2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
April 2nd, 2025
Version: 2
washington university school of medicine
molecular biology
biorxiv

Autoregulation of RPL7B by inhibition of a structural splicing enhancer

Stormo, G. D.Open in Google Scholar•Granas, D.Open in Google Scholar•Hewa, I. G.Open in Google Scholar•White, M. A.Open in Google Scholar

Yeast ribosomal protein gene RPL7B is autoregulated by inhibition of splicing. The first intron has a "zipper stem" that brings the 5' splice near the branch point and serves as an enhancer of splicing that is required for efficient splicing because it has non-consensus branch point sequence of UGCUAAC. The intron also contains an alternative, and mutually exclusive structure, that is conserved across many yeast species. That conserved structure is a binding site for the Rpl7 protein so that when the protein is in excess over what is required for ribosomes, the protein binds to the conserved structure which eliminates the enhancer structure and represses splicing and gene expression.

Similar Papers

biorxiv
Thu Apr 03 2025
CHD7 binds distinct regions in the Sox11 locus to regulate neuronal differentiation
The chromodomain helicase DNA binding protein 7 (CHD7) is a nucleosome repositioner implicated in multiple cellular processes, including neuronal differentiation. We identified CHD7 genome-wide binding sites that regulate neuronal differentiation in an otic stem cell line. We identified CHD7 enrichment at the Sox11 promoter and 3\' untranslated region (UTR). Sox11 is a transcription factor essenti...
Martinez, E.
•
Jadali, A.
•
Qiu, J.
•
Hinman, A. M.
...•
Kwan, K. Y.
biorxiv
Wed Apr 02 2025
AquIRE reveals multiple mechanisms of clinically induced RNA damage and the conservation and dynamics of glycoRNAs
RNA is subject to many modifications, from small chemical changes such as methylation through to conjugation of biomolecules such as glycans. As well as these endogenously written modifications, RNA is also exposed to damage induced by its environment. Certain clinical compounds are known to drive covalent modifications of RNA with a growing appreciation for how these affect function. To understan...
Zhang, Z.
•
Kotopanova, Z. V.
•
Dang, K.
•
Kong, X.
...•
Knight, J. R.
biorxiv
Wed Apr 02 2025
Interleukin-13-mediated alterations in esophageal epithelial mitochondria contribute to tissue remodeling in eosinophilic esophagitis
Background: The significance of mitochondria in EoE pathobiology remains elusive. Objective: To determine the impact of EoE inflammatory mediators upon mitochondrial biology in esophageal epithelium, the mechanisms mediating these effects, and their functional significance to EoE pathobiology. Methods: Mitochondria were evaluated in human biopsies, MC903/Ovalbumin-induced murine EoE, and human eso...
Jackson, J. L.
•
Saxena, R.
•
Murray, M. G.
•
Staub, A. J.
...•
Whelan, K. A.
biorxiv
Wed Apr 02 2025
Genome reannotation and effector candidate identification in Meloidogyne chitwoodi through gland-specific transcriptome analysis
The root-knot nematode (RKN) Meloidogyne chitwoodi is a threat for potato production in the western United States, negatively impacting potato yield and product value. Meloidogyne chitwoodi produce proteins, called effectors, in their esophageal glands that are secreted during parasitism and play integral roles in plant-nematode interactions. Because the esophageal glands are the main effector sec...
Teixeira, M.
•
Ko, I.
•
Bali, S.
•
Vieira, P.
...•
Gleason, C.
biorxiv
Tue Apr 01 2025
A NanoBRET-based assay monitoring interactions in the USP18 signaling hub identifies the first cell-penetrant small molecule compromising USP18/ISG15 binding
Protein modification by interferon-stimulated gene 15 (ISG15), termed ISGylation, exhibits antiviral properties and influences tumorigenesis, genome stability and metabolic processes. ISGylation is counteracted by the specific protease USP18. Likewise, viral proteases such as the papain-like protease (PLpro) from SARS-CoV-2 cleave ISG15 to undermine the host immune response. Beyond its role as a d...
Hess, S.
•
Campos-Alonso, M.
•
Brand, M.
•
Lauw, S.
...•
Knobeloch, K.-P.
biorxiv
Tue Apr 01 2025
Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA
Single-stranded DNA-binding proteins (SSBs) are essential for genome stability, facilitating replication, repair, and recombination by binding ssDNA, recruiting other proteins, and dynamically relocating in response to cellular demands. Using single-molecule fluorescence resonance energy transfer (smFRET) assays, we elucidated the mechanisms underlying direct strand transfer from one locale to ano...
Paul, T.
•
Lee, I.-R.
•
Pangeni, S.
•
Rashid, F.
...•
Ha, T.
biorxiv
Tue Apr 01 2025
The break in the cycle: Inositol pyrophosphate fluxomics disentangled via mathematical modelling
This study investigates the metabolic pathways of inositol pyrophosphates (IPPs) in the yeast cell line {Delta}SPX and the human tumor cell line HCT116. Utilizing pulse-labelling experiments with 18O water and ordinary differential equation (ODE) models, we explore the synthesis and turnover of the highly phosphorylated IPP, 1,5-InsP8. Our findings challenge the notion that 1,5-InsP8 can be synthe...
Hermes, J.
•
Kim, G.-D.
•
Liu, G.
•
De Leo, M. G.
...•
Timmer, J.
biorxiv
Tue Apr 01 2025
Negative regulation of miRNAs sorting in EVs: the RNA-binding protein PCBP2 impairs SYNCRIP-mediated miRNAs EVs loading
While it is accepted that Extracellular Vesicles (EVs)-mediated transfer of microRNAs contributes to intercellular communication, the knowledge about molecular mechanisms controlling the selective and dynamic miRNA-loading in EVs is still limited to few specific RNA-binding proteins interacting with sequence determinants. Moreover, although mutagenesis analysis demonstrated the presence/function o...
Marocco, F.
•
Garbo, S.
•
Montaldo, C.
•
Colantoni, A.
...•
Tripodi, M.
biorxiv
Tue Apr 01 2025
Inherent Specificity and Mutational Sensitivity as Quantitative Metrics for RBP Binding
Interactions between RNAs and RNA binding proteins (RBPs) regulate gene expression in eukaryotic cells. RNA-RBP affinities measured in vitro reveal diverse binding specificities, yet approaches to directly compare specificities across RBPs are lacking. Here, we introduce two quantitative metrics: inherent specificity, which measures how selectively an RBP distinguishes its strongest binding motif ...
Yi, S.
•
Singh, S. S.
•
Ye, X.
•
Krishna, R.
...•
Luna, J. M.