Data set on G4 DNA interactions with human proteins

Vlasenok, Maria; Levchenko, Olga A.; Basmanov, Dmitry; Klinov, Dmitry V.; Varizhuk, Anna M.; Pozmogova, Galina E.

doi:10.1016/j.dib.2018.02.081

Cited by 13 publications

(20 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the human protein microarray (protoarray) assay, [104] three topologically different model G4s were used. Top protein hits for all three or two of the three G4s included the following: ASXL1, a component of the polycomb complex PR-DUB (a histone deubiquitinase that mediates polycomb-target repression [105] ); the linker histone analogs HMGN1 and HMGN3, which modulate histone acetylation; [91,106,107] the linker histone analog HMGB2, which acts similarly to the above-mentioned HMGB1 but also participates in the demarcation of topologically associated chromatin domains by preventing aggregation of CCCTC-binding factor (CTCF); [108] the peptidylarginine deiminase 4 (PADi4), which mediates histone citrullination; [109] histone chaperones FACT (facilitates chromatin transcription) and BRD3 (bromodomain protein 3).…”

Section: G4s Might Directly Engage Architectural Chromatin Proteins mentioning

confidence: 99%

“…[114,115] BRD3 facilitates the transcription of hyperacetylated chromatin [116] and, along with other BET proteins (BRD2 and BRD4), is currently in the limelight with respect to epigenetic therapy (Box 1). Of the several BRD proteins analyzed in the protoarray assay, [104] BRD3 was the only candidate for efficient interaction with G4s (BRD4 and BRD2 were not tested). However, for the accurate evaluation of the binding affinities, future studies are required because protoarray profiling is a semiquantitative method.…”

Section: G4s Might Directly Engage Architectural Chromatin Proteins mentioning

confidence: 99%

See 1 more Smart Citation

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

2019

View full text Add to dashboard Cite

Here, the emerging data on DNA G‐quadruplexes (G4s) as epigenetic modulators are reviewed and integrated. This concept has appeared and evolved substantially in recent years. First, persistent G4s (e.g., those stabilized by exogenous ligands) were linked to the loss of the histone code. More recently, transient G4s (i.e., those formed upon replication or transcription and unfolded rapidly by helicases) were implicated in CpG island methylation maintenance and de novo CpG methylation control. The most recent data indicate that there are direct interactions between G4s and chromatin remodeling factors. Finally, multiple findings support the indirect participation of G4s in chromatin reshaping via interactions with remodeling‐related transcription factors (TFs) or damage responders. Here, the links between the above processes are analyzed; also, how further elucidation of these processes may stimulate the progress of epigenetic therapy is discussed, and the remaining open questions are highlighted.

show abstract

Section: G4s Might Directly Engage Architectural Chromatin Proteins mentioning

confidence: 99%

Section: G4s Might Directly Engage Architectural Chromatin Proteins mentioning

confidence: 99%

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

2019

View full text Add to dashboard Cite

show abstract

“…Thus, CTCF recruitment to D regulated via several interlinked pathways (Figure 1), and G4s may contribute to e them. G4s affect methylation via sequestering DNA methyltransferase DNMT1 fro target sites [4] and may promote chromatin remodeling due to their affinit architectural chromatin proteins and modifiers, including polycomb related comp subunits [18,19]. This study was designed to partially verify the links between G4s, CGIs, chro compactness and CTCF recruitment.…”

Section: Introductionmentioning

confidence: 99%

DNA G-Quadruplexes Contribute to CTCF Recruitment

Tikhonova

Pavlova

Isaakova

et al. 2021

IJMS

View full text Add to dashboard Cite

G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites in CpG islands (CGIs). We aimed to clarify the role of G4s in CTCF positioning. Molecular modeling data suggested direct interactions, so we performed in vitro binding assays with quadruplex-forming sequences from CGIs in the human genome. G4s bound CTCF with Kd values similar to that of the control duplex, while respective i-motifs exhibited no affinity for CTCF. Using ChIP-qPCR assays, we showed that G4-stabilizing ligands enhance CTCF occupancy at a G4-prone site in STAT3 gene. In view of the reportedly increased CTCF affinity for hypomethylated DNA, we next questioned whether G4s also facilitate CTCF recruitment to CGIs via protecting CpG sites from methylation. Bioinformatics analysis of previously published data argued against such a possibility. Finally, we questioned whether G4s facilitate CTCF recruitment by affecting chromatin structure. We showed that three architectural chromatin proteins of the high mobility group colocalize with G4s in the genome and recognize parallel-stranded or mixed-topology G4s in vitro. One of such proteins, HMGN3, contributes to the association between G4s and CTCF according to our bioinformatics analysis. These findings support both direct and indirect roles of G4s in CTCF recruitment.

show abstract

“…Somewhat in line with these studies a large scale screening for G4 structure interacting factors using protein microarrays comprising >9000 human proteins found several factors that are involved in binding nucleosomes [126]. It is also likely that function of the G4 structure helicases like FANCJ [127], BLM [128], WRN [129], and REV-1 [49] would be important in epigenetic modifications in a replication-dependent manner (as demonstrated for REV-1) [49].…”

Section: Promise Of G4 Structure Binding Molecules In Epigenetics mentioning

confidence: 86%

Promise of G-Quadruplex Structure Binding Ligands as Epigenetic Modifiers with Anti-Cancer Effects

2019

View full text Add to dashboard Cite

Evidences from more than three decades of work support the function of non-duplex DNA structures called G-quadruplex (G4) in important processes like transcription and replication. In addition, G4 structures have been studied in connection with DNA base modifications and chromatin/nucleosome arrangements. Recent work, interestingly, shows promise of G4 structures, through interaction with G4 structure-interacting proteins, in epigenetics—in both DNA and histone modification. Epigenetic changes are found to be intricately associated with initiation as well as progression of cancer. Multiple oncogenes have been reported to harbor the G4 structure at regulatory regions. In this context, G4 structure-binding ligands attain significance as molecules with potential to modify the epigenetic state of chromatin. Here, using examples from recent studies we discuss the emerging role of G4 structures in epigenetic modifications and, therefore, the promise of G4 structure-binding ligands in epigenetic therapy.

show abstract

Data set on G4 DNA interactions with human proteins

Cited by 13 publications

References 8 publications

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

DNA G-Quadruplexes Contribute to CTCF Recruitment

Promise of G-Quadruplex Structure Binding Ligands as Epigenetic Modifiers with Anti-Cancer Effects

Contact Info

Product

Resources

About