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Area of Science:

  • Genomics and Molecular Biology
  • Epigenetics and Chromosome Organization

Background:

  • Enhancer-promoter interactions in eukaryotes are typically confined by chromatin insulators, which define topologically associated domains (TADs).
  • Mechanisms allowing enhancer-promoter interactions to bypass these boundaries and span multiple TADs remain largely unknown.
  • Long non-coding RNAs (lncRNAs) are abundant in the genome and are hypothesized to have regulatory functions, including chromatin organization.

Approach:

  • Utilized the well-characterized Drosophila Bithorax complex (BX-C) and its boundary replacement platforms (Fab-7 and F2) to investigate boundary function.
  • Engineered constructs with boundary elements, promoters, and polyadenylation signals in various combinations to assess boundary activity.
  • Assayed for the impact of transcriptional readthrough on boundary function and enhancer activity within the BX-C.

Key Points:

  • Transcriptional readthrough, even at low levels, was found to impair the function of chromatin boundaries within the BX-C.
  • Transcription originating from inserted promoters affected the activity of enhancers located within BX-C regulatory domains.
  • Boundary replacement platforms allowed for the systematic study of transcriptional interference with regulatory element function.

Conclusions:

  • Transcriptional readthrough can interfere with the activity of chromatin insulators, challenging the integrity of topologically associated domains (TADs).
  • This mechanism provides a potential explanation for how enhancer-promoter interactions can occur across TAD boundaries.
  • The findings suggest that lncRNAs, as a significant fraction of Pol II transcripts, may actively regulate chromosome structure and gene expression through transcriptional readthrough.