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Referencias:

• Dunham, I., Kundaje, A., Aldred, S.F., Collins, P.J., Davis, C.A., Doyle, F., Epstein, C.B., Kaul, R., An integrated encyclopedia of DNA elements in the human genome (2012) Nature, 489, pp. 57-74
• Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Knowles, D.G., The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression (2012) Genome Res., 22, pp. 1775-1789
• Quinn, J.J., Chang, H.Y., Unique features of long non-coding RNA biogenesis and function (2016) Nat. Rev. Genet., 17, pp. 47-62
• Kutter, C., Watt, S., Stefflova, K., Wilson, M.D., Goncalves, A., Ponting, C.P., Odom, D.T., Marques, A.C., Rapid turnover of long noncoding RNAs and the evolution of gene expression (2012) PLoS Genet., 8, p. e1002841
• Quinn, J.J., Zhang, Q.C., Georgiev, P., Ilik, I.A., Akhtar, A., Chang, H.Y., Rapid evolutionary turnover underlies conserved lncRNA-genome interactions (2016) Genes Dev., 30, pp. 191-207
• Ulitsky, I., Bartel, D.P., lincRNAs: genomics, evolution, and mechanisms (2013) Cell, 154, pp. 26-46
• Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A., Rinn, J.L., Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses (2011) Genes Dev., 25, pp. 1915-1927
• Washietl, S., Kellis, M., Garber, M., Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals (2014) Genome Res., 24, pp. 616-628
• Batista, P.J., Chang, H.Y., Long noncoding RNAs: cellular address codes in development and disease (2013) Cell, 152, pp. 1298-1307
• Flynn, R.A., Chang, H.Y., Long noncoding RNAs in cell-fate programming and reprogramming (2014) Cell Stem Cell, 14, pp. 752-761
• Ulitsky, I., Shkumatava, A., Jan, C.H., Sive, H., Bartel, D.P., Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution (2011) Cell, 147, pp. 1537-1550
• Hon, C.C., Ramilowski, J.A., Harshbarger, J., Bertin, N., Rackham, O.J., Gough, J., Denisenko, E., Severin, J., An atlas of human long non-coding RNAs with accurate 5′ ends (2017) Nature, 543, pp. 199-204
• Mikhaylichenko, O., Bondarenko, V., Harnett, D., Schor, I.E., Males, M., Viales, R.R., Furlong, E.E.M., The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription (2018) Genes Dev., 32, pp. 42-57
• Guo, H., Ahmed, M., Zhang, F., Yao, C.Q., Li, S., Liang, Y., Hua, J., Langstein, J., Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer (2016) Nat. Genet., 48, pp. 1142-1150
• Schlackow, M., Nojima, T., Gomes, T., Dhir, A., Carmo-Fonseca, M., Proudfoot, N.J., Distinctive patterns of transcription and RNA processing for human lincRNAs (2017) Mol. Cell, 65, pp. 25-38
• Camblong, J., Iglesias, N., Fickentscher, C., Dieppois, G., Stutz, F., Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae (2007) Cell, 131, pp. 706-717
• Hongay, C.F., Grisafi, P.L., Galitski, T., Fink, G.R., Antisense transcription controls cell fate in Saccharomyces cerevisiae (2006) Cell, 127, pp. 735-745
• Ørom, U.A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Huang, Q., Long noncoding RNAs with enhancer-like function in human cells (2010) Cell, 143, pp. 46-58
• Scruggs, B.S., Gilchrist, D.A., Nechaev, S., Muse, G.W., Burkholder, A., Fargo, D.C., Adelman, K., Bidirectional transcription arises from two distinct hubs of transcription factor binding and active chromatin (2015) Mol. Cell, 58, pp. 1101-1112
• Latos, P.A., Pauler, F.M., Koerner, M.V., Şenergin, H.B., Hudson, Q.J., Stocsits, R.R., Allhoff, W., Warczok, K.E., Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing (2012) Science, 338, pp. 1469-1472
• Fatica, A., Bozzoni, I., Long non-coding RNAs: new players in cell differentiation and development (2014) Nat. Rev. Genet., 15, pp. 7-21
