scholarly journals Accessibility and Evolutionary Conservation Mark Bacterial Small-RNA Target-Binding Regions

2011 ◽  
Vol 193 (7) ◽  
pp. 1690-1701 ◽  
Author(s):  
A. Peer ◽  
H. Margalit
Keyword(s):  
Small Rna ◽  
Evolutionary Conservation ◽  
Binding Regions ◽  
Target Binding ◽  
Bacterial Small Rna

scholarly journals A method for in vivo identification of bacterial small RNA ‐binding proteins

2014 ◽  
Vol 3 (6) ◽  
pp. 950-960 ◽  
Author(s):  
Jonathan Osborne ◽  
Louise Djapgne ◽  
Bao Quoc Tran ◽  
Young Ah Goo ◽  
Amanda G. Oglesby‐Sherrouse
Keyword(s):  
Small Rna ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Bacterial Small Rna

scholarly journals Different classes of small RNAs are essential for head regeneration in the planarian Dugesia japonica

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhonghong Cao ◽  
David Rosenkranz ◽  
Suge Wu ◽  
Hongjin Liu ◽  
Qiuxiang Pang ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Evolutionary Conservation ◽  
Body Parts ◽  
Promising Candidate ◽  
Dugesia Japonica ◽  
Head Regeneration

Abstract Background Planarians reliably regenerate all body parts after injury, including a fully functional head and central nervous system. But until now, the expression dynamics and functional role of miRNAs and other small RNAs during the process of head regeneration are not well understood. Furthermore, little is known about the evolutionary conservation of the relevant small RNAs pathways, rendering it difficult to assess whether insights from planarians will apply to other taxa. Results In this study, we applied high throughput sequencing to identify miRNAs, tRNA fragments and piRNAs that are dynamically expressed during head regeneration in Dugesia japonica. We further show that knockdown of selected small RNAs, including three novel Dugesia-specific miRNAs, during head regeneration induces severe defects including abnormally small-sized eyes, cyclopia and complete absence of eyes. Conclusions Our findings suggest that a complex pool of small RNAs takes part in the process of head regeneration in Dugesia japonica and provide novel insights into global small RNA expression profiles and expression changes in response to head amputation. Our study reveals the evolutionary conserved role of miR-124 and brings further promising candidate small RNAs into play that might unveil new avenues for inducing restorative programs in non-regenerative organisms via small RNA mimics based therapies.

scholarly journals Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Anustup Poddar ◽  
Muhammad S. Azam ◽  
Tunc Kayikcioglu ◽  
Maksym Bobrovskyy ◽  
Jichuan Zhang ◽  
...  
Keyword(s):  
Small Rna ◽  
Base Pair ◽  
High Throughput Sequencing ◽  
Base Pairing ◽  
Target Search ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Single Base Pair ◽  
Bacterial Small Rna

AbstractBase-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, kon, and increase the dissociation rate, koff, showing that Hfq directly facilitates sRNA–mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce kon by 24–31% and increase koff by 14–25%, extending the time it takes to find and destroy the target by about a third. The effects of disrupting contiguous base-pairing are much more modest than that expected from thermodynamics, suggesting that Hfq buffers base-pair disruptions.

scholarly journals PresRAT: A server for identification of bacterial small-RNA sequences and their targets with probable binding region

2020 ◽  
Author(s):  
Krishna Kumar ◽  
Abhijit Chakraborty ◽  
Saikat Chakrabarti
Keyword(s):  
Small Rna ◽  
Bacterial Genome ◽  
3D Models ◽  
Bacterial Genomes ◽  
Rna Sequences ◽  
Mrna Targets ◽  
Bacterial Small Rna ◽  
Mrna Binding ◽  
Functional Rnas ◽  
New Procedures

AbstractBacterial small-RNA (sRNA) sequences are functional RNAs, which play an important role in regulating the expression of a diverse class of genes. It is thus critical to identify such sRNA sequences and their probable mRNA targets. Here, we discuss new procedures to identify and characterize sRNA and their targets via the introduction of an integrated online platform named PresRAT (Prediction of sRNA and their Targets). PresRAT uses the primary and secondary structural attributes of sRNA sequences to predict sRNA from a given sequence or bacterial genome. PresRAT also finds probable target mRNAs of sRNA sequences from a given bacterial chromosome and further concentrates on identification of the probable sRNA-mRNA binding regions. Using PresRAT we have identified a total of 60,518 potential sRNA sequences from 54 bacterial genomes and 2447 potential targets from 13 bacterial genomes. We have also implemented a protocol to build and refine 3D models of sRNA and sRNA-mRNA duplex regions and generated 3D models of 50 known sRNAs and 81 sRNA-mRNA duplexes using this platform. Along with the server part, PresRAT also contains a database section, which enlists the predicted sRNA sequences, sRNA targets and their corresponding 3D models with structural dynamics information.

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