On Characterizing the Interactions between Proteins and Guanine Quadruplex Structures of Nucleic Acids

McRae, Ewan K.S.; Booy, Evan P.; Padilla-Meier, G. Pauline; McKenna, Sean Andrew

doi:10.1155/2017/9675348

Cited by 38 publications

(37 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Importantly, the likelihood of G-quadruplexes forming in genomes varies dramatically in different locations of DNA molecules [45]. For example, simple repeats that are rich in G bases are often found at telomeric ends of chromosomes and there is significant evidence that such sequences form complexes of proteins specifically bound to four-stranded structures [46]. Telomeres have been best characterized in the genomes of eukaryotes, including humans, but they also occur in some bacteria [12,13,22].…”

Section: Dna Structures Formed By Dna Repeatsmentioning

confidence: 99%

Structures and stability of simple DNA repeats from bacteria

Brázda

Fojta

Bowater

2020

Biochemical Journal

View full text Add to dashboard Cite

DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

show abstract

Section: Dna Structures Formed By Dna Repeatsmentioning

confidence: 99%

Structures and stability of simple DNA repeats from bacteria

Brázda

Fojta

Bowater

2020

Biochemical Journal

View full text Add to dashboard Cite

show abstract

“…The biotinylation of GQES7-1 did not disrupt the G-quadruplexes (Figure S.5). Several known G-quadruplex-binding proteins were pulled down by this assay (CNBP, YBOX1, hnRP F, hnRP H, DDX21, DDX17) [36][37][38][39][40][41] . Also, a significant number of helicases were identified (DDX3, CNBP, DDX21, DDX17).…”

Section: Absence Of G-quadruplex Sequences In Non-chordate Rrnasmentioning

confidence: 99%

“…Also, a significant number of helicases were identified (DDX3, CNBP, DDX21, DDX17). All these helicases except DDX3 have been reported to unfold Gquadruplexes 36,[40][41] . In addition, a significant number of heterogeneous nuclear ribonucleoproteins (hnRNPs) were bound to GQES7-1, including hnRNP G-T/RMXL2, hnRNP M, hnRNP G/RBMX, hnRNP H2, hnRNP H, hnRNP F, hnRNP H3, and FUS.…”

Section: Absence Of G-quadruplex Sequences In Non-chordate Rrnasmentioning

confidence: 99%

G-quadruplex formation on specific surface-exposed regions of the human ribosomal RNA

Mestre-Fos

Suttapitugsakul

et al. 2018

Preprint

View full text Add to dashboard Cite

Substantial similarities and profound differences mark ribosomes across phylogeny. The ribosomal core is universal, yet mammalian ribosomes are nearly twice as large as those of prokaryotes. This difference in size is predominantly due to the extension of specific rRNA regions called expansion segments. Here, we characterize expansion segment 7 of the 28S rRNA from Homo sapiens by computation, circular dichroism, gel mobility, fluorescent probes, nuclease accessibility, electrophoretic mobility shifts and blotting. Our results indicate that, in a cell-free environment, G-quadruplexes form in human ES7, or 28S rRNA, and in 80S ribosomes or polysomes purified from human cell lines. rRNA G-quadruplex regions are preferentially located on the most surface-exposed regions of the ribosome, near the termini of specific rRNA tentacles in ES7 and ES27. By multiple sequence alignments, we have inferred that G-quadruplex-forming sequences appear to be a general feature of the surfaces of ribosomes of the phylum Chordata. In this study, we also identify the proteins that bind selectively to the rRNA G-quadruplexes, which include several RNA helicases and other RNA remodeling proteins. It is known that G-quadruplexes are contained in telomeres, promoters, and untranslated regions of mRNA but, to our knowledge, they have not been reported to form in ribosomes.

show abstract

“…The repertoire of cellular proteins binding G4s is both structurally and functionally diverse; it comprises a number of zinc-finger transcription factors (SP1, MAZ, PARP, CNBP), splicing factors (U2AF), proteins of the shelterin complex, RNA-binding proteins such as hnRNPs and RHAU, and RGG-box-containing multifunctional proteins, including nucleolin and FMRP [12][13][14]. Persistence of G4 structures can dysregulate the cellular activities they control and also compromise genomic integrity [15,16].…”

mentioning

confidence: 99%

G-Quadruplexes: More Than Just a Kink in Microbial Genomes

Saranathan

Vivekanandan

2019

Trends in Microbiology

View full text Add to dashboard Cite

G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures formed by guanine-rich DNA and RNA sequences. In this review we aim to provide an overview of the biological roles of G4s in microbial genomes with emphasis on recent discoveries. G4s are enriched and conserved in the regulatory regions of microbes, including bacteria, fungi, and viruses. Importantly, G4s in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomes modulate genes crucial for virus replication. Recent studies on Epstein-Barr virus (EBV) shed light on the role of G4s within the microbial transcripts as cis-acting regulatory signals that modulate translation and facilitate immune evasion. Furthermore, G4s in microbial genomes have been linked to radioresistance, antigenic variation, recombination, and latency. G4s in microbial genomes represent novel therapeutic targets for antimicrobial therapy.

show abstract

On Characterizing the Interactions between Proteins and Guanine Quadruplex Structures of Nucleic Acids

Cited by 38 publications

References 69 publications

Structures and stability of simple DNA repeats from bacteria

Structures and stability of simple DNA repeats from bacteria

G-quadruplex formation on specific surface-exposed regions of the human ribosomal RNA

G-Quadruplexes: More Than Just a Kink in Microbial Genomes

Contact Info

Product

Resources

About