Abstract
Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel cDNA sequencing (RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially lincRNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes (21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications (H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis (GSEA) result revealed several sets of lincRNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs.
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Brown, C.J., Hendrich, B.D., Rupert, J.L., Lafrenière, R.G., Xing, Y., Lawrence, J., and Willard, H.F. (1992). 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.
Brown, J.B., Boley, N., Eisman, R., May, G.E., Stoiber, M.H., Duff, M.O., Booth, B.W., Weng, J., Park, S., and Suzuki, A.M. (2014). Diversity and dynamics of the Drosophila transcriptome. Nature 512, 393–399.
Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A., and Rinn, J.L. (2011). Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25, 1915–1927.
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., and Wells, C. (2005). The transcriptional landscape of the mammalian genome. Science 309, 1559–1563.
Clark, M.B., Amaral, P.P., Schlesinger, F.J., Dinger, M.E., Taft, R.J., Rinn, J.L., Ponting, C.P., Stadler, P.F., Morris, K.V., and Morillon, A. (2011). The reality of pervasive transcription. PLoS Biol 9, e1000625.
Cloonan, N., Forrest, A.R., Kolle, G., Gardiner, B.B., Faulkner, G.J., Brown, M.K., Taylor, D.F., Steptoe, A.L., Wani, S., and Bethel, G. (2008). Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5, 613–619.
Cui, P., Lin, Q., Ding, F., Xin, C., Gong, W., Zhang, L., Geng, J., Zhang, B., Yu, X., and Yang, J. (2010). A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics 96, 259–265.
Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., and Knowles, D.G. (2012). The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22, 1775–1789.
Dinger, M.E., Amaral, P.P., Mercer, T.R., Pang, K.C., Bruce, S.J., Gardiner, B.B., Askarian-Amiri, M.E., Ru, K., Soldà, G., and Simons, C. (2008). Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18, 1433–1445.
Djebali, S., Davis, C.A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., and Schlesinger, F. (2012). Landscape of transcription in human cells. Nature 489, 101–108.
ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74.
Forrest, A.R., Kawaji, H., Rehli, M., Baillie, J.K., de Hoon, M.J., Haberle, V., Lassmann, T., Kulakovskiy, I.V., Lizio, M., Itoh, M., Andersson, R., Mungall, C.J., Meehan, T.F., Schmeier, S., Bertin, N., Jorgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U., Medvedeva, Y.A., Plessy, C., Vitezic, M., Severin, J., Semple, C., Ishizu, Y., Young, R.S., Francescatto, M., Alam, I., Albanese, D., Altschuler, G.M., Arakawa, T., Archer, J.A., Arner, P., Babina, M., Rennie, S., Balwierz, P.J., Beckhouse, A.G., Pradhan-Bhatt, S., Blake, J.A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A.M., Califano, A., Cannistraci, C.V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H.C., Dalla, E., Davis, C.A., Detmar, M., Diehl, A.D., Dohi, T., Drablos, F., Edge, A.S., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M.C., Faulkner, G.J., Favorov, A.V., Fisher, M.E., Frith, M.C., Fujita, R., Fukuda, S., Furlanello, C., Furino, M., Furusawa, J., Geijtenbeek, T.B., Gibson, A.P., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T.J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K.J., Ho Sui, S.J., Hofmann, O.M., Hoof, I., Hori, F., Huminiecki, L., Iida, K., Ikawa, T., Jankovic, B.R., Jia, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A.S., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawamoto, H., Kawamura, Y.I., Kawashima, T., Kempfle, J.S., Kenna, T.J., Kere, J., Khachigian, L.M., Kitamura, T., Klinken, S.P., Knox, A.J., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kwon, A.T., Laros, J.F., Lee, W., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Mackay-Sim, A., Manabe, R., Mar, J.C., Marchand, B., Mathelier, A., Mejhert, N., Meynert, A., Mizuno, Y., de Lima Morais, D.A., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C.L., Murata, M., Nagao-Sato, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., van Nimwegen, E., Ninomiya, N., Nishiyori, H., Noma, S., Noma, S., Noazaki, T., Ogishima, S., Ohkura, N., Ohimiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D.A., Pain, A., Passier, R., Patrikakis, M., Persson, H., Piazza, S., Prendergast, J.G., Rackham, O.J., Ramilowski, J.A., Rashid, M., Ravasi, T., Rizzu, P., Roncador, M., Roy, S., Rye, M.B., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sato, H., Savvi, S., Saxena, A., Schneider, C., Schultes, E.A., Schulze-Tanzil, G.G., Schwegmann, A., Sengstag, T., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J.W., Simon, C., Sugiyama, D., Sugiyama, T., Suzuki, M., Suzuki, N., Swoboda, R.K., Hoen, P.A., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Thompson, M., Toyodo, H., Toyoda, T., Valen, E., van de Wetering, M., van den Berg, L.M., Verado, R., Vijayan, D., Vorontsov, I.E., Wasserman, W.W., Watanabe, S., Wells, C.A., Winteringham, L.N., Wolvetang, E., Wood, E.J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Zabierowski, S.E., Zhang, P.G., Zhao, X., Zucchelli, S., Summers, K.M., Suzuki, H., Daub, C.O., Kawai, J., Heutink, P., Hide, W., Freeman, T.C., Lenhard, B., Bajic, V.B., Taylor, M.S., Makeev, V.J., Sandelin, A., Hume, D.A., Carninci, P., and Hayashizaki, Y. (2014). A promoter-level mammalian expression atlas. Nature 507, 462–470.
