Previously unknown mechanism in precision RNA cleaving by Dicer enzyme revealed

By Adnan Saidi On Mar 2, 2023

Previously unknown mechanism in precision RNA cleaving by Dicer enzyme revealed — Purification of hDICER and the hDICER–RNA complex. a, The sequence of pre-let-7a-1^GYM used for structural determination. b, SDS–PAGE of wild-type and mutant hDICER proteins. c, Size-exclusion chromatography of purified proteins. d, In vitro processing of pre-let-7a-1 by purified hDICER. e, Size-exclusion chromatography of the hDICER–pre-let-7a-1^GYM complex. f, SDS–PAGE of the hDICER–pre-let-7a-1^GYM complex visualized by Coomassie blue staining. Protein concentration for each fraction was estimated by Bradford protein assay, and the same amount of protein was loaded for each fraction. g, Urea-PAGE of the hDICER–pre-let-7a-1^GYM complex visualized by SYBR gold staining. RNA concentration for each fraction was estimated by absorbance at 260 nm, and the same amount of RNA was loaded for each fraction. Credit: *Nature* (2023). DOI: 10.1038/s41586-023-05723-3

Researchers at the Center for RNA Research, Institute for Basic Science (IBS), in Seoul, have published a study with critical new insights into the structure and function of the Dicer enzyme. Dicer is an enzyme required for the biogenesis of miRNAs and small interfering RNAs (siRNAs), which in turn are drivers of RNA silencing and post-transcriptional regulating of gene expression, one of the bodies’ many checks on protein production.

RNA silencing requires efficient processing of double-stranded RNA into miRNAs and siRNAs by Dicer. As the name implies, Dicer takes the larger structure, double-stranded RNA, and cuts it into smaller functioning pieces. The specificity of Dicer’s processing has previously only been partially understood, and some of the dicing activity, while functional, needed to be explained.

The study, “Sequence determinant of small RNA production by DICER,” has been published in the journal Nature.

The current research revealed a deeply conserved cis-acting element, termed the “GYM motif,” near the cleavage site. This means that when Dicer cleaves precursor RNA molecules to produce miRNA, it can use landmarks (cis-regulatory elements) within the RNA to know precisely where to cut. This mechanism allows Dicer to override the previously identified mechanism of “ruler”-like counting from the 5′ and 3′ ends of pre-miRNA and solves the mystery around how some of the precision dicings take place.

The study employed massively parallel assays with pre-miRNA variants and human Dicer enzyme (DICER1). The researchers selectively altered the GYM motif, assessed the modified Dicer enzyme’s ability to process double-stranded RNA, and found it to be “a strong determinant of DICER-mediated processing.” The intact GYM motif also improved RNA interference.

Stem recognition by dsRBD and RIIID. The C-terminal dsRBD of DICER shows a large conformational change to accommodate dsRNA in the catalytic valley. Near the cleavage sites, this major groove of the RNA helix is expanded and sandwiched between dsRBD and RIIIDa. The mismatch of the GYM motif is recognized by R1855 of dsRBD. Credit: Nature (2023). DOI: 10.1038/s41586-023-05723-3

The analysis also found that a cancer-associated substitution in Dicer disrupts the recognition of the GYM motif. This discovery could be critically important for future investigations as certain cancers are correlated with increased or decreased Dicer levels, and the association is not currently understood.

Together, the researchers state that their findings “…reveal an integral and conserved mechanism of substrate recognition by DICER and provide a framework to understand how DICER produces small RNAs for biological and therapeutic regulation.”

More information:
Young-Yoon Lee et al, Structure of the human DICER–pre-miRNA complex in a dicing state, Nature (2023). DOI: 10.1038/s41586-023-05723-3

Citation:
Previously unknown mechanism in precision RNA cleaving by Dicer enzyme revealed (2023, March 1)
retrieved 1 March 2023
from https://phys.org/news/2023-03-previously-unknown-mechanism-precision-rna.html

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no
part may be reproduced without the written permission. The content is provided for information purposes only.

For all the latest Science News Click Here

For the latest news and updates, follow us on Google News.

Read original article here

Denial of responsibility! TheDailyCheck is an automatic aggregator around the global media. All the content are available free on Internet. We have just arranged it in one platform for educational purpose only. In each content, the hyperlink to the primary source is specified. All trademarks belong to their rightful owners, all materials to their authors. If you are the owner of the content and do not want us to publish your materials on our website, please contact us by email – [email protected] The content will be deleted within 24 hours.