Microarrays for identifying binding sites and probing structure of RNAs

Abstract

Oligonucleotide microarrays are widely used in various biological studies. In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence. High-throughput methods for determination of secondary structures of RNAs have also been developed. Those methods, however, do not reveal binding sites for oligonucleotides. In contrast, microarrays directly determine binding sites while also providing structural insights. Microarray mapping can be used over a wide range of experimental conditions, including temperature, pH, various cations at different concentrations and the presence of other molecules. Moreover, it is possible to make universal microarrays suitable for investigations of many different RNAs, and readout of results is rapid. Thus, microarrays are used to provide insight into oligonucleotide sequences potentially able to interfere with biological function. Better understanding of structure–function relationships of RNA can be facilitated by using microarrays to find RNA regions capable to bind oligonucleotides. That information is extremely important to design optimal sequences for antisense oligonucleotides and siRNA because both bind to single-stranded regions of target RNAs.

Transcriptional regulation with CRISPR-Cas9: principles, advances, and applications

“…In eukaryotes, efficiency of regulation is diminished by guanine enrichment and adenine depletion of the guide sequence since it decreases sgRNA stability [51]. Chromatin state also affects dCas9 DNA binding: it is much weaker within condensed chromatin regions, therefore very good match between sgRNA and target DNA sequence is required [9,46,52]. Further studies of dCas9 and specificity-improved Cas9 proteins [53,54] in the aforementioned contexts will inform further development of computational algorithms [11,43,51,52,55] that incorporate these effects to precisely select the types and amounts of sgRNAs that are most appropriate to specific applications.…”

HLTF’s Ancient HIRAN Domain Binds 3′ DNA Ends to Drive Replication Fork Reversal

“…Rad5, HLTF, and SHPRH are all members of the SWI/SNF2 family of ATP-dependent DNA translocases involved in chromatin remodeling and DNA repair (Unk et al, 2010). Moreover, the ability of Rad5 and HLTF to promote replication of damaged DNA requires both their ubiquitin ligase and DNA translocase domains (Blastyák et al, 2010; Choi et al, 2015; Gangavarapu et al, 2006; Minca and Kowalski, 2010; Ortiz-Bazán et al, 2014). Indeed, HLTF and Rad5 can directly catalyze replication fork reversal on model DNA substrates (Achar et al, 2011; Blastyák et al, 2010; 2007).…”

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

“…, hydrophobic propensity and surface accessibility), and the evolutionary conservation of the mutated residues across a set of related genes (Reva et al, 2011; Yue et al, 2006; Bromberg et al, 2008; Ng, 2003; Adzhubei et al, 2010). Other approaches analyze mutations across sets of functionally related genes to test for a possible enrichment of mutation events in signaling pathways (Cerami et al, 2010; Ciriello et al, 2012; Hofree et al, 2013; Torkamani and Schork, 2009) or investigate how alterations/modifications alter protein–protein or protein–nucleic interactions (Betts et al, 2015) as well as phosphorylation-dependent signaling motifs (Reimand and Bader, 2013; Reimand et al, 2013). …”