M. B. Clark and J. S. Mattick, Long noncoding RNAs in cell biology, Semin. Cell Dev. Biol, vol.22, pp.366-376, 2011.

L. He and G. J. Hannon, MicroRNAs: small RNAs with a big role in gene regulation, Nat. Rev. Genet, vol.5, pp.522-531, 2004.

E. Berezikov, Evolution of microRNA diversity and regulation in animals, Nat. Rev. Genet, vol.12, pp.846-860, 2011.

H. Pais, S. Moxon, T. Dalmay, and V. Moulton, Small RNA discovery and characterisation in eukaryotes using high-throughput approaches, Adv. Exp. Med. Biol, vol.722, pp.239-254, 2011.

T. Kawamata and Y. Tomari, Making RISC, Trends Biochem. Sci, vol.35, pp.368-376, 2010.

J. S. Mattick and M. J. Gagen, The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms, Mol. Biol. Evol, vol.18, pp.1611-1630, 2001.

J. S. Mattick, Non-coding RNAs: the architects of eukaryotic complexity, EMBO Rep, vol.2, pp.986-991, 2001.

, Nucleic Acids Research, issue.13, 2016.

F. Hube and C. Francastel, Mammalian introns: when the junk generates molecular diversity, Int. J. Mol Sci, vol.16, pp.4429-4452, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02127272

E. Berezikov, W. J. Chung, J. Willis, E. Cuppen, and E. C. Lai, Mammalian mirtron genes, Mol. Cell, vol.28, pp.328-336, 2007.

E. Berezikov, N. Liu, A. S. Flynt, E. Hodges, M. Rooks et al., Evolutionary flux of canonical microRNAs and mirtrons in Drosophila, Nat. Genet, vol.42, pp.6-9, 2010.

W. J. Chung, P. Agius, J. O. Westholm, M. Chen, K. Okamura et al., Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans, Genome Res, vol.21, pp.286-300, 2011.

A. S. Flynt, J. C. Greimann, W. J. Chung, C. D. Lima, and E. C. Lai, MicroRNA biogenesis via splicing and exosome-mediated trimming in Drosophila, Mol. Cell, vol.38, pp.900-907, 2010.

E. A. Glazov, K. Kongsuwan, W. Assavalapsakul, P. F. Horwood, N. Mitter et al., Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection, PLoS One, vol.4, p.6349, 2009.

K. Okamura, J. W. Hagen, H. Duan, D. M. Tyler, and E. C. Lai, The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila, Cell, vol.130, pp.89-100, 2007.

J. G. Ruby, C. H. Jan, and D. P. Bartel, Intronic microRNA precursors that bypass Drosha processing, Nature, vol.448, pp.83-86, 2007.

E. Valen, P. Preker, P. R. Andersen, X. Zhao, Y. Chen et al., Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes, Nat. Struct. Mol. Biol, vol.18, pp.1075-1082, 2011.

M. A. Havens, A. A. Reich, D. M. Duelli, and M. L. Hastings, Biogenesis of mammalian microRNAs by a non-canonical processing pathway, Nucleic Acids Res, vol.40, pp.4626-4640, 2012.

M. M. Janas, M. Khaled, S. Schubert, J. G. Bernstein, D. Golan et al., Feed-forward microprocessing and splicing activities at a microRNA-containing intron, PLoS Genet, vol.7, p.1002330, 2011.

T. B. Hansen, M. T. Veno, T. I. Jensen, A. Schaefer, C. K. Damgaard et al., Argonaute-associated short introns are a novel class of gene regulators, Nat. Commun, vol.7, p.11538, 2016.

C. Ender, A. Krek, M. R. Friedlander, M. Beitzinger, L. Weinmann et al., A human snoRNA with microRNA-like functions, Mol. Cell, vol.32, pp.519-528, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00347390

Y. S. Lee, Y. Shibata, A. Malhotra, and A. Dutta, A novel class of small RNAs: tRNA-derived RNA fragments (tRFs), Genes Dev, vol.23, pp.2639-2649, 2009.