• Bergmann, J.H., Li, J., Eckersley-Maslin, M.A., Rigo, F., Freier, S.M., Spector, D.L., Regulation of the ESC transcriptome by nuclear long noncoding RNAs (2015) Genome Res., 25, pp. 1336-1346
• Schmitt, A.M., Chang, H.Y., Long noncoding RNAs in cancer pathways (2016) Cancer Cell, 29, pp. 452-463
• Schmitz, S.U., Grote, P., Herrmann, B.G., Mechanisms of long noncoding RNA function in development and disease (2016) Cell. Mol. Life Sci., 73, pp. 2491-2509
• Ballabio, A., Willard, H.F., Mammalian X-chromosome inactivation and the XIST gene (1992) Curr. Opin. Genet. Dev., 2, pp. 439-447
• Ilik, I., Akhtar, A., roX RNAs: non-coding regulators of the male X chromosome in flies (2009) RNA Biol., 6, pp. 113-121
• Sauvageau, M., Goff, L.A., Lodato, S., Bonev, B., Groff, A.F., Gerhardinger, C., Sanchez-Gomez, D.B., Spence, M., Multiple knockout mouse models reveal lincRNAs are required for life and brain development (2013) eLife, 2, p. e01749
• Bassett, A.R., Akhtar, A., Barlow, D.P., Bird, A.P., Brockdorff, N., Duboule, D., Ephrussi, A., Haerty, W., Considerations when investigating lncRNA function in vivo (2014) eLife, 3, p. e03058
• Li, L., Liu, B., Wapinski, O.L., Tsai, M.C., Qu, K., Zhang, J., Carlson, J.C., Gupta, R.A., Targeted disruption of Hotair leads to homeotic transformation and gene derepression (2013) Cell Rep., 5, pp. 3-12
• Rinn, J.L., Kertesz, M., Wang, J.K., Squazzo, S.L., Xu, X., Brugmann, S.A., Goodnough, L.H., Chang, H.Y., Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs (2007) Cell, 129, pp. 1311-1323
• Amândio, A.R., Necsulea, A., Joye, E., Mascrez, B., Duboule, D., Hotair is dispensible for mouse development (2016) PLoS Genet., 12, p. e1006232
• Selleri, L., Bartolomei, M.S., Bickmore, W.A., He, L., Stubbs, L., Reik, W., Barsh, G.S., A Hox-embedded long noncoding RNA: is it all hot air? (2016) PLoS Genet., 12, p. e1006485
• Mulvey, B.B., Olcese, U., Cabrera, J.R., Horabin, J.I., An interactive network of long non-coding RNAs facilitates the Drosophila sex determination decision (2014) Biochim. Biophys. Acta, 1839, pp. 773-784
• Petruk, S., Sedkov, Y., Riley, K.M., Hodgson, J., Schweisguth, F., Hirose, S., Jaynes, J.B., Mazo, A., Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference (2006) Cell, 127, pp. 1209-1221
• MNutt, M., Retraction (2014) Science, 344, p. 981
• Wen, K., Yang, L., Xiong, T., Di, C., Ma, D., Wu, M., Xue, Z., Zhang, W., Critical roles of long noncoding RNAs in Drosophila spermatogenesis (2016) Genome Res., 26, pp. 1233-1244
• Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., Booth, B.W., The developmental transcriptome of Drosophila melanogaster (2011) Nature, 471, pp. 473-479
• Young, R.S., Marques, A.C., Tibbit, C., Haerty, W., Bassett, A.R., Liu, J.-L., Ponting, C.P., Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome (2012) Genome Biol. Evol., 4, pp. 427-442
• Brown, J.B., Boley, N., Eisman, R., May, G.E., Stoiber, M.H., Duff, M.O., Booth, B.W., Suzuki, A.M., Diversity and dynamics of the Drosophila transcriptome (2014) Nature, 512, pp. 393-399
• Melé, M., Mattioli, K., Mallard, W., Shechner, D.M., Gerhardinger, C., Rinn, J.L., Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs (2017) Genome Res., 27, pp. 27-37
• Chen, B., Zhang, Y., Zhang, X., Jia, S., Chen, S., Kang, L., Genome-wide identification and developmental expression profiling of long noncoding RNAs during Drosophila metamorphosis (2016) Sci. Rep., 6, p. 23330
• Nyberg, K.G., Machado, C.A., Comparative expression dynamics of intergenic long noncoding RNAs in the genus Drosophila (2016) Genome Biol. Evol., 8, pp. 1839-1858
