RNA Remodeling by RNA Chaperones Monitored by RNA Structure Probing

2019 ◽  
pp. 179-192
Author(s):  
Susann Friedrich ◽  
Tobias Schmidt ◽  
Sven-Erik Behrens
Keyword(s):  
Rna Structure ◽  
Structure Probing ◽  
Rna Remodeling ◽  
Rna Chaperones

scholarly journals FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

2010 ◽  
Vol 7 (12) ◽  
pp. 995-1001 ◽  
Author(s):  
Jason G Underwood ◽  
Andrew V Uzilov ◽  
Sol Katzman ◽  
Courtney S Onodera ◽  
Jacob E Mainzer ◽  
...  
Keyword(s):  
High Throughput ◽  
Rna Structure ◽  
High Throughput Sequencing ◽  
Structure Probing

scholarly journals An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages

2021 ◽  
Author(s):  
Meiling Piao ◽  
Pan Li ◽  
Xiaomin Zeng ◽  
Xi-Wen Wang ◽  
Lan Kang ◽  
...  
Keyword(s):  
Rna Structure ◽  
Low Input ◽  
Input Method ◽  
Structure Probing

scholarly journals Physical and Functional Analysis of Viral RNA Genomes by SHAPE

2019 ◽  
Vol 6 (1) ◽  
pp. 93-117 ◽  
Author(s):  
Mark A. Boerneke ◽  
Jeffrey E. Ehrhardt ◽  
Kevin M. Weeks
Keyword(s):  
Rna Structure ◽  
Rna Viruses ◽  
Genome Structure ◽  
Regulatory Elements ◽  
Viral Rna ◽  
Host Immune Responses ◽  
Linear Sequence ◽  
Structure Probing ◽  
Shape Structure ◽  
Shape Selective

RNA viruses encode the information required to usurp cellular metabolism and gene regulation and to enable their own replication in two ways: in the linear sequence of their RNA genomes and in higher-order structures that form when the genomic RNA strand folds back on itself. Application of high-resolution SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) structure probing to viral RNA genomes has identified numerous new regulatory elements, defined new principles by which viral RNAs interact with the cellular host and evade host immune responses, and revealed relationships between virus evolution and RNA structure. This review summarizes our current understanding of genome structure-function interrelationships for RNA viruses, as informed by SHAPE structure probing, and outlines opportunities for future studies.

scholarly journals mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis inArabidopsis thaliana

2020 ◽  
Vol 117 (35) ◽  
pp. 21785-21795 ◽  
Author(s):  
Susheel Sagar Bhat ◽  
Dawid Bielewicz ◽  
Tomasz Gulanicz ◽  
Zsuzsanna Bodi ◽  
Xiang Yu ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Structure ◽  
Methylation Status ◽  
Mirna Biogenesis ◽  
Stem Loop ◽  
Structure Probing ◽  
Plant Transcriptome ◽  
Loop Regions

InArabidopsis thaliana, the METTL3 homolog, mRNA adenosine methylase (MTA) introducesN6-methyladenosine (m6A) into various coding and noncoding RNAs of the plant transcriptome. Here, we show that an MTA-deficient mutant (mta) has decreased levels of microRNAs (miRNAs) but accumulates primary miRNA transcripts (pri-miRNAs). Moreover, pri-miRNAs are methylated by MTA, and RNA structure probing analysis reveals a decrease in secondary structure within stem–loop regions of these transcripts inmtamutant plants. We demonstrate interaction between MTA and both RNA Polymerase II and TOUGH (TGH), a plant protein needed for early steps of miRNA biogenesis. Both MTA and TGH are necessary for efficient colocalization of the Microprocessor components Dicer-like 1 (DCL1) and Hyponastic Leaves 1 (HYL1) with RNA Polymerase II. We propose that secondary structure of miRNA precursors induced by their MTA-dependent m6A methylation status, together with direct interactions between MTA and TGH, influence the recruitment of Microprocessor to plant pri-miRNAs. Therefore, the lack of MTA inmtamutant plants disturbs pri-miRNA processing and leads to the decrease in miRNA accumulation. Furthermore, our findings reveal that reduced miR393b levels likely contributes to the impaired auxin response phenotypes ofmtamutant plants.

scholarly journals Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments

2016 ◽  
Vol 14 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Alina Selega ◽  
Christel Sirocchi ◽  
Ira Iosub ◽  
Sander Granneman ◽  
Guido Sanguinetti
Keyword(s):  
Statistical Modeling ◽  
High Throughput ◽  
Rna Structure ◽  
Structure Probing

scholarly journals RNA structure probing to characterize RNA-protein interactions on a low abundance pre-mRNA in living cells

RNA ◽  
2020 ◽  
pp. rna.077263.120
Author(s):  
Jodi L Bubenik ◽  
Melissa Hale ◽  
Ona McConnell ◽  
Eric Wang ◽  
Maurice S. Swanson ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Rna Structure ◽  
Living Cells ◽  
Structure Probing

Light-based RNA structure probing

2018 ◽  
Vol 15 (3) ◽  
pp. 163-163
Keyword(s):  
Rna Structure ◽  
Structure Probing
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