Hypermethylated LTR retrotransposon exhibits enhancer activity

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• Long terminal repeat (LTR) retrotransposons constitute a significant portion of the human genome.
• These elements are typically silenced through DNA methylation but possess potential regulatory functions.
• Understanding the paradox of silenced yet active LTRs is crucial for genome regulation insights.

Purpose of the Study:

• To investigate the transcriptional activity of hypermethylated ERV-9 LTR retrotransposons.
• To resolve the apparent contradiction between LTR hypermethylation and enhancer function.
• To elucidate the mechanism by which hypermethylated LTRs influence cis-linked gene transcription.

Main Methods:

• CRISPR-cas9 mediated in vivo deletion of ERV-9 LTR.
• Chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR) and sequencing (ChIP-seq).
• Electrophoretic mobility shift assays (EMSA) using methylated and unmethylated LTR probes.

Main Results:

• Hypermethylated ERV-9 LTR demonstrated significant enhancer activity, suppressing globin gene transcription by over 50% upon deletion.
• ChIP studies revealed reduced binding of transcription factors NF-Y and GATA-1/2 to methylated LTR motifs compared to unmethylated ones.
• EMSA confirmed that hypermethylation decreased the binding affinity of these key transcription factors to the LTR enhancer.

Conclusions:

• Hypermethylated LTRs retain enhancer function by interacting with transcription factors, although at a reduced capacity.
• DNA methylation of LTRs drastically diminishes but does not eliminate their ability to activate transcription of nearby genes.
• This finding challenges the view of LTRs as purely parasitic elements and highlights their role in gene regulation.