Chapter 33 : Structure and Interaction Prediction in Prokaryotic RNA Biology

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For over a decade, prokaryotic and eukaryotic RNA biology exploration has unveiled the multifaceted and central contribution of RNA-based control in all domains of life. RNA interactions are at the core of many regulative processes and have hence been heavily studied by wet-lab and biocomputational researchers alike. Within this review, we focus on biocomputational methods and outline the technical details of standard algorithms for RNA secondary structure and RNA-RNA interaction prediction. Furthermore, we highlight their application in the context of prokaryotic RNA biology.

Citation: Wright* P, Mann* M, Backofen* R. 2019. Structure and Interaction Prediction in Prokaryotic RNA Biology, p 563-579. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0001-2017
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Image of Figure 1
Figure 1

Loop decomposition of a nested RNA structure into hairpin loops (H; dark gray), multiloops (M; light gray), stackings (S; light blue), bulges (B; dark blue), and interior loops (I; dark blue). Initials of the loop types are placed in white next to the enclosing base pair (black).

Citation: Wright* P, Mann* M, Backofen* R. 2019. Structure and Interaction Prediction in Prokaryotic RNA Biology, p 563-579. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0001-2017
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Figure 2

Graphical depiction of the Nussinov-like recursion from equation 1 .

Citation: Wright* P, Mann* M, Backofen* R. 2019. Structure and Interaction Prediction in Prokaryotic RNA Biology, p 563-579. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0001-2017
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Figure 3

Potential interactions for two identical RNA molecules (blue and green) as predicted by the RNAhybrid web server (A) ( ) and IntaRNA web server (B) ( ) (intramolecular base pairs subsequently added, which form a kissing hairpin interaction). Inter- and intramolecular base pairs are indicated by vertical pipe symbols and arches, respectively.

Citation: Wright* P, Mann* M, Backofen* R. 2019. Structure and Interaction Prediction in Prokaryotic RNA Biology, p 563-579. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0001-2017
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Figure 4

Recursion depiction of interaction prediction via (A) and (B).

Citation: Wright* P, Mann* M, Backofen* R. 2019. Structure and Interaction Prediction in Prokaryotic RNA Biology, p 563-579. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0001-2017
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Figure 5

(A) Intramolecular structure-enclosing interaction predictable by concatenation-based approaches. (B) Double kissing hairpin interaction that be predicted since it forms a pseudoknot when linked. The red dotted line denotes the linker, and blue and green denote the first and second sequences, respectively. Base pairs are indicated by pipe or dash symbols.

Citation: Wright* P, Mann* M, Backofen* R. 2019. Structure and Interaction Prediction in Prokaryotic RNA Biology, p 563-579. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0001-2017
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Figure 6

The ensemble-based approach for interaction prediction. Instead of considering only a single individual structure for the RNAs and , RNAup and IntaRNA introduce a sequence-specific accessibility term, which represents all structures with an accessible (i.e., not covered by intramolecular base pairs) interaction site .. and ... These are incorporated into a modified duplex calculation.

Citation: Wright* P, Mann* M, Backofen* R. 2019. Structure and Interaction Prediction in Prokaryotic RNA Biology, p 563-579. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0001-2017
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Figure 7

(Left) accessibility scenario without consideration of RNA-binding factors (A, B). Here, region .. is accessible, while ′..′ is blocked by intramolecular base pairs. (Right) Putative situation with bound factors A and B. The accessible site .. is blocked by A, while ′..′ becomes accessible due to structural reconfiguration upon binding of A and B.

Citation: Wright* P, Mann* M, Backofen* R. 2019. Structure and Interaction Prediction in Prokaryotic RNA Biology, p 563-579. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0001-2017
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