Results 71 to 80 of about 15,140,513 (376)

A comparative analysis of mRNA enrichment strategies and guidance for improving their efficiency

Scientific Reports
The pervasive presence of ribosomal RNA (rRNA) in total RNA poses a considerable challenge to the accurate analysis of cellular transcriptomes. In this study, we comprehensively analyze strategies for Saccharomyces cerevisiae mRNA enrichment, aiming to ...
Angelika Andrzejewska-Romanowska, Ewa Tykwińska, Paweł Śledziński, Katarzyna Pachulska-Wieczorek   +3 more
doaj   +1 more source

Ab initio RNA folding

, 2014
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and
Cragnolini, Tristan, Derreumaux, Philippe, Pasquali, Samuela   +2 more
core   +1 more source

Estimating the power of sequence covariation for detecting conserved RNA structure

bioRxiv, 2019
Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment ...
Elena Rivas, J. Clements, S. Eddy
semanticscholar   +1 more source

Reciprocal control of viral infection and phosphoinositide dynamics

FEBS Letters, EarlyView.
Phosphoinositides, although scarce, regulate key cellular processes, including membrane dynamics and signaling. Viruses exploit these lipids to support their entry, replication, assembly, and egress. The central role of phosphoinositides in infection highlights phosphoinositide metabolism as a promising antiviral target.
Marie Déborah Bancilhon, Bruno Mesmin
wiley   +1 more source

Interplay between single-stranded binding proteins on RNA secondary structure

, 2013
RNA protein interactions control the fate of cellular RNAs and play an important role in gene regulation. An interdependency between such interactions allows for the implementation of logic functions in gene regulation.
Bundschuh, Ralf, Lin, Yi-Hsuan
core   +1 more source

Flexible RNA design under structure and sequence constraints using formal languages [PDF]

, 2013
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure.
Denise, Alain, Ponty, Yann, Vialette, Stéphane, Waldispühl, Jérôme, Zhang, Yi, Zhou, Yu   +5 more
core   +5 more sources

RNApdbee 2.0: multifunctional tool for RNA structure annotation

Nucleic Acids Res., 2018
In the field of RNA structural biology and bioinformatics, an access to correctly annotated RNA structure is of crucial importance, especially in the secondary and 3D structure predictions.
T. Zok, Maciej Antczak, Michal Zurkowski, M. Popenda, J. Błażewicz, R. Adamiak, Marta Szachniuk   +6 more
semanticscholar   +1 more source

The anti‐CRISPR protein AcrIE8.1 inhibits the type I‐E CRISPR‐Cas system by directly binding to the Cascade subunit Cas11

FEBS Letters, EarlyView.
In this study, we present the structure of AcrIE8.1, a previously uncharacterized anti‐CRISPR protein that inhibits the type I‐E CRISPR‐Cas system. Through a combination of structural and biochemical analyses, we demonstrate that AcrIE8.1 directly binds to the Cas11 subunit of the Cascade complex to inhibit the CRISPR‐Cas system.
Young Woo Kang, Hyun Ho Park
wiley   +1 more source

The dual role of Spn-E in supporting heterotypic ping-pong piRNA amplification in silkworms

EMBO Reports
The PIWI-interacting RNA (piRNA) pathway plays a crucial role in silencing transposons in the germline. piRNA-guided target cleavage by PIWI proteins triggers the biogenesis of new piRNAs from the cleaved RNA fragments.
Natsuko Izumi, Keisuke Shoji, Lumi Negishi, Yukihide Tomari   +3 more
doaj   +1 more source

Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure

Nature Communications, 2022
The authors present DiffScan, an advanced tool for normalization and differential analysis of RNA structure probing experiments, combining their power in deciphering the dynamic RNA structurome and facilitating the discovery of RNA regulatory functions.
Bo Yu, Pan Li, Qiangfeng Cliff Zhang, Lin Hou   +3 more
doaj   +1 more source