Faulkner, G.J., Forrest, A.R., Chalk, A.M., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D.A., and Grimmond, S.M. (2008). A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics 91, 281–288.
Gupta, R.A., Shah, N., Wang, K.C., Kim, J., Horlings, H.M., Wong, D.J., Tsai, M.C., Hung, T., Argani, P., and Rinn, J.L. (2010). Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071–1076.
Guttman, M., Amit, I., Garber, M., French, C., Lin, M., Feldser, D., Huarte, M., Zuk, O., Carey, B., and Cassady, J. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227.
Guttman, M., Donaghey, J., Carey, B.W., Garber, M., Grenier, J.K., Munson, G., Young, G., Lucas, A.B., Ach, R., and Bruhn, L. (2011). lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477, 295–300.
Guttman, M., Garber, M., Levin, J.Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M.J., Gnirke, A., Nusbaum, C., Rinn, J.L., Lander, E.S., and Regev, A. (2010). Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28, 503–510.
Hüttenhofer, A., and Vogel, J. (2006). Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 34, 635–646.
Haas, B.J., and Zody, M.C. (2010). Advancing RNA-seq analysis. Nat Biotechnol 28, 421.
Hangauer, M.J., Vaughn, I.W., and McManus, M.T. (2013). Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genetics 9, e1003569.
Hawkins, P.G., and Morris, K.V. (2010). Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription 1, 165–175.
Heard, E., and Disteche, C.M. (2006). Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 20, 1848–1867.
Hu, W., Alvarez-Dominguez, J.R., and Lodish, H.F. (2012). Regulation of mammalian cell differentiation by long non-coding RNAs. EMBO Rep 13, 971–983.
Karolchik, D., Barber, G.P., Casper, J., Clawson, H., Cline, M.S., Diekhans, M., Dreszer, T.R., Fujita, P.A., Guruvadoo, L., Haeussler, M., Harte, R.A., Heitner, S., Hinrichs, A.S., Learned, K., Lee, B.T., Li, C.H., Raney, B.J., Rhead, B., Rosenbloom, K.R., Sloan, C.A., Speir, M.L., Zweig, A.S., Haussler, D., Kuhn, R.M., and Kent, W.J. (2014). The UCSC Genome Browser database: 2014 update. Nucleic Acids Res 42, D764–D770.
Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nashida, H., Yap, C., Suzuki, M., and Kawai, J. (2005). Antisense transcription in the mammalian transcriptome. J Biol Chem 309, 1564–1566.
Kuhn, R.M., Karolchik, D., Zweig, A.S., Wang, T., Smith, K.E., Rosenbloom, K.R., Rhead, B., Raney, B.J., Pohl, A., and Pheasant, M. (2009). The UCSC genome browser database: update 2009. Nucleic acids Res 37, D755–D761.
Li, G., Ruan, X., Auerbach, R.K., Sandhu, K.S., Zheng, M., Wang, P., Poh, H.M., Goh, Y., Lim, J., and Zhang, J. (2012). Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98.
Liu, J., Jung, C., Xu, J., Wang, H., Deng, S., Bernad, L., Arenas-Huertero, C., and Chua, N.-H. (2012). Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24, 4333–4345.
Liu, W., Zhao, Y., Cui, P., Lin, Q., Ding, F., Xin, C., Tan, X., Song, S., Yu, J., and Hu, S. (2011). Thousands of novel transcripts identified in mouse cerebrum, testis, and EScells based on ribo-minus RNA sequencing. Front Genet 2, 93.
Luo, H., Sun, S., Li, P., Bu, D., Cao, H., and Zhao, Y. (2013). Comprehensive characterization of 10,571 mouse large intergenic noncoding RNAs from whole transcriptome sequencing. PLoS One 8, e70835.
Lv, J., Liu, H., Huang, Z., Su, J., He, H., Xiu, Y., Zhang, Y., and Wu, Q. (2013). Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Res, 41, 10044–10061.
