (gain or loss of individual chromosomes) causes greater genomic instability than changes in complete chromosome sets (haploidy/polyploidy).
• Genomic imbalance disrupts macromolecular stoichiometry, affecting protein-coding genes (PCGs), microRNAs, and transposable elements (TEs).
• The role of long non-coding RNAs (lncRNAs) in response to genomic imbalance is largely unknown.

Purpose of the Study:

• To investigate and compare the effects of aneuploidy versus haploidy/polyploidy on lncRNA expression in maize.
• To determine if lncRNAs act as dosage-sensitive regulators under genomic stress.

Main Methods:

• RNA sequencing (RNA-seq) was used to analyze lncRNA expression in maize mature leaf tissue across different ploidy levels.
• Analysis included comparing cis-located and trans-located lncRNAs relative to chromosomal dosage.
• Co-expression networks of cis-acting and trans-acting lncRNAs were constructed.

Main Results:

• Aneuploidy induced significant modulation of both cis- and trans-located lncRNAs, with cis-acting lncRNAs shifting from dosage compensation to a gene dosage effect.
• Trans-located lncRNAs showed varied responses, including inverse effects and positive correlations with chromosomal dosage.
• LncRNAs exhibited greater sensitivity to dosage changes than PCGs and showed similar modulation trends to TEs.
• Ploidy series (haploidy/polyploidy) resulted in less lncRNA modulation compared to aneuploidy.

Conclusions:

• LncRNAs are sensitive, dosage-dependent regulators of gene expression in the context of genomic imbalance.
• LncRNAs may play crucial roles in mediating the biological consequences of aneuploidy.
• This study provides insights into lncRNA function and their potential as regulators of PCGs under genomic stress.