Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse

Abstract

Background: MicroRNAs (miRNAs) regulate target gene expression at post-transcriptional level. Intense research has been conducted for miRNA identification and the target finding. However, much less is known about the transcriptional regulation of miRNA genes themselves. Recently, a special group of pre-miRNAs that are produced directly by transcription without Drosha processing were validated in mouse, indicating the complexity of miRNA biogenesis.

Methods: In this work, we detect clusters of aligned Cap-seq reads to find the transcription start sites (TSSs) for intergenic miRNAs and study their transcriptional regulation in Caenorhabditis elegans and mouse.

Results: In both species, we have identified a class of special pre-miRNAs whose 5′ ends are capped, and are most probably generated directly by transcription. Furthermore, we distinguished another class of special pre-miRNAs that are 5′-capped but are also part of longer primary miRNAs, suggesting they may have more than one transcription mechanism. We detected multiple cap reads peaks within miRNA clusters in C. elegans. We surmised that the miRNAs in a cluster may either be transcribed independently or be re-capped during the microprocessor cleavage process. We also observed that H3K4me3 and Pol II are enriched at those identified miRNA TSSs.

Conclusions: The Cap-seq datasets enabled us to annotate the primary TSSs for miRNA genes with high resolution. Special class of 5′-capped pre-miRNAs have been identified in both C. elegans and mouse. The capping patter of miRNAs in a cluster indicate that clustered miRNA transcripts probably undergo a re-capping procedure during the microprocessor cleavage process.

Graphical abstract

Keywords

miRNA / Cap-seq / transcriptional regulation

References

[1] Kim, V. N. and Nam, J.-W. (2006) Genomics of microRNA. Trends Genet., 22, 165–173

[2] Krol, J., Loedige, I. and Filipowicz, W. (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat. Rev. Genet., 11, 597–610

[3] Berezikov, E. (2011) Evolution of microRNA diversity and regulation in animals. Nat. Rev. Genet., 12, 846–860

[4] Mallanna, S. K. and Rizzino, A. (2010) Emerging roles of microRNAs in the control of embryonic stem cells and the generation of induced pluripotent stem cells. Dev. Biol., 344, 16–25

[5] Collins, F. S. and Varmus, H. (2015) A new initiative on precision medicine. N. Engl. J. Med., 372, 793–795

[6] Larry Jameson, J. and Longo, D. L. (2015) Precision medicine—personalized, problematic, and promising. Obstet. Gynecol. Surv., 70, 612–614

[7] Lüscher, T. F. (2016) Frontiers in precision medicine: genes and their modulation by miRNAs. Eur. Heart J., 37, 3247–3250

[8] Willeit, P., Skroblin, P., Kiechl, S., Fernández-Hernando, C. and Mayr, M. (2016) Liver microRNAs: potential mediators and biomarkers for metabolic and cardiovascular disease? Eur. Heart J., 37, 3260–3266

[9] Matin, F., Jeet, V., Clements, J. A., Yousef, G. M. and Batra, J. (2016) MicroRNA theranostics in prostate cancer precision medicine. Clin. Chem., 62, 1318–1333

[10] Coronnello, C. and Benos, P. V. (2013) ComiR: combinatorial microRNA target prediction tool. Nucleic Acids Res., 41, W159– W164

[11] Yuan, C. and Sun, Y. (2013) RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes. PLoS One, 8, e77596

[12] Lei, J. and Sun, Y. (2014) miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data. Bioinformatics, 30, 2837–2839

[13] Lee, Y., Kim, M., Han, J., Yeom, K.-H., Lee, S., Baek, S. H. and Kim, V. N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 23, 4051–4060

[14] Borchert, G. M., Lanier, W. and Davidson, B. L. (2006) RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol., 13, 1097–1101

[15] Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Rådmark, O., Kim, S., (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415–419

[16] Chendrimada, T. P., Gregory, R. I., Kumaraswamy, E., Norman, J., Cooch, N., Nishikura, K. and Shiekhattar, R. (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature, 436, 740–744

[17] Kuehbacher, A., Urbich, C., Zeiher, A. M. and Dimmeler, S. (2007) Role of Dicer and Drosha for endothelial microRNA expression and angiogenesis. Circ. Res., 101, 59–68

[18] Berezikov, E., Chung, W.-J., Willis, J., Cuppen, E. and Lai, E. C. (2007) Mammalian mirtron genes. Mol. Cell, 28, 328–336

[19] Ruby, J. G., Jan, C. H. and Bartel, D. P. (2007) Intronic microRNA precursors that bypass Drosha processing. Nature, 448, 83–86

[20] Chang, T.-C., Pertea, M., Lee, S., Salzberg, S. L. and Mendell, J. T. (2015) Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms. Genome Res., 25, 1401–1409

