Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats

Thumbnail Image
D'Souza, Michael H.
Mrozowich, Tyler
Badmalia, Maulik D.
Geeraert, Mitchell
Frederickson, Angela
Henrickson, Amy
Demeler, Borries
Wolfinger, Michael T.
Patel, Trushar R.
Journal Title
Journal ISSN
Volume Title
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.