scholarly journals A Fiedler Vector Scoring Approach for Novel RNA Motif Selection

2021 ◽  
Vol 125 (4) ◽  
pp. 1144-1155
Author(s):  
Qiyao Zhu ◽  
Tamar Schlick
Keyword(s):  
Fiedler Vector ◽  
Rna Motif

Structures of Artificially Designed RNA Nanoarchitectures at Near-Atomic Resolution

2020 ◽  
Author(s):  
Di Liu ◽  
Yaming Shao ◽  
Joseph A. Piccirilli ◽  
Yossi Weizmann
Keyword(s):  
Nucleic Acid ◽  
High Resolution ◽  
Single Strand ◽  
Atomic Resolution ◽  
Rna Motifs ◽  
X Ray ◽  
Structural Details ◽  
Rna Motif

<p>Though advances in nanotechnology have enabled the construction of synthetic nucleic acid based nanoarchitectures with ever-increasing complexity for various applications, high-resolution structures are lacking due to the difficulty of obtaining good diffracting crystals. Here we report the design of RNA nanostructures based on homooligomerizable tiles from an RNA single-strand for X-ray determination. Three structures are solved to near-atomic resolution: a 2D parallelogram, an unexpectedly formed 3D nanobracelet, and a 3D nanocage. Structural details of their constituent motifs—such as kissing loops, branched kissing-loops and T-junctions—that resemble natural RNA motifs and resisted X-ray determination are revealed. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanostructure design and suggests a novel route to investigate RNA motif structures by configuring them into nanoarchitectures.</p>

scholarly journals Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
E. Agirre ◽  
A. J. Oldfield ◽  
N. Bellora ◽  
A. Segelle ◽  
R. F. Luco
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Embryonic Stem ◽  
Chromatin Modifications ◽  
Histone Marks ◽  
Splicing Regulators ◽  
Machine Learning Approach ◽  
Alternatively Spliced ◽  
Rna Motif ◽  
Regulation Changes

AbstractAlternative splicing relies on the combinatorial recruitment of splicing regulators to specific RNA binding sites. Chromatin has been shown to impact this recruitment. However, a limited number of histone marks have been studied at a global level. In this work, a machine learning approach, applied to extensive epigenomics datasets in human H1 embryonic stem cells and IMR90 foetal fibroblasts, has identified eleven chromatin modifications that differentially mark alternatively spliced exons depending on the level of exon inclusion. These marks act in a combinatorial and position-dependent way, creating characteristic splicing-associated chromatin signatures (SACS). In support of a functional role for SACS in coordinating splicing regulation, changes in the alternative splicing of SACS-marked exons between ten different cell lines correlate with changes in SACS enrichment levels and recruitment of the splicing regulators predicted by RNA motif search analysis. We propose the dynamic nature of chromatin modifications as a mechanism to rapidly fine-tune alternative splicing when necessary.

scholarly journals Fiedler Vector Approximation via Interacting RandomWalks

2020 ◽  
Vol 48 (1) ◽  
pp. 101-102
Author(s):  
Vishwaraj Doshi ◽  
Do Young Eun
Keyword(s):  
Fiedler Vector ◽  
Vector Approximation

scholarly journals RNA motif discovery: a computational overview

2015 ◽  
Vol 10 (1) ◽  
Author(s):  
Avinash Achar ◽  
Pål Sætrom
Keyword(s):  
Motif Discovery ◽  
Rna Motif
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