Ender, C. & Meister, G. Argonaute proteins at a glance. J. Cell Sci. 123, 1819–1823 (2010).

Article  CAS  Google Scholar 

Wassarman, K. M., Zhang, A. & Storz, G. Small RNAs in Escherichia coli. Trends Microbiol. 7, 37–45 (1999).

Article  CAS  Google Scholar 

Watanabe, Y. & Yamamoto, M. S. pombe mei2+ encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA. Cell 78, 487–498 (1994).

Article  CAS  Google Scholar 

Lakhotia, S. C. & Sharma, A. The 93D (hsr-omega) locus of Drosophila: non-coding gene with house-keeping functions. Genetica 97, 339–348 (1996).

Article  CAS  Google Scholar 

Kelley, R. L. et al. Epigenetic spreading of the Drosophila dosage compensation complex from roX RNA genes into flanking chromatin. Cell 98, 513–522 (1999).

Article  CAS  Google Scholar 

Bartolomei, M. S., Zemel, S. & Tilghman, S. M. Parental imprinting of the mouse H19 gene. Nature 351, 153–155 (1991).

Article  CAS  Google Scholar 

Brown, C. J. et al. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71, 527–542 (1992).

Article  CAS  Google Scholar 

Rodriguez, A., Griffiths-Jones, S., Ashurst, J. L. & Bradley, A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14, 1902–1910 (2004).

Article  CAS  Google Scholar 

He, D. et al. miRNA-independent function of long noncoding pri-miRNA loci. Proc. Natl Acad. Sci. USA 118, e2017562118 (2021).

Article  CAS  Google Scholar 

Askarian-Amiri, M. E. et al. SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 17, 878–891 (2011).

Article  CAS  Google Scholar 

Lambert, M., Benmoussa, A. & Provost, P. Small non-coding RNAs derived from eukaryotic ribosomal RNA. Noncoding RNA 5, 16 (2019).

Article  CAS  Google Scholar 

Kawaji, H. et al. Hidden layers of human small RNAs. BMC Genomics 9, 157 (2008).

Article  Google Scholar 

Krishna, S. et al. Dynamic expression of tRNA-derived small RNAs define cellular states. EMBO Rep. 20, e47789 (2019).

Article  Google Scholar 

Taft, R. J. et al. Small RNAs derived from snoRNAs. RNA 15, 1233–1240 (2009).

Article  CAS  Google Scholar 

Chen, Q. et al. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science 351, 397–400 (2016).

Article  CAS  Google Scholar 

Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916–919 (2002).

Article  CAS  Google Scholar 

Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573 (2002).

Article  Google Scholar 

Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005).

Article  CAS  Google Scholar 

Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149–1154 (2005).

Article  CAS  Google Scholar 

Sender, R., Fuchs, S. & Milo, R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14, e1002533 (2016).

Article  Google Scholar 

Hahn, M. W. & Wray, G. A. The g-value paradox. Evol. Dev. 4, 73–75 (2002).

Article  Google Scholar 

Liu, G., Mattick, J. S. & Taft, R. J. A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle 12, 2061–2072 (2013).

Article  CAS  Google Scholar 

Mercer, T. R., Dinger, M. E. & Mattick, J. S. Long noncoding RNAs: insights into function. Nat. Rev. Genet. 10, 155–159 (2009).

Article  CAS  Google Scholar 

Parrott, A. M. et al. The evolution and expression of the snaR family of small non-coding RNAs. Nucleic Acids Res. 39, 1485–1500 (2011).

Article  CAS  Google Scholar 

Täuber, H., Hüttelmaier, S. & Köhn, M. POLIII-derived non-coding RNAs acting as scaffolds and decoys. J. Mol. Cell Biol. 11, 880–885 (2019).

Article  Google Scholar 

Hahne, J. C., Lampis, A. & Valeri, N. Vault RNAs: hidden gems in RNA and protein regulation. Cell. Mol. Life Sci. 78, 1487–1499 (2021).

Article  CAS  Google Scholar 

Kapranov, P. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484–1488 (2007).

Article  CAS  Google Scholar 

Fejes-Toth, K. et al. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457, 1028–1032 (2009).

Article  CAS  Google Scholar 

Preker, P. et al. PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters. Nucleic Acids Res. 39, 7179–7193 (2011).

Article  CAS  Google Scholar 

Castelo-Branco, G. et al. The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells. Genome Biol. 14, R98 (2013).

Article  Google Scholar 

Flynn, R. A. et al. 7SK-BAF axis controls pervasive transcription at enhancers. Nat. Struct. Mol. Biol. 23, 231–238 (2016).

Article  CAS  Google Scholar 

Gussakovsky, D. & McKenna, S. A. Alu RNA and their roles in human disease states. RNA Biol. 18, 574–585 (2021).

Article  CAS  Google Scholar 

Ullu, E. & Tschudi, C. Alu sequences are processed 7SL RNA genes. Nature 312, 171–172 (1984).

Article  CAS  Google Scholar 

Tsirigos, A. & Rigoutsos, I. Alu and B1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput. Biol. 5, e1000610 (2009).

Article  Google Scholar 

Zhang, X.-O., Gingeras, T. R. & Weng, Z. Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function. Genome Res. 29, 1402–1414 (2019).

Article  CAS  Google Scholar 

Deng, W. et al. Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Res. 16, 20–29 (2006).

Article  CAS  Google Scholar 

Dieci, G., Conti, A., Pagano, A. & Carnevali, D. Identification of RNA polymerase III-transcribed genes in eukaryotic genomes. Biochim. Biophys. Acta 1829, 296–305 (2013).

Article  CAS  Google Scholar 

Jawdekar, G. W. & Henry, R. W. Transcriptional regulation of human small nuclear RNA genes. Biochim. Biophys. Acta 1779, 295–305 (2008).

Article  CAS  Google Scholar 

Kufel, J. & Grzechnik, P. Small nucleolar RNAs tell a different tale. Trends Genet. 35, 104–117 (2019).

Article  CAS  Google Scholar 

Wilusz, J. E., Freier, S. M. & Spector, D. L. 3’ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135, 919–932 (2008).

Article  CAS  Google Scholar 

Yin, Q.-F. et al. Long noncoding RNAs with snoRNA ends. Mol. Cells 48, 219–230 (2012).

Article  CAS  Google Scholar 

Wu, H. et al. Unusual processing generates SPA lncRNAs that sequester multiple RNA binding proteins. Mol. Cells 64, 534–548 (2016).

Article  CAS  Google Scholar 

Gingeras, T. R. Origin of phenotypes: genes and transcripts. Genome Res. 17, 682–690 (2007).

Article  CAS  Google Scholar 

Cheetham, S. W., Faulkner, G. J. & Dinger, M. E. Overcoming challenges and dogmas to understand the functions of pseudogenes. Nat. Rev. Genet. 21, 191–201 (2020).

Article  CAS  Google Scholar 

Frith, M. C. et al. Pseudo–messenger RNA: phantoms of the transcriptome. PLoS Genet. 2, e23 (2006).

Article  Google Scholar 

Frankish, A. et al. GENCODE 2021. Nucleic Acids Res. 49, D916–D923 (2021).

Article  CAS  Google Scholar 

Ma, Y. et al. Genome-wide analysis of pseudogenes reveals HBBP1’s human-specific essentiality in erythropoiesis and implication in β-thalassemia. Dev. Cell 56, 478–493 (2021).

Article  CAS  Google Scholar 

Patop, I. L., Wüst, S. & Kadener, S. Past, present, and future of circRNAs. EMBO J. 38, e100836 (2019).

Article  Google Scholar