Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Issue 10 (25th May 2022)

• Record Type: Journal Article
• Authors: D'Souza, Michael H; Mrozowich, Tyler; Badmalia, Maulik D; Geeraert, Mitchell; Frederickson, Angela; Henrickson, Amy; Demeler, Borries; Wolfinger, Michael T; Patel, Trushar R
• Is Part Of: Nucleic acids research. Volume 50:Issue 10(2022)
• Page Start: 5881
• Page End: 5898
• Publication Date: 2022-05-25
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac414
• Languages: English
• ISSNs: 0305-1048

Abstract

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.