Biology subjects

Nicholson-Shaw, T.

Publications and source records attributed to Nicholson-Shaw, T..

4 recordsLinked to original sources

bioRxiv2025

Post-transcriptional monoadenylation by TENT2 terminates human RNA polymerase III transcript 3' end processing and promotes 7SL RNA biogenesis

Small non-coding RNAs (sncRNAs) are subject to 3 end trimming and tailing activities that impact maturation versus degradation decisions during biogenesis. To investigate the dynamics of human sncRNA 3 end processing at a global level we performed genome-wide 3 end sequencing of nascently-transcribed and steady-state sncRNAs. This revealed widespread post-transcriptional adenylation of nascent sncRNAs, which came in two distinct varieties. One is characterized by oligoadenylation, which is transient, promoted by TENT4A/4B polymerases, and most commonly observed on unstable snoRNAs that are not fully processed at their 3 ends. The other is characterized by monoadenylation, which is broadly catalyzed by TENT2 and, in contrast to oligoadenylation, stably accumulates at the 3-end of sncRNAs, including Polymerase-III-transcribed (Pol-III) RNAs and a subset of small nuclear RNAs. Monoadenylation inhibits Pol-III RNA post-transcriptional 3 uridine trimming and extension and, in the case of 7SL RNAs, prevents their accumulation with nuclear La protein and promotes their biogenesis towards assembly into cytoplasmic signal recognition particles. Thus, the biogenesis of human sncRNAs involves widespread mono- or oligo-adenylation with divergent impacts on sncRNA fates.

molecular biology↗

bioRxiv2024

A Dose-Response Model for Accurate Detection and Quantification of Transcriptome-Wide Gene Knockdown for Oligonucleotide-Based Medicines

Synthetic antisense oligonucleotides and siRNAs are a class of Oligonucleotide-Based Medicines (OBMs) that can hybridize with pre-mRNA and mRNA, recruit a mechanism-of-action specific enzymatic complex, and knockdown target gene expression. This class of molecules provides an excellent substrate for designing precision gene-modulatory therapeutics; however, quantifying on- and off-target dose response as measured by next-generation sequencing for this class of therapeutics has remained under-powered and ambiguous. Often in silico predictions of off-targets (ranked by edit tolerance) are used as putative off-target analysis in ASO and siRNA drug design. We construct a simple, effective theory of transcriptional dynamics and enzymatic activity in order to describe the transcriptome-wide response to these oligonucleotides. We establish rigorous quantification methods of off-target analysis in oligonucleotide drug design. We also extend the DESeq work [1, 2] of Negative Binomial noise in gene expression measurements to describe noise, including outliers, in OBM-dose response NGS experiments. We demonstrate the performance of our model on both synthetic and experimental Digital Gene Expression (DGE) data of dose response in ASO-treated cells. We present our analysis package, DoReSeq, as a freely available resource for the community. We hope this will elevate the standards of off-target analysis for such an important class of precision therapeutics.

pharmacology and toxicology↗

bioRxiv2022

The 2',3' cyclic phosphatase Angel1 facilitates mRNA degradation during human ribosome-associated quality control

Translation elongation stalls trigger mRNA decay and degradation of the nascent polypeptide via translation-dependent quality control pathways. One such pathway, non-stop mRNA decay (NSD), targets aberrant mRNAs that lack stop codons for example due to premature polyadenylation. Here we identify Angel1, a CCR4 deadenylase homolog whose biochemical activity remains poorly defined, as a rate-limiting factor for NSD in human cells. Angel1 associates with mRNA coding regions and proteins involved in ribosome-associated quality control and mRNA decay, consistent with a factor that monitors translation elongation stalls. Depletion of Angel1 causes stabilization of reporter mRNAs that are targeted for NSD by the absence of stop codons, but not an mRNA targeted for nonsense-mediated decay. A conserved catalytic residue of Angel1 is critical for its function in NSD. Our findings identify Angel1 as a human NSD factor and suggest that Angel1 catalytic activity plays a critical role in the NSD pathway.

molecular biology↗

bioRxiv2021

Tailer: A Pipeline for Sequencing-Based Analysis of Non-Polyadenylated RNA 3' End Processing

Post-transcriptional trimming and tailing of RNA 3 ends play key roles in the processing and quality control of non-coding RNAs (ncRNAs). However, bioinformatic tools to examine changes in the RNA 3 "tailome" are sparse and not standardized. Here we present Tailer, a bioinformatic pipeline in two parts that allows for robust quantification and analysis of tail information from next generation sequencing experiments that preserve RNA 3 end information. The first part of Tailer, Tailer-Processing, uses genome annotation or reference FASTA gene sequences to quantify RNA 3 ends from SAM-formatted alignment files or FASTQ sequence read files produced from sequencing experiments. The second part, Tailer-Analysis, uses the output of Tailer-Processing to identify statistically significant RNA targets of trimming and tailing and create graphs for data exploration. We apply Tailer to RNA 3 end sequencing experiments from three published studies and find that it accurately and reproducibly recapitulates key findings. Thus, Tailer should be a useful and easily accessible tool to globally investigate tailing dynamics of non-polyadenylated RNAs and conditions that perturb them.

molecular biology↗