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

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Backe, 2005, X-ray crystallographic and NMR studies of the third KH domain of hnRNP K in complex with single-stranded nucleic acids, Structure, 13, 1055, 10.1016/j.str.2005.04.008 Blume, 2015 Braddock, 2002, Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA, EMBO J, 21, 3476, 10.1093/emboj/cdf352 Cabili, 2011, Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses, Gene Dev., 25, 1915, 10.1101/gad.17446611 Cesana, 2011, A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA, Cell, 147, 358, 10.1016/j.cell.2011.09.028 Chen, 2015, High speed BLASTN: an accelerated MegaBLAST search tool, Nucleic Acids Res., 43, 7762, 10.1093/nar/gkv784 Derrien, 2012, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res., 22, 1775, 10.1101/gr.132159.111 Dimitrova, 2014, LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint, Mol. Cell, 54, 777, 10.1016/j.molcel.2014.04.025 Duret, 2006, The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene, Science, 312, 1653, 10.1126/science.1126316 el, 1992, Definition of a consensus binding site for p53, Nat. Genet., 1, 45, 10.1038/ng0492-45 Elisaphenko, 2008, A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements, PLoS One, 3, 10.1371/journal.pone.0002521 Funk, 1992, A transcriptionally active DNA-binding site for human p53 protein complexes, Mol. Cell Biol., 12, 2866 Gupta, 2010, Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis, Nature, 464, 1071, 10.1038/nature08975 Guttman, 2009, Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature, 458, 223, 10.1038/nature07672 Guttman, 2011, lincRNAs act in the circuitry controlling pluripotency and differentiation, Nature, 477, 295, 10.1038/nature10398 He, 2014, Association between long non-coding RNA and human rare diseases, Biomed. Rep., 2, 19, 10.3892/br.2013.191 He, 2011, The sequence, structure and evolutionary features of HOTAIR in mammals, BMC Evol. Biol., 11, 102, 10.1186/1471-2148-11-102 Hrdlickova, 2014, Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity, Genome Med., 6, 88, 10.1186/s13073-014-0088-0 Huarte, 2015, The emerging role of lncRNAs in cancer, Nat. Med., 21, 1253, 10.1038/nm.3981 Huarte, 2010, A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response, Cell, 142, 409, 10.1016/j.cell.2010.06.040 Huarte, 2010, Large non-coding RNAs: missing links in cancer?, Hum. Mol. Genet., 19, R152, 10.1093/hmg/ddq353 Isin, 2015, Exosomal lncRNA-p21 levels may help to distinguish prostate cancer from benign disease, Front. Genet., 6, 168 Ji, 2003, MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer, Oncogene, 22, 8031, 10.1038/sj.onc.1206928 Kent, 2002, BLAT--the BLAST-like alignment tool, Genome Res., 12, 656 Kent, 2002, The human genome browser at UCSC, Genome Res., 12, 996, 10.1101/gr.229102 Khalil, 2009, Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression, vol. 106, 11667 Kim, 2008, Isolation and characterization of a novel H1.2 complex that acts as a repressor of p53-mediated transcription, J. Biol. Chem., 283, 9113, 10.1074/jbc.M708205200 Kretz, 2013, Control of somatic tissue differentiation by the long non-coding RNA TINCR, Nature, 493, 231, 10.1038/nature11661 Lee, 2015, NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy, Bioinformatics, 31, 1325, 10.1093/bioinformatics/btu830 Ma, 2013, On the classification of long non-coding RNAs, RNA Biol., 10, 925, 10.4161/rna.24604 Madeira, 2019, The EMBL-EBI search and sequence analysis tools APIs in 2019, Nucleic Acids Res., 47, W636, 10.1093/nar/gkz268 Matouk, 2007, The H19 non-coding RNA is essential for human tumor growth, PLoS One, 2, e845, 10.1371/journal.pone.0000845 Moumen, 2005, hnRNP K: an HDM2 target and transcriptional coactivator of p53 in response to DNA damage, Cell, 123, 1065, 10.1016/j.cell.2005.09.032 Nakamoto, 2020, hnRNPK recognition of the B motif of Xist and other biological RNAs, Nucleic Acids Res., 48, 9320, 10.1093/nar/gkaa677 Nawrocki, 2013, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, 29, 2933, 10.1093/bioinformatics/btt509 Nesterova, 2001, Characterization of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence, Genome Res., 11, 833, 10.1101/gr.174901 Pang, 2006, Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function, Trends Genet., 22, 1, 10.1016/j.tig.2005.10.003 Penny, 1996, Requirement for Xist in X chromosome inactivation, Nature, 379, 131, 10.1038/379131a0 Poliseno, 2010, A coding-independent function of gene and pseudogene mRNAs regulates tumour biology, Nature, 465, 1033, 10.1038/nature09144 Raveh, 2015, The H19 Long non-coding RNA in cancer initiation, progression and metastasis - a proposed unifying theory, Mol. Cancer, 14, 184, 10.1186/s12943-015-0458-2 Riley, 2008, Transcriptional control of human p53-regulated genes, Nat. Rev. Mol. Cell Biol., 9, 402, 10.1038/nrm2395 Rivas, 2017, A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs, Nat. Methods, 14, 45, 10.1038/nmeth.4066 Sidiqi, 2005, Structure and RNA binding of the third KH domain of poly(C)-binding protein 1, Nucleic Acids Res., 33, 1213, 10.1093/nar/gki265 Sumazin, 2011, An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma, Cell, 147, 370, 10.1016/j.cell.2011.09.041 Tang, 2015, LincRNA-p21: implications in human diseases, Int. J. Mol. Sci., 16, 18732, 10.3390/ijms160818732 Torarinsson, 2006, Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure, Genome Res., 16, 885, 10.1101/gr.5226606 Ulitsky, 2013, lincRNAs: genomics, evolution, and mechanisms, Cell, 154, 26, 10.1016/j.cell.2013.06.020 Vazquez, 2008, The genetics of the p53 pathway, apoptosis and cancer therapy, Nat. Rev. Drug Discov., 7, 979, 10.1038/nrd2656 Wang, 2014, LincRNA-p21 enhances the sensitivity of radiotherapy for human colorectal cancer by targeting the Wnt/beta-catenin signaling pathway, Oncol. Rep., 31, 1839, 10.3892/or.2014.3047 Will, 2007, Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering, PLoS Comput. Biol., 3, e65, 10.1371/journal.pcbi.0030065 Winkler, 2022, Functional elements of the cis-regulatory lincRNA-p21, Cell Rep., 39, 10.1016/j.celrep.2022.110687 Yoon, 2012, LincRNA-p21 suppresses target mRNA translation, Mol. Cell, 47, 648, 10.1016/j.molcel.2012.06.027 Zampetaki, 2018, Long non-coding RNA structure and function: is there a link?, Front. Physiol., 9, 1201, 10.3389/fphys.2018.01201 Zhai, 2013, Clinical significance of long intergenic noncoding RNA-p21 in colorectal cancer, Clin. Colorectal Cancer, 12, 261, 10.1016/j.clcc.2013.06.003 Zhang, 2017, The interplay of LncRNA-H19 and its binding partners in physiological process and gastric carcinogenesis, Int. J. Mol. Sci., 18 Zhang, 2017, The long noncoding RNA Malat1: its physiological and pathophysiological functions, RNA Biol., 14, 1705, 10.1080/15476286.2017.1358347