A. M. Abdelfattah, C. Park, and M. Y. Choi, Update on non-canonical microRNAs, Biomol. Concepts, vol.5, pp.275-287, 2014.

A. Jha, G. Panzade, R. Pandey, and R. Shankar, A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm, Nucleic Acids Res, vol.43, pp.8713-8724, 2015.

D. Cifuentes, H. Xue, D. W. Taylor, H. Patnode, Y. Mishima et al., A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity, Science, vol.328, pp.1694-1698, 2010.

S. Cheloufi, C. O. Santos, M. M. Chong, and G. J. Hannon, A dicer-independent miRNA biogenesis pathway that requires Ago catalysis, Nature, vol.465, pp.584-589, 2010.

M. A. Havens, A. A. Reich, and M. L. Hastings, Drosha promotes splicing of a pre-microRNA-like alternative exon, PLoS Genet, vol.10, p.1004312, 2014.

J. Liu and E. S. Maxwell, Mouse U14 snRNA is encoded in an intron of the mouse cognate hsc70 heat shock gene, Nucleic Acids Res, vol.18, pp.6565-6571, 1990.

J. S. Mattick and I. V. Makunin, Small regulatory RNAs in mammals, Hum. Mol. Genet, vol.14, issue.1, pp.121-132, 2005.

E. S. Lander, L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody et al., Initial sequencing and analysis of the human genome, Nature, vol.409, pp.860-921, 2001.

F. Hube, J. Guo, S. Chooniedass-kothari, C. Cooper, M. K. Hamedani et al., Alternative splicing of the first intron of the steroid receptor RNA activator (SRA) participates in the generation of coding and noncoding RNA isoforms in breast cancer cell lines, DNA Cell Biol, vol.25, pp.418-428, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02127748

F. Hube, G. Velasco, J. Rollin, D. Furling, and C. Francastel, Steroid receptor RNA activator protein binds to and counteracts SRA RNA-mediated activation of MyoD and muscle differentiation, Nucleic Acids Res, vol.39, pp.513-525, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02127321

D. Furling, L. Coiffier, V. Mouly, J. P. Barbet, J. L. St-guily et al., Defective satellite cells in congenital myotonic dystrophy, Hum. Mol. Genet, vol.10, pp.2079-2087, 2001.

G. Velasco, F. Hube, J. Rollin, D. Neuillet, C. Philippe et al., Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues, Proc. Natl. Acad. Sci. U.S.A, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02127331

G. S. Pall and A. J. Hamilton, Improved northern blot method for enhanced detection of small RNA, Nat. Protoc, vol.3, pp.1077-1084, 2008.

F. Hube and C. Francastel, Pocket-sized RNA-Seq": a method to capture new mature microRNA produced from a genomic region of interest, Non-Coding RNA, vol.1, pp.127-138, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02127269

F. Ferri, H. Bouzinba-segard, G. Velasco, F. Hube, and C. Francastel, Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase, Nucleic Acids Res, vol.37, pp.5071-5080, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02127333

E. Varkonyi-gasic and R. P. Hellens, Quantitative stem-loop RT-PCR for detection of microRNAs, Methods Mol. Biol, vol.744, pp.145-157, 2011.

C. Cooper, J. Guo, Y. Yan, S. Chooniedass-kothari, F. Hube et al., Increasing the relative expression of endogenous non-coding Steroid Receptor RNA Activator (SRA) in human breast cancer cells using modified oligonucleotides, Nucleic Acids Res, vol.37, pp.4518-4531, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02127334

C. W. Sugnet, W. J. Kent, M. Ares, and D. Haussler, Transcriptome and genome conservation of alternative splicing events in humans and mice, Pac. Symp. Biocomput, pp.66-77, 2004.