• Bonn, S., Zinzen, R.P., Girardot, C., Gustafson, E.H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Furlong, E.E.M., Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development (2012) Nat. Genet., 44, pp. 148-156
• Lu, B., Zeng, Z., Shi, T., Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-seq (2013) Sci. China Life Sci., 56, pp. 143-155
• Delás, M.J., Sabin, L.R., Dolzhenko, E., Knott, S.R., Munera Maravilla, E., Jackson, B.T., Wild, S.A., Zhou, M., lncRNA requirements for mouse acute myeloid leukemia and normal differentiation (2017) eLife, 6, p. e25607
• Liu, S.J., Nowakowski, T.J., Pollen, A.A., Lui, J.H., Horlbeck, M.A., Attenello, F.J., He, D., Lim, D.A., Single-cell analysis of long non-coding RNAs in the developing human neocortex (2016) Genome Biol., 17, p. 67
• Mirsafian, H., Manda, S.S., Mitchell, C.J., Sreenivasamurthy, S., Ripen, A.M., Mohamad, S.B., Merican, A.F., Pandey, A., Long non-coding RNA expression in primary human monocytes (2016) Genomics, 108, pp. 37-45
• Wang, L., Park, H.J., Dasari, S., Wang, S., Kocher, J.P., Li, W., CPAT: coding-potential assessment tool using an alignment-free logistic regression model (2013) Nucleic Acids Res., 41, p. e74
• Lin, M.F., Jungreis, I., Kellis, M., PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions (2011) Bioinformatics, 27, pp. i275-i282
• Plaza, S., Menschaert, G., Payre, F., In search of lost small peptides (2017) Annu. Rev. Cell Dev. Biol., 33, pp. 391-416
• Heyn, P., Kircher, M., Dahl, A., Kelso, J., Tomancak, P., Kalinka, A.T., Neugebauer, K.M., The earliest transcribed zygotic genes are short, newly evolved, and different across species (2014) Cell Rep., 6, pp. 285-292
• Artieri, C.G., Fraser, H.B., Transcript length mediates developmental timing of gene expression across Drosophila (2014) Mol. Biol. Evol., 31, pp. 2879-2889
• Wilk, R., Hu, J., Blotsky, D., Krause, H.M., Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs (2016) Genes Dev., 30, pp. 594-609
• Gratz, S.J., Ukken, F.P., Rubinstein, C.D., Thiede, G., Donohue, L.K., Cummings, A.M., O'Connor-Giles, K.M., Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila (2014) Genetics, 196, pp. 961-971
• Quintero-Cadena, P., Sternberg, P.W., Enhancer sharing promotes neighborhoods of transcriptional regulation across eukaryotes (2016) G3 (Bethesda), 6, pp. 4167-4174
• Sigova, A.A., Mullen, A.C., Molinie, B., Gupta, S., Orlando, D.A., Guenther, M.G., Almada, A.E., Young, R.A., Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells (2013) Proc. Natl. Acad. Sci. USA, 110, pp. 2876-2881
• Core, L.J., Waterfall, J.J., Gilchrist, D.A., Fargo, D.C., Kwak, H., Adelman, K., Lis, J.T., Defining the status of RNA polymerase at promoters (2012) Cell Rep., 2, pp. 1025-1035
• Reim, I., Frasch, M., The Dorsocross T-box genes are key components of the regulatory network controlling early cardiogenesis in Drosophila (2005) Development, 132, pp. 4911-4925
• Hamaguchi, T., Yabe, S., Uchiyama, H., Murakami, R., Drosophila Tbx6-related gene, Dorsocross, mediates high levels of Dpp and Scw signal required for the development of amnioserosa and wing disc primordium (2004) Dev. Biol., 265, pp. 355-368
• Reim, I., Lee, H.H., Frasch, M., The T-box-encoding Dorsocross genes function in amnioserosa development and the patterning of the dorsolateral germ band downstream of Dpp (2003) Development, 130, pp. 3187-3204
• Lagha, M., Bothma, J.P., Levine, M., Mechanisms of transcriptional precision in animal development (2012) Trends Genet., 28, pp. 409-416
• Mackay, T.F., Richards, S., Stone, E.A., Barbadilla, A., Ayroles, J.F., Zhu, D., Casillas, S., Cridland, J.M., The Drosophila melanogaster genetic reference panel (2012) Nature, 482, pp. 173-178