Maamar, H., Cabili, M.N., Rinn, J., and Raj, A. (2013). linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes Dev 27, 1260–1271.
Mattick, J.S. (2009). The genetic signatures of noncoding RNAs. PLoS Genet 5, e1000459.
Mercer, T.R., Dinger, M.E., and Mattick, J.S. (2009). Long non-coding RNAs: insights into functions. Nat Rev Genet 10, 155–159.
Meyer, L.R., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Kuhn, R.M., Wong, M., Sloan, C.A., Rosenbloom, K.R., Roe, G., and Rhead, B. (2013). The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 41, D64–D69.
Stamatoyannopoulos, J.A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D.M., Groudine, M., Bender, M., Kaul, R., and Canfield, T. (2012). An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol 13, 418.
Nakaya, H.I., Amaral, P.P., Louro, R., Lopes, A., Fachel, A.A., Moreira, Y.B., El-Jundi, T.A., da Silva, A.M., Reis, E.M., and Verjovski-Almeida, S. (2007). Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol 8, R43.
Nam, J.W., and Bartel, D. (2012). Long non-coding RNAs in C. elegans. Genome Res 22, 2529–2540.
Barbosa-Morais, N.L., Irimia, M., Pan, Q., Xiong, H.Y., Gueroussov, S., Lee, L.J., Slobodeniuc, V., Kutter, C., Watt, S., Colak, R., Kim, T., Misquitta-Ali, C.M., Wilson, M.D., Kim, P.M., Odom, D.T., Frey, B.J., and Blencowe, B.J. (2012). The evolutionary landscape of alternative splicing in verterbrate species. Science 338, 1587–1593.
Okazaki, Y., Furuno, M., Kasukawa, T., and Adachi, J. (2002). Analysis of the mouse transcriptome based on functional annotation of 60770 full-length cDNAs. Nature 420, 563–573.
Ørom, U.A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., and Huang, Q. (2010). Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46–58.
Pan, L., Gong, W., Zhou, Y., Li, X., Yu, J., and Hu, S. (2014). A comprehensive transcriptomic analysis of infant and adult mouse ovary. Genomics Proteomics Bioinformatics 12, 239–248.
Pauli, A., Rinn, J.L., and Schier, A.F. (2011). Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet 12, 136–149.
Pauli, A., Valen, E., Lin, M.F., Garber, M., Vastenhouw, N.L., Levin, J.Z., Fan, L., Sandelin, A., Rinn, J.L., and Regev, A. (2012). Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 22, 577–591.
Pervouchine, D.D., Djebali, S., Breschi, A., Davis, C.A., Barja, P.P., Dobin, A., Tanzer, A., Lagarde, J., Zaleski, C., See, L.H., Fastuca, M., Drenkow, J., Wang, H., Bussotti, G., Pei, B., Balasubramanian, S., Monlong, J., Harmanci, A., Gerstein, M., Beer, M.A., Notredame, C., Guigo, R., and Gingeras, T.R. (2015). Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat Commun 6, 5903.
Qu, Z., and Adelson, D.L. (2012). Identification and comparative analysis of ncRNAs in human, mouse and zebrafish indicate a conserved role in regulation of genes expressed in brain. PLoS One 7, e52275.
Ramskld, D., Wang, E., Burge, C., and Sandberg, R. (2009). An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5, e1000598.
Rinn, J.L., Kertesz, M., Wang, J.K., and Squazzo, S.L. (2007). Functional demarcation of active and silent chromatin domains in human HOX Loci by non-coding RNAs. Cell 129, 1311–1323.
Sasaki, Y.T., Ideue, T., Sano, M., Mituyama, T., and Hirose, T. (2009). MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci USA 106, 2525–2530.
Sati, S., Ghosh, S., Jain, V., Scaria, V., and Sengupta, S. (2012). Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. Nucleic Acids Res 40, 10018–10031.
Sauvageau, M., Goff, L.A., Lodato, S., Bonev, B., Groff, A.F., Gerhardinger, C., Sanchez-Gomez, D.B., Hacisuleyman, E., Li, E., and Spence, M. (2013). Multiple knockout mouse models reveal lincRNAs are required for life and brain development. ELife 2, e01749.
Sigova, A.A., Mullen, A.C., Molinie, B., Gupta, S., Orlando, D.A., Guenther, M.G., Almada, A.E., Lin, C., Sharp, P.A., and Giallourakis, C.C. (2013). Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci USA 110, 2876–2881.
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., and Lander, E.S. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102, 15545–15550.
The ENCODE Project Consortium. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816.
Tan, M.H., Au, K.F., Yablonovitch, A.L., Wills, A.E., Chuang, J., Baker, J.C., Wong, W.H., and Li, J.B. (2013). RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res 23, 201–216.
