ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Pennisi, E. Genomics. ENCODE project writes eulogy for junk DNA. Science 337, 1159–1161 (2012).
Article CAS PubMed Google Scholar
Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854 (1993).
Article CAS PubMed Google Scholar
Wightman, B., Ha, I. & Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855–862 (1993).
Article CAS PubMed Google Scholar
Neppl, R. L. & Wang, D. Z. The myriad essential roles of microRNAs in cardiovascular homeostasis and disease. Genes. Dis. 1, 18–39 (2014).
Article PubMed PubMed Central Google Scholar
Amaral, P. P., Clark, M. B., Gascoigne, D. K., Dinger, M. E. & Mattick, J. S. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res. 39, D146–D151 (2011).
Article CAS PubMed Google Scholar
Quek, X. C. et al. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res. 43, D168–D173 (2015).
Article CAS PubMed Google Scholar
Wang, K. C. & Chang, H. Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904–914 (2011).
Article CAS PubMed PubMed Central Google Scholar
Ma, L., Bajic, V. B. & Zhang, Z. On the classification of long non-coding RNAs. RNA Biol. 10, 925–933 (2013).
Statello, L., Guo, C. J., Chen, L. L. & Huarte, M. Gene regulation by long non-coding RNAs and its biological functions. Nat. Rev. Mol. Cell Biol. 22, 96–118 (2021).
Article CAS PubMed Google Scholar
Noh, J. H., Kim, K. M., McClusky, W. G., Abdelmohsen, K. & Gorospe, M. Cytoplasmic functions of long noncoding RNAs. Wiley Interdiscip. Rev. RNA 9, e1471 (2018).
Article PubMed PubMed Central Google Scholar
Qin, T., Li, J. & Zhang, K. Q. Structure, regulation, and function of linear and circular long non-coding RNAs. Front. Genet. 11, 150 (2020).
Article CAS PubMed PubMed Central Google Scholar
Wu, S., Chen, L. & Zhou, X. Circular RNAs in the regulation of cardiac hypertrophy. Mol. Ther. Nucleic Acids 27, 484–490 (2022).
Article CAS PubMed Google Scholar
Darbellay, F. & Necsulea, A. Comparative transcriptomics analyses across species, organs, and developmental stages reveal functionally constrained lncRNAs. Mol. Biol. Evol. 37, 240–259 (2020).
Article CAS PubMed Google Scholar
Gao, J. et al. Integrated transcriptomics and epigenomics reveal chamber-specific and species-specific characteristics of human and mouse hearts. PLoS Biol. 19, e3001229 (2021).
Article CAS PubMed PubMed Central Google Scholar
Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775–1789 (2012).
Article CAS PubMed PubMed Central Google Scholar
Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005).
Article CAS PubMed Google Scholar
See, K. et al. Single cardiomyocyte nuclear transcriptomes reveal a lincRNA-regulated de-differentiation and cell cycle stress-response in vivo. Nat. Commun. 8, 225 (2017).
Article PubMed PubMed Central Google Scholar
Yan, Y. et al. The cardiac translational landscape reveals that micropeptides are new players involved in cardiomyocyte hypertrophy. Mol. Ther. 29, 2253–2267 (2021).
Article CAS PubMed PubMed Central Google Scholar
van Heesch, S. et al. The translational landscape of the human heart. Cell 178, 242–260.e29 (2019).
Ounzain, S. et al. Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs. Eur. Heart J. 36, 353–368 (2015).
Article CAS PubMed Google Scholar
Matkovich, S. J., Edwards, J. R., Grossenheider, T. C., de Guzman Strong, C. & Dorn, G. W. II Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs. Proc. Natl Acad. Sci. USA 111, 12264–12269 (2014).
Article CAS PubMed PubMed Central Google Scholar
Izumo, S. et al. Myosin heavy chain messenger RNA and protein isoform transitions during cardiac hypertrophy. Interaction between hemodynamic and thyroid hormone-induced signals. J. Clin. Invest. 79, 970–977 (1987).
Article CAS PubMed PubMed Central Google Scholar
Izumo, S., Nadal-Ginard, B. & Mahdavi, V. Protooncogene induction and reprogramming of cardiac gene expression produced by pressure overload. Proc. Natl Acad. Sci. USA 85, 339–343 (1988).
Article CAS PubMed PubMed Central Google Scholar
Yang, K. C. et al. Deep RNA sequencing reveals dynamic regulation of myocardial noncoding RNAs in failing human heart and remodeling with mechanical circulatory support. Circulation 129, 1009–1021 (2014).
Article CAS PubMed PubMed Central Google Scholar
Xiao, X. G., Touma, M. & Wang, Y. Decoding the noncoding transcripts in human heart failure. Circulation 129, 958–960 (2014).
Li, Z. et al. LncExpDB: an expression database of human long non-coding RNAs. Nucleic Acids Res. 49, D962–D968 (2021).
Article CAS PubMed Google Scholar
Mas-Ponte, D. et al. LncATLAS database for subcellular localization of long noncoding RNAs. RNA 23, 1080–1087 (2017).
Article CAS PubMed PubMed Central Google Scholar
Bridges, M. C., Daulagala, A. C. & Kourtidis, A. LNCcation: lncRNA localization and function. J. Cell Biol. 220, e202009045 (2021).
Article CAS PubMed PubMed Central Google Scholar
Carlevaro-Fita, J. & Johnson, R. Global positioning system: understanding long noncoding RNAs through subcellular localization. Mol. Cell 73, 869–883 (2019).
Article CAS PubMed Google Scholar
Yu, B. & Shan, G. Functions of long noncoding RNAs in the nucleus. Nucleus 7, 155–166 (2016).
Article CAS PubMed PubMed Central Google Scholar
Rashid, F., Shah, A. & Shan, G. Long non-coding RNAs in the cytoplasm. Genomics Proteom. Bioinforma. 14, 73–80 (2016).
Olgun, G., Sahin, O. & Tastan, O. Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes. BMC Genomics 19, 650 (2018).
Article PubMed PubMed Central Google Scholar
Wang, Y. et al. Long non-coding RNA DSCR8 acts as a molecular sponge for miR-485-5p to activate Wnt/β-catenin signal pathway in hepatocellular carcinoma. Cell Death Dis. 9, 851 (2018).
Article PubMed PubMed Central Google Scholar
Gil, N. & Ulitsky, I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat. Rev. Genet. 21, 102–117 (2020).
Article CAS PubMed Google Scholar
Ma, W., Liu, Y., Ma, H., Ren, Z. & Yan, J. Cis-acting: a pattern of lncRNAs for gene regulation in induced pluripotent stem cells from patients with Down syndrome determined by integrative analysis of lncRNA and mRNA profiling data. Exp. Ther. Med. 22, 701 (2021).
Article CAS PubMed PubMed Central Google Scholar
Yan, P., Luo, S., Lu, J. Y. & Shen, X. Cis- and trans-acting lncRNAs in pluripotency and reprogramming. Curr. Opin. Genet. Dev. 46, 170–178 (2017).
Comments (0)