• Kaessmann, H., Origins, evolution, and phenotypic impact of new genes (2010) Genome Res., 20, pp. 1313-1326
• Kondo, S., Vedanayagam, J., Mohammed, J., Eizadshenass, S., Kan, L., Pang, N., Aradhya, R., Lai, E.C., New genes often acquire male-specific functions but rarely become essential in Drosophila (2017) Genes Dev., 31, pp. 1841-1846
• Chen, S., Zhang, Y.E., Long, M., New genes in Drosophila quickly become essential (2010) Science, 330, pp. 1682-1685
• Rossi, A., Kontarakis, Z., Gerri, C., Nolte, H., Hölper, S., Krüger, M., Stainier, D.Y., Genetic compensation induced by deleterious mutations but not gene knockdowns (2015) Nature, 524, pp. 230-233
• Mercer, T.R., Dinger, M.E., Sunkin, S.M., Mehler, M.F., Mattick, J.S., Specific expression of long noncoding RNAs in the mouse brain (2008) Proc. Natl. Acad. Sci. USA, 105, pp. 716-721
• Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Gingeras, T.R., STAR: ultrafast universal RNA-seq aligner (2013) Bioinformatics, 29, pp. 15-21
• Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P.D., Bowden, J., Couger, M.B., Lieber, M., De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis (2013) Nat. Protoc., 8, pp. 1494-1512
• Wu, T.D., Watanabe, C.K., GMAP: a genomic mapping and alignment program for mRNA and EST sequences (2005) Bioinformatics, 21, pp. 1859-1875
• Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Pachter, L., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation (2010) Nat. Biotechnol., 28, pp. 511-515
• Love, M.I., Huber, W., Anders, S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 (2014) Genome Biol., 15, p. 550
• Khodor, Y.L., Rodriguez, J., Abruzzi, K.C., Tang, C.H.A., Marr, M.T., 2nd, Rosbash, M., Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila (2011) Genes Dev., 25, pp. 2502-2512
• Schor, I.E., Degner, J.F., Harnett, D., Cannavò, E., Casale, F.P., Shim, H., Garfield, D.A., Furlong, E.E., Promoter shape varies across populations and affects promoter evolution and expression noise (2017) Nat. Genet., 49, pp. 550-558
• Arvey, A., Hermann, A., Hsia, C.C., Ie, E., Freund, Y., McGinnis, W., Minimizing off-target signals in RNA fluorescent in situ hybridization (2010) Nucleic Acids Res., 38, p. e115
• Cannavò, E., Koelling, N., Harnett, D., Garfield, D., Casale, F.P., Ciglar, L., Gustafson, H.E., Degner, J.F., Genetic variants regulating expression levels and isoform diversity during embryogenesis (2017) Nature, 541, pp. 402-406
• Davis, M.P., Carrieri, C., Saini, H.K., van Dongen, S., Leonardi, T., Bussotti, G., Monahan, J.M., Rappsilber, J., Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution (2017) EMBO Rep., 18, pp. 1231-1247
• Pauli, A., Valen, E., Lin, M.F., Garber, M., Vastenhouw, N.L., Levin, J.Z., Fan, L., Schier, A.F., Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis (2012) Genome Res., 22, pp. 577-591
• Zinzen, R.P., Girardot, C., Gagneur, J., Braun, M., Furlong, E.E.M., Combinatorial binding predicts spatio-temporal cis-regulatory activity (2009) Nature, 462, pp. 65-70
• Junion, G., Spivakov, M., Girardot, C., Braun, M., Gustafson, E.H., Birney, E., Furlong, E.E., A transcription factor collective defines cardiac cell fate and reflects lineage history (2012) Cell, 148, pp. 473-486
• Gallo, S.M., Gerrard, D.T., Miner, D., Simich, M., Des Soye, B., Bergman, C.M., Halfon, M.S., REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila (2011) Nucleic Acids Res., 39, pp. D118-D123
• Kvon, E.Z., Kazmar, T., Stampfel, G., Yáñez-Cuna, J.O., Pagani, M., Schernhuber, K., Dickson, B.J., Stark, A., Genome-scale functional characterization of Drosophila developmental enhancers in vivo (2014) Nature, 512, pp. 91-95

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