Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation

Isiktas, Atagun U.; Eshov, Aziz; Yang, Suzhou; Guo, Junjie U.

doi:10.1016/j.crmeth.2022.100334

Cited by 10 publications

(31 citation statements)

References 33 publications

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“…4,7 (2) The presence of a single strand in the ground state (lowest free energy state) that could engage in Watson-Crick (WC) base pair formation with other RNA chains is not always required. Even if the ground state is perfectly ordered, with no discernible disordered regions, phase separation does take place, as was shown in experiments 8,10 and confirmed using simulations 13 for repeat RNA sequences. (3) Because RNA is a polyanion, it stands to reason that cations could be efficacious in promoting phase separation by forming bridging interactions across RNA chains, although the mechanism of how this could be achieved is unknown.…”

Section: Introductionsupporting

confidence: 61%

Section: Introductionsupporting

confidence: 60%

“…Finally, for a fixed n and identical sequence composition, the approximate dimer formation rate maybe altered by changing the sequence. Thus, the exact sequence, 10 in addition to n , salt concentration and other environmental factors, determine the tendency to self-associate.…”

Section: Discussionmentioning

confidence: 99%

“…However, it is only recently the importance of condensate formation involving RNA molecules in a variety of contexts is starting to be appreciated. [2][3][4][5][6][7][8][9][10] The diversity of RNA sequences as well as the myriad structures an isolated RNA (a self-organizing polymer) adopts make it difficult to uncover the molecular features that drive phase separation. Nevertheless, one could anticipate a few scenarios for phase separation by favorable RNA-RNA interactions.…”

Section: Introductionmentioning

confidence: 99%

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Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

Maity

Nguyên

Hori

et al. 2023

Preprint

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Low complexity nucleotide repeat sequences, which are implicated in several neurological disorders, undergo liquid-liquid phase separation (LLPS) provided the number of repeat units, n, exceeds a critical value. Here, we establish a link between the folding landscapes of the monomers of trinucleotide repeats and their propensity to self-associate. Simulations using a coarse-grained Self-Organized Polymer (SOP) model for (CAG)n repeats in monovalent salt solutions reproduce experimentally measured melting temperatures, which are available only for small n. By extending the simulations to large n, we show that the free energy gap, ∆GS, between the ground state (GS) and slipped hairpin (SH) states is a predictor of aggregation propensity. The GS for even n is a perfect hairpin (PH) whereas it is a SH when n is odd. The value of ∆GS (zero for odd n) is larger for even n than for odd n. As a result, the rate of dimer formation is slower in (CAG)30 relative to (CAG)31, thus linking ∆GS to RNA-RNA association. The yield of the dimer decreases dramatically, compared to the wild type, in mutant sequences in which the population of the SH is decreases substantially. Association between RNA chains is preceded by a transition to the SH even if the GS is a PH. The finding that the excitation spectra, which depends on the exact sequence, n, and ionic conditions, is a predictor of self-association, should also hold for other RNAs (mRNA for example) that undergo LLPS.

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Section: Introductionsupporting

confidence: 61%

Section: Introductionsupporting

confidence: 60%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

Maity

Nguyên

Hori

et al. 2023

Preprint

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“…A series of experiments − have established that low-complexity repeat RNA sequences, such as (CAG) n and (CUG) n (where n is the number of repeat units), undergo phase separation. In the two phase region, the high-density droplet coexists with the sol or low-density dispersed phase.…”

mentioning

confidence: 99%

Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences

Maity,

Nguyen,

Hori

et al. 2024

J. Phys. Chem. Lett.

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Repeat RNA sequences self-associate to form condensates. Simulations of a coarse-grained single-interaction site model for (CAG) n (n = 30 and 31) show that the salt-dependent free energy gap, ΔG S , between the ground (perfect hairpin) and the excited state (slipped hairpin (SH) with one CAG overhang) of the monomer for (n even) is the primary factor that determines the rates and yield of self-assembly. For odd n, the free energy (G S ) of the ground state, which is an SH, is used to predict the self-association kinetics. As the monovalent salt concentration, C S , increases, ΔG S and G S increase, which decreases the rates of dimer formation. In contrast, ΔG S for shuffled sequences, with the same length and sequence composition as (CAG) 31 , is larger, which suppresses their propensities to aggregate. Although demonstrated explicitly for (CAG) polymers, the finding of inverse correlation between the free energy gap and RNA aggregation is general.

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Accelerated Simulations Reveal Physicochemical Factors Governing Stability and Composition of RNA Clusters

Aierken,

Joseph

2024

J. Chem. Theory Comput.

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Under certain conditions, RNA repeat sequences phase separate, yielding protein-free biomolecular condensates. Importantly, RNA repeat sequences have also been implicated in neurological disorders, such as Huntington's disease. Thus, mapping repeat sequences to their phase behavior, functions, and dysfunctions is an active area of research. However, despite several advances, it remains challenging to characterize the RNA phase behavior at a submolecular resolution. Here, we have implemented a residue-resolution coarsegrained model in LAMMPS�that incorporates both the RNA sequence and structure�to study the clustering propensities of protein-free RNA systems. Importantly, we achieve a multifold speedup in the simulation time compared to previous work. Leveraging this efficiency, we study the clustering propensity of all 20 nonredundant trinucleotide repeat sequences. Our results align with findings from experiments, emphasizing that canonical base-pairing and G−U wobble pairs play dominant roles in regulating cluster formation of RNA repeat sequences. Strikingly, we find strong entropic contributions to the stability and composition of RNA clusters, which is demonstrated for single-component RNA systems as well as binary mixtures of trinucleotide repeats. Additionally, we investigate the clustering behaviors of trinucleotide (odd) repeats and their quadranucleotide (even) counterparts. We observe that odd repeats exhibit stronger clustering tendencies, attributed to the presence of consecutive base pairs in their sequences that are disrupted in even repeat sequences. Altogether, our work extends the set of computational tools for probing RNA cluster formation at submolecular resolution and uncovers physicochemical principles that govern the stability and composition of the resulting clusters.

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Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation

Cited by 10 publications

References 33 publications

Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences

Accelerated Simulations Reveal Physicochemical Factors Governing Stability and Composition of RNA Clusters

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