Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids

Zhang, Jiahui; Fakharzadeh, Ashkan; Pan, Feng; Roland, Christopher; Sagui, Celeste

doi:10.1093/nar/gkaa665

Cited by 30 publications

(40 citation statements)

References 106 publications

(112 reference statements)

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“…We now know that R-loops are key regulatory intermediates of epigenetic states, telomere maintenance, DNA repair reactions, mitochondrial DNA replication, and more (Aguilera and García-Muse 2012 ; Crossley et al 2019 ). At the same time dysregulation of normal R-loop formation and dynamics is associated with genome instability, potentially impacting cancers and diseases of trinucleotide repeat-expansion ( Stirling and Hieter 2017 ; Zhang et al 2020 ). Given the breadth of these functions and the pervasive transcription of the human genome, there is likely to be a large number of factors that regulate R-loop formation, bind R-loops, and resolve R-loops.…”

Section: Introductionmentioning

confidence: 99%

Integrative analysis and prediction of human R-loop binding proteins

Kumar

Fournier

Stirling

2022

G3 Genes|Genomes|Genetics

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In the past decade there has been a growing appreciation for R-loop structures as important regulators of the epigenome, telomere maintenance, DNA repair and replication. Given these numerous functions, dozens, or potentially hundreds, of proteins could serve as direct or indirect regulators of R-loop writing, reading, and erasing. In order to understand common properties shared amongst potential R-loop binding proteins (RLBPs) we mined published proteomic studies and distilled 10 features that were enriched in RLBPs compared to the rest of the proteome. Applying an easy-ensemble machine learning approach, we used these RLBP-specific features along with their amino acid composition to create random forest classifiers that predict the likelihood of a protein to bind to R-loops. Known R-loop regulating pathways such as splicing, DNA damage repair and chromatin remodeling are highly enriched in our datasets, and we validate two new R-loop binding proteins LIG1 and FXR1 in human cells. Together these datasets provide a reference to pursue analyses of novel R-loop regulatory proteins.

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Section: Introductionmentioning

confidence: 99%

Integrative analysis and prediction of human R-loop binding proteins

Kumar

Fournier

Stirling

2022

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

show abstract

“…We now know that R-loops are key regulatory intermediates of epigenetic states, telomere maintenance, DNA repair reactions, mitochondrial DNA replication, and more (4,5). At the same time dysregulation of normal R-loop formation and dynamics is associated with genome instability, potentially impacting cancers and diseases of trinucleotide repeat-expansion (6,7). Given the breadth of these functions and the pervasive transcription of the human genome, there is likely to be a large number of factors that regulate R-loop formation, bind R-loops, and resolve R-loops.…”

Section: Introductionmentioning

confidence: 99%

Global prediction of candidate R-loop binding and R-loop regulatory proteins

Fournier

Kumar

Smith

et al. 2021

Preprint

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In the past decade there has been a growing appreciation for R-loop structures as important regulators of the epigenome, telomere maintenance, DNA repair and replication. Given these numerous functions, dozens, or potentially hundreds, of proteins could serve as direct or indirect regulators of R-loop writing, reading, and erasing. In order to understand common properties shared amongst potential R-loop binding proteins (RLBPs) we mined published proteomic studies and distilled 10 features that were enriched in RLBPs compared to the rest of the proteome. We used these RLBP-specific features along with their amino acid composition to create a random forest classifier which predicts the likelihood of a protein to bind to R-loops. In parallel, we employed a whole-genome CRISPR screen coupled with flow-cytometry using the S9.6 monoclonal antibody to sort guide RNAs associated with induction of high S9.6 staining. Known R-loop regulating pathways such as splicing and DNA damage repair are highly enriched in our datasets, and we validate two new R-loop modulating proteins. Together these resources provide a reference to pursue analyses of novel R-loop regulatory proteins.

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“…While H-y (Y*RY) triplex structures are usually pH dependent, for the GAA•TTC run, they are stable at neutral pH 21,23 . Consequently, formation of both Py/Pu/Py and Pu/Pu/Py triplex was reported for this repeat at various ambient conditions in supercoiled DNA 21,77-79 .…”

Section: Discussionmentioning

confidence: 73%

Large-scale expansions of Friedreich’s ataxia GAA•TTC repeats in human cells are prevented by LNA-DNA oligonucleotides and PNA oligomers

Rastokina

Mozafari

Cebrián

et al. 2022

Preprint

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The human disease Friedreich’s ataxia (FRDA) is caused by expansions of GAA•TTC repeats in the first intron intron of the frataxin (FXN) gene, and both intergenerational and somatic expansions are crucial for disease development. We and others have shown earlier that expanded GAA•TTC repeats can form an intramolecular triplex structure (H-DNA). Here we studied the effects of locked nucleic acid (LNA)-DNA mixmer oligonucleotides and peptide nucleic acid (PNA) oligomers on the expansion of GAA•TTC repeats in cultured human cells. Our experimental system employes a mammalian/yeast shuttle plasmid containing a selectable cassette to detect repeat expansions. Using our in-house in vitro triplex-specific DNA cleavage assay, we first confirmed H-DNA formation by the (GAA)100•(TTC)100 repeat in the selectable cassette and demonstrated that the designed LNA-DNA oligonucleotides as well as PNA oligomers are able to disrupt this structure. We then found that both LNA-DNA mixmers and PNA oligomers prevent repeat expansions in human cells. In the accompanying paper, we show that expansions of GAA•TTC repeats in this experimental system occur during replication fork stalling, regression and restart at the repetitive run. We hypothesize, therefore, that triplex DNA formation by the GAA•TTC repeats is a key to their instability, while LNA-DNA oligonucleotides and PNA oligomers counteract repeat expansions by disrupting the triplex at the fork or preventing triplex formation upon fork reversal.

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Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids

Cited by 30 publications

References 106 publications

Integrative analysis and prediction of human R-loop binding proteins

Integrative analysis and prediction of human R-loop binding proteins

Global prediction of candidate R-loop binding and R-loop regulatory proteins

Large-scale expansions of Friedreich’s ataxia GAA•TTC repeats in human cells are prevented by LNA-DNA oligonucleotides and PNA oligomers

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