[21] Dai, L., Chen, K., Youngren, B., Kulina, J., Yang, A., Guo, Z., Li, J., Yu, P. and Gu, S. (2016) Cytoplasmic Drosha activity generated by alternative splicing. Nucleic Acids Res., 44, 10454–10466

[22] Xie, M., Li, M., Vilborg, A., Lee, N., Shu, M.-D., Yartseva, V., Šestan, N. and Steitz, J. A. (2013) Mammalian 5′-capped microRNA precursors that generate a single microRNA. Cell, 155, 1568–1580

[23] Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A. and Enright, A. J. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34, D140–D144

[24] Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57–63

[25] Saini, H. K., Griffiths-Jones, S. and Enright, A. J. (2007) Genomic analysis of human microRNA transcripts. Proc. Natl. Acad. Sci. USA, 104, 17719–17724

[26] Ozsolak, F., Poling, L. L., Wang, Z., Liu, H., Liu, X. S., Roeder, R. G., Zhang, X., Song, J. S. and Fisher, D. E. (2008) Chromatin structure analyses identify miRNA promoters. Genes Dev., 22, 3172–3183

[27] Corcoran, D. L., Pandit, K. V., Gordon, B., Bhattacharjee, A., Kaminski, N. and Benos, P. V. (2009) Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One, 4, e5279

[28] Chien, C.-H., Sun, Y.-M., Chang, W.-C., Chiang-Hsieh, P.-Y., Lee, T.-Y., Tsai, W.-C., Horng, J.-T., Tsou, A.-P. and Huang, H.-D. (2011) Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res., 39, 9345–9356

[29] Wang, G., Wang, Y., Shen, C., Huang, Y. W., Huang, K., Huang, T. H., Nephew, K. P., Li, L. and Liu, Y. (2010) RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS One, 5, e13798

[30] Saini, H. K., Enright, A. J. and Griffiths-Jones, S. (2008) Annotation of mammalian primary microRNAs. BMC Genomics, 9, 564

[31] Kodzius, R., Kojima, M., Nishiyori, H., Nakamura, M., Fukuda, S., Tagami, M., Sasaki, D., Imamura, K., Kai, C., Harbers, M., (2006) CAGE: cap analysis of gene expression. Nat. Methods, 3, 211–222

[32] de Hoon, M. and Hayashizaki, Y. (2008) Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference. Biotechniques, 44, 627–632

[33] Gu, W., Lee, H.-C., Chaves, D., Youngman, E. M., Pazour, G. J., Conte, D. Jr and Mello, C. C. (2012) CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell, 151, 1488–1500

[34] Corsi, A. K. (2006) A biochemist’s guide to Caenorhabditis elegans. Anal. Biochem., 359, 1–17

[35] Chen, R. A.-J., Down, T. A., Stempor, P., Chen, Q. B., Egelhofer, T. A., Hillier, L. W., Jeffers, T. E. and Ahringer, J. (2013) The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Genome Res., 23, 1339–1347

[36] Kruesi, W. S., Core, L. J., Waters, C. T., Lis, J. T. and Meyer, B. J. (2013) Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. eLife, 2, e00808

[37] Spieth, J., Lawson, D., Davis, P., Williams, G. and Howe, K. (2014) Overview of gene structure in C. elegans. In WormBook, 1–18.

[38] Büssing, I., Yang, J. S. Jr, Lai, E. C. and Grosshans, H. (2010) The nuclear export receptor XPO-1 supports primary miRNA processing in C. elegans and Drosophila. EMBO J., 29, 1830–1839

[39] Li, N., You, X., Chen, T., Mackowiak, S. D., Friedländer, M. R., Weigt, M., Du, H., Gogol-Döring, A., Chang, Z., Dieterich, C., (2013) Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery. Nucleic Acids Res., 41, 3619–3634

[40] Fejes-Toth, K., Sotirova, V., Sachidanandam, R., Assaf, G., Hannon, G. J., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., Dumais, E., (2009) Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature, 457, 1028–1032

[41] Crooks, G. E., Hon, G., Chandonia, J.-M. and Brenner, S. E. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188–1190

[42] Abeel, T., Van Parys, T., Saeys, Y., Galagan, J. and Van de Peer, Y. (2012) GenomeView: a next-generation genome browser. Nucleic Acids Res., 40, e12

[43] Bracht, J., Hunter, S., Eachus, R., Weeks, P. and Pasquinelli, A. E. (2004) Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA, 10, 1586–1594

[44] Davuluri, R. V., Suzuki, Y., Sugano, S., Plass, C. and Huang, T. H.-M. (2008) The functional consequences of alternative promoter use in mammalian genomes. Trends Genet., 24, 167–177

