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A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK

Maulik, A and Bandopadhyay, D and Singh, M (2023) A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK. In: Current Research in Structural Biology, 5 .

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Official URL: https://doi.org/10.1016/j.crstbi.2023.100099


Long Intergenic Non-coding RNAs (lincRNAs) are the largest class of long non-coding RNAs in eukaryotes, originating from the genome's intergenic regions. A ∼4 ​kb long lincRNA-p21 is derived from a transcription unit next to the p21/Cdkn1a gene locus. LincRNA-p21 plays regulatory roles in p53-dependent transcriptional and translational repression through its physical association with proteins such as hnRNPK and HuR. It is also involved in the aberrant gene expression in different cancers. In this study, we have carried out a bioinformatics-based gene analysis and annotation of lincRNA-p21 to show that it is highly conserved in primates and identified two conserved domains in its sequence at the 5′ and 3′ terminal regions. hnRNPK has previously been shown to interact specifically with the 5′ conserved region of lincRNA-p21. hnRNPK is known to bind preferentially to the pyrimidine-rich (poly C) nucleotide sequences in RNAs. Interestingly, we observed a single occurrence of a cytosine-rich patch (C-patch) consisting of a CUCCCGC sequence in the 5′ conserved region of human lincRNA-p21, making it a putative hnRNPK binding motif. Using NMR and ITC experiments, we showed that the single-stranded C-patch containing RNA sequence motif interacts specifically with the KH3 domain of hnRNPK.

Item Type: Journal Article
Publication: Current Research in Structural Biology
Publisher: Elsevier B.V.
Additional Information: The copyright for this article belongs to the Authors.
Keywords: Bioinformatics; hnRNPK; ITC; lincRNA-p21; NMR CSP; Sequence conservation
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 18 Apr 2023 10:22
Last Modified: 18 Apr 2023 10:22
URI: https://eprints.iisc.ac.in/id/eprint/81336

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