Biophysical Characterisation of Human LincRNA-p21 Sense and Antisense Alu Inverted Repeats

D'Souza, M.; Mrozowich, T.; Badmalia, M. D.; Geeraert, M.; Frederickson, A.; Henrickson, A.; Demeler, B.; Wolfinger, M. T.; Patel, T. R.

doi:10.1101/2021.12.08.471813

bioRxiv · 10.1101/2021.12.08.471813

Biophysical Characterisation of Human LincRNA-p21 Sense and Antisense Alu Inverted Repeats

D'Souza, M.·Mrozowich, T.·Badmalia, M. D.·Geeraert, M.·Frederickson, A.·Henrickson, A.·Demeler, B.·Wolfinger, M. T.·Patel, T. R.

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Abstract

Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also critical in down-regulating many p53 target genes through its interaction with a p53 repressive complex. The interaction between LincRNA-p21 and the repressive complex is likely dependent on the RNA tertiary structure. Previous studies have determined the two-dimensional secondary structures of the sense and antisense human LincRNA-p21 AluSx1 IRs using SHAPE. However, there were no insights into its three-dimensional structure. Therefore, we in vitro transcribed the sense and antisense regions of LincRNA-p21 AluSx1 Inverted Repeats (IRs) and performed analytical ultracentrifugation, size exclusion chromatography, light scattering, and small angle X-ray scattering (SAXS) studies. Based on these studies, we determined low-resolution, three-dimensional structures of sense and antisense LincRNA-p21. By adapting previously known two-dimensional information, we calculated their sense and antisense high-resolution models and determined that they agree with the low-resolution structures determined using SAXS. Thus, our integrated approach provides insights into the structure of LincRNA-p21 Alu IRs. Our study also offers a viable pipeline for combining the secondary structure information with biophysical and computational studies to obtain high-resolution atomistic models for long noncoding RNAs.

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D'Souza, M., Mrozowich, T., Badmalia, M. D., Geeraert, M., Frederickson, A., Henrickson, A., Demeler, B., Wolfinger, M. T., Patel, T. R.. 2021-12-08. Biophysical Characterisation of Human LincRNA-p21 Sense and Antisense Alu Inverted Repeats. https://doi.org/10.1101/2021.12.08.471813

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