[45] Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., (2012) Landscape of transcription in human cells. Nature, 489, 101–108

[46] Sigova, A. A., Mullen, A. C., Molinie, B., Gupta, S., Orlando, D. A., Guenther, M. G., Almada, A. E., Lin, C., Sharp, P. A., 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

[47] Wei, Y., Zhang, S., Shang, S., Zhang, B., Li, S., Wang, X., Wang, F., Su, J., Wu, Q., Liu, H., (2016) SEA: a super-enhancer archive. Nucleic Acids Res., 44, D172–D179

[48] Biasiolo, M., Sales, G., Lionetti, M., Agnelli, L., Todoerti, K., Bisognin, A., Coppe, A., Romualdi, C., Neri, A. and Bortoluzzi, S. (2011) Impact of host genes and strand selection on miRNA and miRNA* expression. PLoS One, 6, e23854

[49] Meijer, H. A., Smith, E. M. and Bushell, M. (2014) Regulation of miRNA strand selection: follow the leader? Biochem. Soc. Trans., 42, 1135–1140

[50] Lau, N. C., Lim, L. P., Weinstein, E. G. and Bartel, D. P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858–862

[51] Otsuka, Y., Kedersha, N. L. and Schoenberg, D. R. (2009) Identification of a cytoplasmic complex that adds a cap onto 5′-monophosphate RNA. Mol. Cell. Biol., 29, 2155–2167

[52] Schoenberg, D. R. and Maquat, L. E. (2009) Re-capping the message. Trends Biochem. Sci., 34, 435–442

[53] Mukherjee, C., Patil, D. P., Kennedy, B. A., Bakthavachalu, B., Bundschuh, R. and Schoenberg, D. R. (2012) Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability. Cell Rep., 2, 674–684

[54] Kiss, D. L., Oman, K., Bundschuh, R. and Schoenberg, D. R. (2015) Uncapped 5′ ends of mRNAs targeted by cytoplasmic capping map to the vicinity of downstream CAGE tags. FEBS Lett., 589, 279–284

[55] Rouha, H., Thurner, C. and Mandl, C. W. (2010) Functional microRNA generated from a cytoplasmic RNA virus. Nucleic Acids Res., 38, 8328–8337

[56] Shapiro, J. S., Langlois, R. A., Pham, A. M. and Tenoever, B. R. (2012) Evidence for a cytoplasmic microprocessor of pri-miRNAs. RNA, 18, 1338–1346

[57] Sandelin, A., Carninci, P., Lenhard, B., Ponjavic, J., Hayashizaki, Y. and Hume, D. A. (2007) Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat. Rev. Genet., 8, 424–436

[58] Frith, M. C., Valen, E., Krogh, A., Hayashizaki, Y., Carninci, P. and Sandelin, A. (2008) A code for transcription initiation in mammalian genomes. Genome Res., 18, 1–12

[59] Sandelin, A., Alkema, W., Engström, P., Wasserman, W. W. and Lenhard, B. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32, D91–D94

[60] Winter, J., Jung, S., Keller, S., Gregory, R. I. and Diederichs, S. (2009) Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat. Cell Biol., 11, 228–234

[61] Song, G. and Wang, L. (2008) MiR-433 and miR-127 arise from independent overlapping primary transcripts encoded by the miR-433-127 locus. PLoS One, 3, e3574

[62] Murphy, D., Dancis, B. and Brown, J. R. (2008) The evolution of core proteins involved in microRNA biogenesis. BMC Evol. Biol., 8, 92

[63] Kiezun, A., Artzi, S., Modai, S., Volk, N., Isakov, O. and Shomron, N. (2012) miRviewer: a multispecies microRNA homologous viewer. BMC Res. Notes, 5, 92

[64] Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A., Taylor, M. S., Engström, P. G., Frith, M. C., (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet., 38, 626–635

[65] Danino, Y. M., Even, D., Ideses, D. and Juven-Gershon, T. (2015) The core promoter: at the heart of gene expression. Biochim. Biophys. Acta, 1849, 1116–1131

[66] Landry, J.-R., Mager, D. L. and Wilhelm, B. T. (2003) Complex controls: the role of alternative promoters in mammalian genomes. Trends Genet., 19, 640–648

[67] Baek, D., Davis, C., Ewing, B., Gordon, D. and Green, P. (2007) Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res., 17, 145–155

[68] Staff, S. (2011) Using the sra toolkit to convert. sra files into other formats.National Center for Biotechnology Information (US)

[69] Langmead, B., Trapnell, C., Pop, M. and Salzberg, S. L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25

[70] Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137

RIGHTS & PERMISSIONS

Higher Education Press and Springer-Verlag GmbH Germany