Biology subjects

Shine, M.

Publications and source records attributed to Shine, M..

3 recordsLinked to original sources

bioRxiv2025

Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib

Cellular stresses induce transcription readthrough, whereby RNA polymerase II elongates past a genes polyadenylation cleavage site without RNA cleavage. Readthrough has been reported in several cancer types. Here, we use long-read sequencing of nascent RNA to quantify transcriptional readthrough in chronic myelogenous leukemia (CML) cells and characterize early responses to the targeted therapeutic, imatinib. We show that the amount, length, and gene-specificity of readthrough increase within 1 hour, while gene expression and alternative splicing alterations emerge later. Strikingly, imatinib-dependent mRNA isoform changes involved "readthrough chimeras", in which exons from an upstream gene are alternatively spliced to exons in a downstream gene. Modifications in mRNA isoforms and chimera levels detected at 18 hours were also found in imatinib-resistant K562 as well as CML patient cells, suggesting a cascade of early changes in the fidelity of transcription and splicing, leading to long-term adjustment in gene expression and the development of therapy resistance. TeaserPrecision RNA sequencing was used to discover the earliest response of leukemia cells treated with targeted therapy: transcriptional readthrough.

molecular biology↗

bioRxiv2023

Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p

The stem loop 2 motif (s2m), a highly conserved 41-nucleotide hairpin structure in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome, serves as an attractive therapeutic target that may have important roles in the virus life cycle or interactions with the host. However, the conserved s2m in Delta SARS-CoV-2, a previously dominant variant characterized by high infectivity and disease severity, has received relatively less attention than that of the original SARS-CoV-2 virus. The focus of this work is to identify and define the s2m changes between Delta and SARS-CoV-2 and subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the GISAID database targeting the s2m element reveals a greater than 99% correlation of a single nucleotide mutation at the 15th position (G15U) in Delta SARS-CoV-2. Based on 1H NMR assignments comparing the imino proton resonance region of s2m and the G15U at 19{degrees}C, we find that the U15-A29 base pair closes resulting in a stabilization of the upper stem without overall secondary structure deviation. Increased stability of the upper stem did not affect the chaperone activity of the viral N protein, as it was still able to convert the kissing dimers formed by s2m G15U into a stable duplex conformation, consistent with the s2m reference. However, we find that the s2m G15U mutation drastically reduces the binding affinity of the host miR-1307-3p. These findings demonstrate that the observed G15U mutation alters the secondary structure of s2m with subsequent impact on viral binding of host miR-1307-3p, with potential consequences on the immune response.

biochemistry↗

bioRxiv2022

US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes

Structure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules (proteins, RNAs, and DNAs). The pipeline is built on a uniform TM-score objective function coupled with a heuristic alignment searching algorithm. Large-scale benchmarks demonstrated significant advantages of US-align over state-of-the-art methods in pairwise and multiple structure alignments of different molecules. Detailed analyses showed that the major advantage of US-align lies in the extensive optimization of the unified objective function powered by efficient heuristic search iterations, which significantly improve the accuracy and speed of the structural alignment process. Meanwhile, the universal protocol fusing different molecular and structural types helps facilitate the heterogeneous oligomer structure comparison and template-based protein-protein and protein-RNA/DNA docking.

bioinformatics↗