Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats
D'Souza, Michael H.
Badmalia, Maulik D.
Wolfinger, Michael T.
Patel, Trushar R.
Oxford University Press
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.
Open access article. Creative Commons Attribution-NonCommercial 4.0 International license (CC BY-NC 4.0) applies
RNA characterisation , RNA manipulation , Long noncoding RNA , Three-dimensional structure
D'Souza, M. H., Mrozowich, T., Badmalia, M. D., Geeraert, M., Frederickson, A., Henrickson, A., Demeler, B., Wolfinger, M. T., & Patel, T. R. (2022). Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Nucleic Acids Research, 50(10), 5881-5898. https://doi.org/10.1093/nar/gkac414