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Identification of cis-Elements for RNA Subcellular Localization Through REL-seq

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RNA-Chromatin Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2161))

Abstract

The subcellular localization of RNAs is regulated by cis-regulatory elements together with interacting trans factors. Here we describe a high-throughput sequencing-based method named REL-seq (RNA elements for subcellular localization by sequencing) to identify the cis-elements that contribute to RNA subcellular localization. By coupling REL-seq with random mutagenesis (mutREL-seq), we can further narrow down the cis-elements to key motifs at single-nucleotide resolution.

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References

  1. Kohler A, Hurt E (2007) Exporting RNA from the nucleus to the cytoplasm. Nat Rev Mol Cell Biol 8(10):761–773. https://doi.org/10.1038/nrm2255

    Article  CAS  PubMed  Google Scholar 

  2. Boutz PL, Bhutkar A, Sharp PA (2015) Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes Dev 29(1):63–80. https://doi.org/10.1101/gad.247361.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ (2014) Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res 24(11):1774–1786. https://doi.org/10.1101/gr.177790.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A (2015) Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol 16:20. https://doi.org/10.1186/s13059-015-0586-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Schlackow M, Nojima T, Gomes T, Dhir A, Carmo-Fonseca M, Proudfoot NJ (2017) Distinctive patterns of transcription and RNA processing for human lincRNAs. Mol Cell 65(1):25–38. https://doi.org/10.1016/j.molcel.2016.11.029

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigo R (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res 22(9):1616–1625. https://doi.org/10.1101/gr.134445.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Hammarskjold ML (2001) Constitutive transport element-mediated nuclear export. Curr Top Microbiol Immunol 259:77–93

    CAS  PubMed  Google Scholar 

  8. Nappi F, Schneider R, Zolotukhin A, Smulevitch S, Michalowski D, Bear J, Felber BK, Pavlakis GN (2001) Identification of a novel posttranscriptional regulatory element by using a rev- and RRE-mutated human immunodeficiency virus type 1 DNA proviral clone as a molecular trap. J Virol 75(10):4558–4569. https://doi.org/10.1128/JVI.75.10.4558-4569.2001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Zhang B, Gunawardane L, Niazi F, Jahanbani F, Chen X, Valadkhan S (2014) A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA. Mol Cell Biol 34(12):2318–2329. https://doi.org/10.1128/MCB.01673-13

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Miyagawa R, Tano K, Mizuno R, Nakamura Y, Ijiri K, Rakwal R, Shibato J, Masuo Y, Mayeda A, Hirose T, Akimitsu N (2012) Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles. RNA 18(4):738–751. https://doi.org/10.1261/rna.028639.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Ridings-Figueroa R, Stewart ER, Nesterova TB, Coker H, Pintacuda G, Godwin J, Wilson R, Haslam A, Lilley F, Ruigrok R, Bageghni SA, Albadrani G, Mansfield W, Roulson JA, Brockdorff N, Ainscough JFX, Coverley D (2017) The nuclear matrix protein CIZ1 facilitates localization of **st RNA to the inactive X-chromosome territory. Genes Dev 31(9):876–888. https://doi.org/10.1101/gad.295907.117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Sunwoo H, Colognori D, Froberg JE, Jeon Y, Lee JT (2017) Repeat E anchors **st RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1). Proc Natl Acad Sci U S A 114(40):10654–10659. https://doi.org/10.1073/pnas.1711206114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Wutz A, Rasmussen TP, Jaenisch R (2002) Chromosomal silencing and localization are mediated by different domains of **st RNA. Nat Genet 30(2):167–174. https://doi.org/10.1038/ng820

    Article  CAS  PubMed  Google Scholar 

  14. Lubelsky Y, Ulitsky I (2018) Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Nature 555(7694):107–111. https://doi.org/10.1038/nature25757

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL (2018) High-throughput identification of RNA nuclear enrichment sequences. EMBO J 37(6). https://doi.org/10.15252/embj.201798452

  16. Yin Y, Lu JY, Zhang X, Shao W, Xu Y, Li P, Hong Y, Cui L, Shan G, Tian B, Zhang QC U1 snRNP regulates chromatin retention of noncoding RNAs. Submitted

    Google Scholar 

  17. Arnold CD, Gerlach D, Stelzer C, Boryn LM, Rath M, Stark A (2013) Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339(6123):1074–1077. https://doi.org/10.1126/science.1232542

    Article  CAS  PubMed  Google Scholar 

  18. Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST (2012) Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150(2):279–290. https://doi.org/10.1016/j.cell.2012.05.043

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. McCullum EO, Williams BA, Zhang J, Chaput JC (2010) Random mutagenesis by error-prone PCR. Methods Mol Biol 634:103–109. https://doi.org/10.1007/978-1-60761-652-8_7

    Article  CAS  PubMed  Google Scholar 

  20. Chujo T, Yamazaki T, Kawaguchi T, Kurosaka S, Takumi T, Nakagawa S, Hirose T (2017) Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs. EMBO J 36(10):1447–1462. https://doi.org/10.15252/embj.201695848

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work is supported by the National Natural Science Foundation of China (20161310854, 31471219), the National Basic Research Program of China (2017YFA0504204, 2018YFA0107603), and the Center for Life Sciences at Tsinghua University. Y.Y. is supported by the Outstanding Postdoctoral Program of Tsinghua-Peking Joint Center for Life Sciences.

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Authors and Affiliations

  1. Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Bei**g, China

    Yafei Yin & **aohua Shen

Authors
  1. Yafei Yin
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  2. **aohua Shen
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Corresponding author

Correspondence to **aohua Shen .

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Editors and Affiliations

  1. Department for Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark

    Ulf Andersson Vang Ørom

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Yin, Y., Shen, X. (2020). Identification of cis-Elements for RNA Subcellular Localization Through REL-seq. In: Ørom, U. (eds) RNA-Chromatin Interactions. Methods in Molecular Biology, vol 2161. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0680-3_11

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  • DOI: https://doi.org/10.1007/978-1-0716-0680-3_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0679-7

  • Online ISBN: 978-1-0716-0680-3

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