M. J. Moore, Nuclear RNA turnover. Cell, vol.108, pp.431-434, 2002.

B. Zhang, D. Han, Y. Korostelev, Z. Yan, N. Shao et al., Changes in snoRNA and snRNA abundance in the human, chimpanzee, macaque, and mouse brain, Genome Biol. Evol, vol.8, pp.840-850, 2016.

H. Quach, L. B. Barreiro, G. Laval, N. Zidane, E. Patin et al., Signatures of purifying and local positive selection in human miRNAs, Am. J. Hum. Genet, vol.84, pp.316-327, 2009.

D. Bhartiya, J. Talwar, Y. Hasija, and V. Scaria, Systematic curation and analysis of genomic variations and their potential functional consequences in snoRNA loci, Hum. Mutat, vol.33, pp.2367-2374, 2012.

J. Wen, E. Ladewig, S. Shenker, J. Mohammed, and E. C. Lai, Analysis of nearly one thousand mammalian mirtrons reveals novel features of dicer substrates, PLoS Comput. Biol, vol.11, p.1004441, 2015.

R. I. Gregory, K. P. Yan, G. Amuthan, T. Chendrimada, B. Doratotaj et al., The Microprocessor complex mediates the genesis of microRNAs, Nature, vol.432, pp.235-240, 2004.

H. C. Kim, G. M. Kim, J. M. Yang, and J. W. Ki, Cloning, expression, and complementation test of the RNA lariat debranching enzyme cDNA from mouse, Mol. Cell, vol.11, pp.198-203, 2001.

I. J. Macrae, E. Ma, M. Zhou, C. V. Robinson, and J. A. Doudna, In vitro reconstitution of the human RISC-loading complex, Proc. Natl. Acad. Sci. U.S.A, vol.105, pp.512-517, 2008.

T. P. Chendrimada, R. I. Gregory, E. Kumaraswamy, J. Norman, N. Cooch et al., TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing, Nature, vol.436, pp.740-744, 2005.

G. Tang, siRNA and miRNA: an insight into RISCs, Trends Biochem. Sci, vol.30, pp.106-114, 2005.

E. Maniataki and Z. Mourelatos, A human, ATP-independent, RISC assembly machine fueled by pre-miRNA, Genes Dev, vol.19, pp.2979-2990, 2005.

E. Kozlowska, W. J. Krzyzosiak, and E. Koscianska, Regulation of huntingtin gene expression by miRNA-137, -214, -148a, and their respective isomiRs, Int. J. Mol. Sci, vol.14, pp.16999-17016, 2013.

H. Y. Jin, A. Gonzalez-martin, A. V. Miletic, M. Lai, S. Knight et al.,

C. Xiao, Transfection of microRNA mimics should be used with caution, Front. Genet, vol.6, p.340, 2015.

M. Ohno, C. Shibata, T. Kishikawa, T. Yoshikawa, A. Takata et al., The flavonoid apigenin improves glucose tolerance through inhibition of microRNA maturation in miRNA103 transgenic mice, Sci. Rep, vol.3, p.2553, 2013.

S. Chooniedass-kothari, E. Emberley, M. K. Hamedani, S. Troup, X. Wang et al., The steroid receptor RNA activator is the first functional RNA encoding a protein, FEBS Lett, vol.566, pp.43-47, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02127389

S. Y. Jung, A. Malovannaya, J. Wei, B. W. O'malley, and J. Qin, Proteomic analysis of steady-state nuclear hormone receptor coactivator complexes, Mol. Endocrinol, vol.19, pp.2451-2465, 2005.

A. Kapusta and C. Feschotte, Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications, Trends Genet, vol.30, pp.439-452, 2014.

