TERRA transcripts and promoters from telomeric and interstitial sites

Area of Science:

• Genomics and Molecular Biology
• Noncoding RNA Research
• Epigenetics and Chromosome Biology

Background:

• TERRA (Telomeric Repeat-containing RNA) are long noncoding RNAs transcribed from human telomeres.
• Previous studies identified TERRA promoters in subtelomeres, driven by CpG island repeat sequences.
• The T2T-CHM13v2.0 genome assembly provides a more complete view of subtelomeric and intrachromosomal regions.

Purpose of the Study:

• To comprehensively identify and characterize TERRA promoters using the T2T-CHM13v2.0 human reference genome.
• To investigate the genomic organization and evolutionary origins of TERRA promoters.
• To determine the transcriptional activity of interstitial telomeric sequences (ITSs) and their contribution to TERRA production.

Main Methods:

• Genome-wide analysis of the T2T-CHM13v2.0 human reference genome to locate TERRA promoters.
• Classification of identified promoters based on their genomic organization (subtelomeric vs. intrachromosomal).
• Comparative sequence analysis to trace promoter origins.
• RT-PCR and RNA-seq experiments to assess TERRA transcript synthesis from ITSs across various cell lines.

Main Results:

• 39 out of 46 subtelomeres harbor TERRA promoters, categorized by their organization.
• 106 intrachromosomal TERRA-like promoters were discovered, with 47 potentially regulating nearby genes.
• Subtelomeric and interstitial promoters originate from a novel family of segmental duplications.
• TERRA transcripts can be synthesized from ITSs, and their transcription levels correlate with telomeric repeat length.
• TERRA expression varies significantly across different cell types, including telomerase-positive and -negative lines.

Conclusions:

• The human genome contains a substantial number of TERRA promoters in both subtelomeric and intrachromosomal locations.
• TERRA promoters represent a newly identified class of segmental duplications with ancient origins.
• Interstitial telomeric sequences are significant sources of TERRA transcripts, contributing to the overall TERRA pool.