Abstract
With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their genome-wide chromatin binding regions and mode of action. Evidence from these new technologies emphasize that chromatin targeting of lncRNAs is a prominent mechanism and that these chromatin targeted lncRNAs exert their functionality by fine tuning chromatin architecture resulting in an altered transcriptional readout. Currently, there are no unifying principles that define chromatin association of lncRNAs, however, evidence from a few chromatin-associated lncRNAs show presence of a short common sequence for chromatin targeting. In this article, we review how technological advancements contributed in characterizing chromatin associated lncRNAs, and discuss the potential mechanisms by which chromatin associated lncRNAs execute their functions.
Highlights
RNA, considered a potential primordial molecule of life, has been serving as a central molecule in molecular biology research due to its ability store information and execute catalytic functions in diverse biological contexts
The question in that case remains whether any long ncRNA (lncRNA) with triplex forming capability can be targeted to all the “triplex targetable” i.e TFRs at genomic locations? and secondly, which factors initiate, promote and maintain triplex formation at target locations and that in principle is there a possibility of any difference between cis and trans targeting of triplexes lncRNAs (Figure 2)?
With the development of novel technologies to probe lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we realize the extent of lncRNA involvement in chromatin organization
Summary
In the early 1980s, elegant genetic and molecular studies identified a phenomenon of parent-of-origin-specific allelic expression called genomic imprinting which explained in part the molecular mechanism of dosage compensation [60]. RIPiT-Seq: RNA: Protein immunoprecipitation in tandem (RIPiT) is suitable for RBPs with poor inherent ultraviolet (UV) crosslink ability This method yields highly specific RNA binding footprints of any cellular RNPs and the resulted RNA footprints can be combined with high-throughput sequencing (RIPiT-Seq) thereby providing a means to map the RNA binding sites of such RBPs [73]. MRNA Interactome Capture (MIC): mRNA Interactome Capture (MIC) is an oligo dT-based capture of global mRNA protein-interactome from cells cross linked with complementary crosslinking chemistries: with UV (at 254 nm) or photoactivatable-ribonucleoside (4SU, 4 thiouridine)-enhanced crosslinking (PAR-CL) at 265 nm This method characterized global mRNA proteome comprising novel RNA binding proteins, including metabolic enzymes. RBDmap: RNA Binding Domain map (RBDmap) is an improved protocol of RIC, which finemaps the protein domains that interacts with mRNAs. UV irradiated cells were given stringent denaturing washes to purify the resulting covalently linked RBP–RNA complexes with oligo(dT) magnetic beads. The need for such an approach possibly led to the gradual development of several techniques for identification of global targeting of RNAs to chromatin as we shall discuss
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