Non-coding RNAs match the deleted genomic regions in humans

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• RNA is transcribed from DNA, implying no RNA should exist from deleted DNA regions.
• Previous research has not extensively explored the presence of RNA transcripts mapping to deleted genomic areas in human cells.

Purpose of the Study:

• To investigate the presence and characteristics of RNA transcripts mapping to deleted DNA regions in human cells.
• To determine if a residual RNA cache exists within human cells and its potential origins.

Main Methods:

• Utilized whole genome, ncRNA, and mRNA sequence data from the 1000 Genomes Project (CEU and YRI populations).
• Aligned ncRNA reads against individual genomic DNA sequences to identify transcripts mapping to homozygous deletions.
• Analyzed the distribution and enrichment of ncRNA reads around deletion sites and genic regions.

Main Results:

• Identified ncRNA reads mapping to 229 out of 1114 homozygous deletions across analyzed samples.
• Observed enrichment of these ncRNA reads at the ends of deletions and within genic regions.
• The enrichment pattern at deletion ends suggests a potential link to double-strand break repair mechanisms.

Conclusions:

• Human cells may harbor a residual ncRNA cache, with transcripts mapping to deleted genomic regions.
• These ncRNAs might originate from double-strand break-induced RNA (dsRNA) species involved in DNA repair.
• The findings suggest this ncRNA cache could be a heritable molecular signature, possibly propagated across generations.