A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK
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-d...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Current Research in Structural Biology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2665928X23000053 |
| _version_ | 1797796360192262144 |
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| author | Aditi Maulik Devleena Bandopadhyay Mahavir Singh |
| author_facet | Aditi Maulik Devleena Bandopadhyay Mahavir Singh |
| author_sort | Aditi Maulik |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-13T03:31:54Z |
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| id | doaj.art-f0889f51bb4148ca8f887df0879fb88d |
| institution | Directory Open Access Journal |
| issn | 2665-928X |
| language | English |
| last_indexed | 2024-03-13T03:31:54Z |
| publishDate | 2023-01-01 |
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| series | Current Research in Structural Biology |
| spelling | doaj.art-f0889f51bb4148ca8f887df0879fb88d2023-06-24T05:19:04ZengElsevierCurrent Research in Structural Biology2665-928X2023-01-015100099A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPKAditi Maulik0Devleena Bandopadhyay1Mahavir Singh2Corresponding author.; Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, IndiaMolecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, IndiaCorresponding author.; Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, IndiaLong 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.http://www.sciencedirect.com/science/article/pii/S2665928X23000053lincRNA-p21Sequence conservationBioinformaticshnRNPKNMR CSPITC |
| spellingShingle | Aditi Maulik Devleena Bandopadhyay Mahavir Singh A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK Current Research in Structural Biology lincRNA-p21 Sequence conservation Bioinformatics hnRNPK NMR CSP ITC |
| title | A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK |
| title_full | A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK |
| title_fullStr | A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK |
| title_full_unstemmed | A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK |
| title_short | A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK |
| title_sort | cytosine patch sequence motif identified in the conserved region of lincrna p21 interacts with the kh3 domain of hnrnpk |
| topic | lincRNA-p21 Sequence conservation Bioinformatics hnRNPK NMR CSP ITC |
| url | http://www.sciencedirect.com/science/article/pii/S2665928X23000053 |
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