D. Ulveling, C. Francastel, and F. Hube, When one is better than two: RNA with dual functions, Biochimie, vol.93, pp.633-644, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02127323

D. Ulveling, C. Francastel, and F. Hube, Identification of potentially new bifunctional RNA based on genome-wide data-mining of alternative splicing events, Biochimie, vol.93, pp.2024-2027, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02127774

J. S. Mattick and I. V. Makunin, Non-coding RNA, Hum. Mol. Genet., 15 Spec, issue.1, pp.17-29, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02127407

D. Rearick, A. Prakash, A. Mcsweeny, S. S. Shepard, L. Fedorova et al., Critical association of ncRNA with introns, Nucleic Acids Res, vol.39, pp.2357-2366, 2011.

J. W. Brown, D. F. Marshall, and M. Echeverria, Intronic noncoding RNAs and splicing, Trends Plant Sci, vol.13, pp.335-342, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00297288

C. H. Jung, M. A. Hansen, I. V. Makunin, D. J. Korbie, and J. S. Mattick, Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data, BMC. Genomics, p.77, 2010.

H. Zhou and K. Lin, Excess of microRNAs in large and very 5 biased introns, Biochem. Biophys. Res. Commun, vol.368, pp.709-715, 2008.

D. Chen, Y. Meng, C. Yuan, L. Bai, D. Huang et al., Plant siRNAs from introns mediate DNA methylation of host genes, RNA, vol.17, pp.1012-1024, 2011.

P. K. Joshi, D. Gupta, U. K. Nandal, Y. Khan, S. K. Mukherjee et al., Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons, Genomics, vol.99, pp.370-375, 2012.

E. Ladewig, K. Okamura, A. S. Flynt, J. O. Westholm, and E. C. Lai, Discovery of hundreds of mirtrons in mouse and human small RNA data, Genome Res, vol.22, pp.1634-1645, 2012.

Y. Meng and C. Shao, Large-scale identification of mirtrons in Arabidopsis and rice, PLoS One, vol.7, p.31163, 2012.

A. Schamberger, B. Sarkadi, and T. I. Orban, Human mirtrons can express functional microRNAs simultaneously from both arms in a flanking exon-independent manner, RNA. Biol, vol.9, pp.1177-1185, 2012.

L. G. St, D. Shtokalo, M. R. Tackett, Z. Yang, T. Eremina et al., Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells, BMC. Genomics, p.504, 2012.

Q. H. Zhu, A. Spriggs, L. Matthew, L. Fan, G. Kennedy et al., A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains, Genome Res, vol.18, pp.1456-1465, 2008.

C. R. Mandel, Y. Bai, and L. Tong, Protein factors in pre-mRNA 3 -end processing, Cell Mol. Life Sci, vol.65, pp.1099-1122, 2008.

D. Thierry-mieg and J. Thierry-mieg, AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biol, vol.7, pp.12-14, 2006.

J. Grimwood, L. A. Gordon, A. Olsen, A. Terry, J. Schmutz et al., The DNA sequence and biology of human chromosome 19, Nature, vol.428, pp.529-535, 2004.

M. L. Bortolin-cavaille, M. Dance, M. Weber, and J. Cavaille, C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts, Nucleic Acids Res, vol.37, pp.3464-3473, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00611749

T. R. Mercer, M. E. Dinger, C. P. Bracken, G. Kolle, J. M. Szubert et al.,

S. M. Grimmond, Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome, Genome Res, vol.20, pp.1639-1650, 2010.

T. R. Mercer, D. J. Gerhardt, M. E. Dinger, J. Crawford, C. Trapnell et al., Targeted RNA sequencing reveals the deep complexity of the human transcriptome, Nat. Biotechnol, 2011.

G. T. Williams, M. Mourtada-maarabouni, and F. Farzaneh, A critical role for non-coding RNA GAS5 in growth arrest and rapamycin inhibition in human T-lymphocytes, Biochem. Soc. Trans, vol.39, pp.482-486, 2011.