Ulitsky, I., and Bartel, D.P. (2013). lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26–46.
Ulitsky, I., Shkumatava, A., Jan, C.H., Sive, H., and Bartel, D.P. (2011). Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147, 1537–1550.
Wang, K.C., and Chang, H.Y. (2011). Molecular mechanisms of long noncoding RNAs. Mol Cell 43, 904–914.
Werner, A. (2013). Biological functions of natural antisense transcripts. BMC Biol 11, 31.
Wetterbom, A., Ameur, A., Feuk, L., Gyllensten, U., and Cavelier, L. (2010). Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing. Genome Biol 11, R78.
Yang, L., Duff, M.O., Graveley, B.R., Carmichael, G.G., and Chen, L.-L. (2011). Genomewide characterization of non-polyadenylated RNAs. Genome Biol 12, R16.
Yang, P.K., and Kuroda, M.I. (2007). Noncoding RNAs and intranuclear positioning in monoallelic gene expression. Cell 128, 777–786.
Yassour, M., Kaplan, T., Fraser, H.B., Levin, J.Z., Pfiffner, J., Adiconis, X., Schroth, G., Luo, S., Khrebtukova, I., and Gnirke, A. (2009). Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci USA 106, 3264–3269.
Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B.D., Shen, Y., Pervouchine, D.D., Djebali, S., Thurman, R.E., Kaul, R., Rynes, E., Kirilusha, A., Marinov, G.K., Williams, B.A., Trout, D., Amrhein, H., Fisher-Aylor, K., Antoshechkin, I., DeSalvo, G., See, L.H., Fastuca, M., Drenkow, J., Zaleski, C., Dobin, A., Prieto, P., Lagarde, J., Bussotti, G., Tanzer, A., Denas, O., Li, K., Bender, M.A., Zhang, M., Byron, R., Groudine, M.T., McCleary, D., Pham, L., Ye, Z., Kuan, S., Edsall, L., Wu, Y.C., Rasmussen, M.D., Bansal, M.S., Kellis, M., Keller, C.A., Morrissey, C.S., Mishra, T., Jain, D., Dogan, N., Harris, R.S., Cayting, P., Kawli, T., Boyle, A.P., Euskirchen, G., Kundaje, A., Lin, S., Lin, Y., Jansen, C., Malladi, V.S., Cline, M.S., Erickson, D.T., Kirkup, V.M., Learned, K., Sloan, C.A., Rosenbloom, K.R., Lacerda de Sousa, B., Beal, K., Pignatelli, M., Flicek, P., Lian, J., Kahveci, T., Lee, D., James Kent, W., Ramalho Santos, M., Herrero, J., Notredame, C., Johnson, A., Vong, S., Lee, K., Bates, D., Neri, F., Diegel, M., Canfield, T., Sabo, P.J., Wilken, M.S., Reh, T.A., Giste, E., Shafer, A., Kutyavin, T., Haugen, E., Dunn, D., Reynolds, A.P., Neph, S., Humbert, R., Scott Hansen, R., De Bruijn, M., Selleri, L., Rudensky, A., Josefowicz, S., Samstein, R., Eichler, E.E., Orkin, S.H., Levasseur, D., Papayannopoulou, T., Chang, K.H., Skoultchi, A., Gosh, S., Disteche, C., Treuting, P., Wang, Y., Weiss, M.J., Blobel, G.A., Cao, X., Zhong, S., Wang, T., Good, P.J., Lowdon, R.F., Adams, L.B., Zhou, X.Q., Pazin, M.J., Feingold, E.A., Wold, B., Taylor, J., Mortazavi, A., Weissman, S.M., Stamatoyannopoulos, J.A., Snyder, M.P., Guigo, R., Gingeras, T.R., Gilbert, D.M., Hardison, R.C., Beer, M.A., Ren, B., and Mouse, E.C. (2014). A comparative encyclopedia of DNA elements in the mouse genome. Nature 515, 355–364.
Zheng, D., Frankish, A., Baertsch, R., Kapranov, P., Reymond, A., Choo, S.W., Lu, Y., Denoeud, F., Antonarakis, S.E., and Snyder, M. (2007). Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 17, 839–851.
Zhou, Y., Gong, W., Xiao, J., Wu, J., Pan, L., Li, X., Wang, X., Wang, W., Hu, S., and Yu, J. (2014). Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle. Sci China Life Sci 57, 340–355.
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Zhao, Y., Liu, W., Zeng, J. et al. Identification and analysis of mouse non-coding RNA using transcriptome data. Sci. China Life Sci. 59, 589–603 (2016). https://doi.org/10.1007/s11427-015-4929-x
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DOI: https://doi.org/10.1007/s11427-015-4929-x