bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2021.07.22.451324

Systematic mapping of small nucleolar RNA targets in human cells

Dunn-Davies, H.·Dudnakova, T.·Langhendries, J.-L.·Watkins, N.·Lafontaine, D. L.·Tollervey, D.
View original source ↗Export metadata ↓

Abstract

Altered expression of box C/D small nucleolar RNAs (snoRNAs) is implicated in human diseases, including cancer. Box C/D snoRNAs canonically direct site-specific, 2-O-methylation but the extent to which they participate in other functions remains unclear. To identify RNA targets of box C/D snoRNAs in human cells, we applied two techniques based on UV crosslinking, proximity ligation and sequencing of RNA hybrids (CLASH and FLASH). These identified hundreds of novel snoRNA interactions with rRNA, snoRNAs and mRNAs. We developed an informatic pipeline to rigorously call interactions predicted to direct methylation. Multiple snoRNA-rRNA interactions identified were not predicted to direct RNA methylation. These potentially modulate methylation efficiency and/or contribute to folding dynamics. snoRNA-mRNA hybrids included 1,300 interactions between 117 snoRNA families and 940 mRNAs. Human U3 is substantially more abundant than other snoRNAs and represented about 50% of snoRNA-mRNA hybrids. The distribution of U3 interactions across mRNAs also differed from other snoRNAs. Following U3 depletion, mRNAs showing altered abundance were strongly enriched for U3 CLASH targets. Most human snoRNAs are excised from pre-mRNA introns. Enrichment for snoRNA association with branch point regions of introns that contain snoRNA genes was common, suggesting widespread regulation of snoRNA maturation.

Explore related subjects

cell biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Dunn-Davies, H., Dudnakova, T., Langhendries, J.-L., Watkins, N., Lafontaine, D. L., Tollervey, D.. 2021-07-22. Systematic mapping of small nucleolar RNA targets in human cells. https://doi.org/10.1101/2021.07.22.451324

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

The yeast Gcn2 protein kinase mediates P-body formation both through its activity with eIF2α and with non-canonical substrates

P-bodies (PBs) are control hubs for RNA processing and storage that form when translation initiation is inhibited, including during stress. In yeast, Gcn2 is the sole eIF2 alpha kinase that inhibits translation initiation in response to diverse stresses. We show that PB formation depends strongly on Gcn2 during amino acid starvation but only partially during oxidative stress. Constitutively active Gcn2 also induces PB formation in unstressed cells. Surprisingly, PBs are still constitutively formed in a gcn3 mutant strain that is insensitive to eIF2 alpha phosphorylation suggesting that Gcn2 also promotes PB formation independently of eIF2 alpha phosphorylation. Analysis of several putative Gcn2-substrates involved in RNA metabolism identified several proteins required for Gcn2-mediated PB formation. Among these, Smu2, which was not previously implicated in PB formation, localises to PBs and is required for stress-induced coalescence of mRNA granules into PBs. Together, our findings indicate that Gcn2 promotes PB formation via two complementary routes: eIF2 alpha phosphorylation, which generates untranslated mRNAs, and Smu2-dependent maturation of mRNA granules into PBs.

cell biology↗
bioRxiv2026

Quantitative Head-to-Tail Analysis Reveals Heterogeneous Cellular Organization and Connexin Expression in the Porcine Sinoatrial Node

Background: The sinoatrial node (SAN) is an integral component of the cardiac conduction system that dictates heart rhythm. Optical mapping studies have demonstrated functional differences between the superior and inferior leading pacemaking sites in the human SAN; however, the mechanistic connections between structure and function in the SAN through intra-tissue and inter-tissue current source-sink relationships have not been fully resolved. Methods: Porcine SAN longitudinal cryosections along the head-to-tail axis were immunostained and analyzed for regional cell organization and connexin (CX) isoform expression. Results: Quantification of pacemaking cardiomyocyte (PCM) density revealed >9-fold more PCMs within a SAN volume than suggested by a widely cited estimate, assuming comparable PCM densities across species. The SAN head region consisted of large PCM clusters with low aspect ratios, high PCM density, low fibroblast density, and PCMs with the highest HCN4 expression and lowest CX40 and CX43 expression. These characteristics are consistent with an electrically well-insulated, strong current-source that supports pacemaking function. Although the SAN tail also exhibited high local PCM density, its smaller PCM clusters, lower HCN4 expression, and higher CX40, CX43, and CX45 expression rendered it a weaker current source. The SAN mid-region exhibited large PCM clusters aligned in the head-to-tail axis and the highest expression of CX40 and CX45, an expression profile that suggests a fast-conducting intra-tissue pathway that electrically links the leading pacemaking sites at the head and tail. The peripheral SAN at the head and tail also exhibited higher CX expression of all isoforms than the central subregions, an organization consistent with enhanced inter-tissue coupling required for proper pacing function. Conclusions: Our data provide novel insights into the distinct regional micro-organization of the SAN along the head-to-tail axis, which through intra-tissue and inter-tissue coupling, likely modulates the balance of current source-sink relationships that supports robust pacemaking and pacing functions.

cell biology↗
bioRxiv2026

Inference of cell division parameters in bacteria under transient growth conditions

Most quantitative models of bacterial cell division assume steady-state growth, yet natural environments are highly dynamic. Here, we infer division control parameters of E. coli from single-cell size trajectories under nonsteady growth. We describe growth as a continuous process interrupted by stochastic divisions, whose propensity depends on cell size and on the size added since birth. Combining an estimation of time-dependent single-cell growth rates with a maximum-likelihood estimator that we previously validated on synthetic data, we obtain time-resolved estimates of the mean added size at division, its noise, and a strategy parameter that measures how added size depends on birth size. This parameter vanishes for the adder, in which cells add, on average, a fixed size regardless of their size at birth, and is negative for sizer-adder control, in which larger-born cells add less size. We apply this approach to published single-cell data covering steady exponential growth, gradual nutrient depletion, and exit from starvation. We implement a time-resolved model selection based on the Akaike information criterion, concluding that the adder is sufficient during steady growth, whereas size dynamics during entry into and exit from stationary phase are better explained by transient deviations toward sizer-adder control. The framework provides a general method to quantify time-resolved changes in the scale, stochasticity, and strategy of division in nonsteady environments.

cell biology↗