P. L. De, E. Yao, P. Callier, L. Faivre, V. Drouin et al., Germline deletion of the miR-17 approximately 92 cluster causes skeletal and growth defects in humans, Nat. Genet, vol.43, pp.1026-1030, 2011.

D. P. Bartel, MicroRNAs: genomics, biogenesis, mechanism, and function, Cell, vol.116, pp.281-297, 2004.

Y. K. Kim and V. N. Kim, Processing of intronic microRNAs, EMBO J, vol.26, pp.775-783, 2007.

A. M. Monteys, R. M. Spengler, J. Wan, L. Tecedor, K. A. Lennox et al., Structure and activity of putative intronic miRNA promoters, RNA, vol.16, pp.495-505, 2010.

P. Ramalingam, J. K. Palanichamy, A. Singh, P. Das, M. Bhagat et al., Biogenesis of intronic miRNAs located in clusters by independent transcription and alternative splicing, RNA, vol.20, pp.76-87, 2014.

M. J. Fitch, L. Campagnolo, F. Kuhnert, and H. Stuhlmann, Egfl7, a novel epidermal growth factor-domain gene expressed in endothelial cells, Dev. Dyn, vol.230, pp.316-324, 2004.

Z. Szweykowska-kulinska, A. Jarmolowski, and F. Vazquez, The crosstalk between plant microRNA biogenesis factors and the spliceosome, Plant Signal. Behav, vol.8, p.26955, 2013.

C. Mattioli, G. Pianigiani, and F. Pagani, Cross talk between spliceosome and microprocessor defines the fate of pre-mRNA, Interdiscip. Rev. RNA, vol.5, pp.647-658, 2014.

Z. Melamed, A. Levy, R. Fluss, G. Lev-maor, K. Mekahel et al., Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions, Mol. Cell, vol.50, pp.869-881, 2013.

L. Agranat-tamir, N. Shomron, J. Sperling, and R. Sperling, Interplay between pre-mRNA splicing and microRNA biogenesis within the supraspliceosome, Nucleic Acids Res, vol.42, pp.4640-4651, 2014.

M. Ha and V. N. Kim, Regulation of microRNA biogenesis, Nat. Rev. Mol Cell Biol, vol.15, pp.509-524, 2014.

H. Seitz and P. D. Zamore, Rethinking the microprocessor, Cell, vol.125, pp.827-829, 2006.

R. B. Lanz, N. J. Mckenna, S. A. Onate, U. Albrecht, J. Wong et al., A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex, Cell, vol.97, pp.17-27, 1999.

S. M. Colley and P. J. Leedman, Steroid receptor RNA activator -a nuclear receptor coregulator with multiple partners: Insights and challenges, Biochimie, vol.93, pp.1966-1972, 2011.

C. Cooper, D. Vincett, Y. Yan, M. K. Hamedani, Y. Myal et al., Steroid receptor RNA activator bi-faceted genetic system: heads or tails?, Biochimie, vol.93, 1973.

D. Zhao, A. Pond, B. Watkins, D. Gerrard, Y. Wen et al., Peripheral endocannabinoids regulate skeletal muscle development and maintenance, Eur. J. Transl. Myol, vol.1, pp.167-179, 2010.

Y. Takai, W. Ikeda, H. Ogita, and Y. Rikitake, The immunoglobulin-like cell adhesion molecule nectin and its associated protein afadin, Annu. Rev. Cell Dev. Biol, vol.24, pp.309-342, 2008.

Y. Takai, J. Miyoshi, W. Ikeda, and H. Ogita, Nectins and nectin-like molecules: roles in contact inhibition of cell movement and proliferation, Nat. Rev. Mol Cell Biol, vol.9, pp.603-615, 2008.

A. Brero, H. P. Easwaran, D. Nowak, I. Grunewald, T. Cremer et al., Methyl CpG-binding proteins induce large-scale chromatin reorganization during terminal differentiation, J. Cell Biol, vol.169, pp.733-743, 2005.