G-quadruplexes originating from evolutionary conserved L1 elements interfere with neuronal gene expression in Alzheimer\u2019s disease

Roy Hanna,Gilbert Bernier,Anthony Flamier,Andrea Barabino

doi:10.1038/s41467-021-22129-9

Abstract

DNA sequences containing consecutive guanines organized in 4-interspaced tandem repeats can form stable single-stranded secondary structures, called G-quadruplexes (G4). Herein, we report that the Polycomb group protein BMI1 is enriched at heterochromatin regions containing putative G4 DNA sequences, and that G4 structures accumulate in cells with reduced BMI1 expression and/or relaxed chromatin, including sporadic Alzheimer’s disease (AD) neurons. In AD neurons, G4 structures preferentially accumulate in lamina-associated domains, and this is rescued by re-establishing chromatin compaction. ChIP-seq analyses reveal that G4 peaks correspond to evolutionary conserved Long Interspersed Element-1 (L1) sequences predicted to be transcriptionally active. Hence, G4 structures co-localize with RNAPII, and inhibition of transcription can reverse the G4 phenotype without affecting chromatin’s state, thus uncoupling both components. Intragenic G4 structures affecting splicing events are furthermore associated with reduced neuronal gene expression in AD. Active L1 sequences are thus at the origin of most G4 structures observed in human neurons.

Highlights

DNA sequences containing consecutive guanines organized in 4-interspaced tandem repeats can form stable single-stranded secondary structures, called G-quadruplexes (G4)
When we analyzed genes with an intragenic G4 structure that was associated with an alternative splicing event, we found that these were significantly downregulated in Alzheimer’s disease (AD) neurons (Fig. 5e and Supplementary Figs. 11c, 13c, and 14c)
We report here that BMI1 inactivation in human cells or mouse photoreceptors resulted in heterochromatin relaxation and induction of G4 structures

Summary

Introduction

DNA sequences containing consecutive guanines organized in 4-interspaced tandem repeats can form stable single-stranded secondary structures, called G-quadruplexes (G4). We report that the Polycomb group protein BMI1 is enriched at heterochromatin regions containing putative G4 DNA sequences, and that G4 structures accumulate in cells with reduced BMI1 expression and/or relaxed chromatin, including sporadic Alzheimer’s disease (AD) neurons. BMI1 inactivation in human dermal fibroblasts (HDFs) results in loss of heterochromatin and transcriptional de-repression of repetitive DNA sequences[9]. Loss of heterochromatin and genomic instability at repetitive DNA sequences were described as new molecular characteristics present in cortical neurons from both Bmi1+/– mice and AD cases[11,12]. Most genetically inherited progeroid syndromes, such as Hutchinson–Gilford progeria, Werner, Bloom, and Xeroderma pigmentosum, present heterochromatin relaxation and genomic instability phenotypes[21,22,23]. Werner (WRN), Xeroderma pigmentosum (XPB, XPD), and Bloom (BLM) gene products encode DNA helicases that can resolve G-quadruplex (G4) DNA’s secondary structures ( called structured DNA or G-quadruplexes) stabilized by Hoogsteen hydrogen bonds between guanines (G)[24,25,26]

Methods

Results

Conclusion