Hypermethylated LTR retrotransposon exhibits enhancer activity

Tianxiang Hu, Xingguo Zhu, Wenhu Pi, Miao Yu, Huidong Shi, Dorothy Tuan Lo

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

LTR retrotransposons are repetitive DNA elements comprising ∼10% of the human genome. They are silenced by hypermethylation of cytosines in CpG dinucleotides and are considered parasitic DNA serving no useful function for the host genome. However, hypermethylated LTRs contain enhancer and promoter sequences and can promote tissue-specific transcription of cis-linked genes. To resolve the apparent paradox of hypermethylated LTRs possessing transcriptional activities, we studied the ERV-9 LTR retrotransposon located at the 5′ border of the transcriptionally active β-globin gene locus in human erythroid progenitor and erythroleukemia K562 cells. We found that the ERV-9 LTR, containing 65 CpGs in 1.7 kb DNA, was hypermethylated (with > 90% methylated CpGs). Hypermethylated LTR possessed transcriptional enhancer activity, since in vivo deletion of the LTR by CRISPR-cas9 suppressed transcription of the globin genes by > 50%. ChIP-qPCR and ChIP-seq studies showed that the hypermethylated LTR enhancer spanning recurrent CCAATCG and GATA motifs associated respectively with key transcription factors (TFs) NF-Y and GATA-1 and -2 at reduced levels, compared with the unmethylated LTR in transfected LTR-reporter gene plasmids. Electrophoretic mobility shift assays with methylated LTR enhancer probe showed that the methylated probe bound both NF-Y and GATA-1 and -2 with lower affinities than the unmethylated enhancer probe. Thus, hypermethylation drastically reduced, but did not totally abolish, the binding affinities of the enhancer motifs to the key TFs to assemble the LTR-pol II transcription complex that activated transcription of cis-linked genes at reduced efficiency.

Original languageEnglish (US)
Pages (from-to)226-237
Number of pages12
JournalEpigenetics
Volume12
Issue number3
DOIs
StatePublished - Mar 4 2017

Fingerprint

Retroelements
Endogenous Retroviruses
Globins
Genes
DNA
Transcription Factors
Clustered Regularly Interspaced Short Palindromic Repeats
Leukemia, Erythroblastic, Acute
K562 Cells
Cytosine
Electrophoretic Mobility Shift Assay
Human Genome
Reporter Genes
Plasmids
Genome

Keywords

  • CRISPR-cas9
  • ChIP/EMSA
  • LTR enhancer
  • LTR hypermethylation
  • retrotransposon
  • transcription factor binding to methylated DNA

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research

Cite this

Hypermethylated LTR retrotransposon exhibits enhancer activity. / Hu, Tianxiang; Zhu, Xingguo; Pi, Wenhu; Yu, Miao; Shi, Huidong; Tuan Lo, Dorothy.

In: Epigenetics, Vol. 12, No. 3, 04.03.2017, p. 226-237.

Research output: Contribution to journalArticle

Hu, Tianxiang ; Zhu, Xingguo ; Pi, Wenhu ; Yu, Miao ; Shi, Huidong ; Tuan Lo, Dorothy. / Hypermethylated LTR retrotransposon exhibits enhancer activity. In: Epigenetics. 2017 ; Vol. 12, No. 3. pp. 226-237.
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