Skip to main content
SpringerLink
Log in

Identification of Imprinted Loci by Transcriptome Sequencing

  • Protocol
  • First Online:
Genomic Imprinting

Part of the book series: Methods in Molecular Biology ((MIMB,volume 925))

Abstract

Enabled by high-throughput technologies that are capable of generating millions of sequencing reads, transcriptome sequencing is emerging as an important approach for mapping allelic imbalance (AI), where transcription is biased toward one allele in a diploid system. AI is identified by counting sequencing reads that map to genomic regions containing heterozygous SNPs, where the base identity of the SNP is used to distinguish allelic origin. Genomic imprinting is a special case of AI where bias is toward parental sex and can be identified by transcriptome sequencing of systems that represent reciprocally inherited loci. The focus of this protocol is on experimental design, analysis, and interpretation of genomic imprint discovery using whole transcriptome sequencing.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Cattanach BM, Kirk M (1985) Differential activity of maternally and paternally derived chromosome regions in mice. Nature 315:496–498

    Article  PubMed  CAS  Google Scholar 

  2. Surani MA, Reik W, Allen ND (1988) Transgenes as molecular probes for genomic imprinting. Trends Genet 4:59–62

    Article  PubMed  CAS  Google Scholar 

  3. Nicholls RD, Knoll JH, Butler MG, Karam S, Lalande M (1989) Genetic imprinting suggested by maternal heterodisomy in nondeletion Prader-Willi syndrome. Nature 342:281–285

    Article  PubMed  CAS  Google Scholar 

  4. Choi JD, Underkoffler LA, Collins JN, Marchegiani SM, Terry NA, Beechey CV, Oakey RJ (2001) Microarray expression profiling of tissues from mice with uniparental duplications of chromosomes 7 and 11 to identify imprinted genes. Mamm Genome 12:758–764

    Article  PubMed  CAS  Google Scholar 

  5. Mizuno Y, Sotomaru Y, Katsuzawa Y, Kono T, Meguro M, Oshimura M, Kawai J, Tomaru Y, Kiyosawa H, Nikaido I, Amanuma H, Hayashizaki Y, Okazaki Y (2002) Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray. Biochem Biophys Res Commun 290:1499–1505

    Article  PubMed  CAS  Google Scholar 

  6. Plass C, Shibata H, Kalcheva I, Mullins L, Kotelevtseva N, Mullins J, Kato R, Sasaki H, Hirotsune S, Okazaki Y, Held WA, Hayashizaki Y, Chapman VM (1996) Identification of Grf1 on mouse chromosome 9 as an imprinted gene by RLGS-M. Nat Genet 14:106–109

    Article  PubMed  CAS  Google Scholar 

  7. Morcos L, Ge B, Koka V, Lam KC, Pokholok DK, Gunderson KL, Montpetit A, Verlaan DJ, Pastinen T (2011) Genome-wide assessment of imprinted expression in human cells. Genome Biol 12:R25

    Article  PubMed  CAS  Google Scholar 

  8. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    Article  PubMed  CAS  Google Scholar 

  9. http://www.illumina.com

  10. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464:768–772

    Article  PubMed  CAS  Google Scholar 

  11. Morison IM, Ramsay JP, Spencer HG (2005) A census of mammalian imprinting. Trends Genet 21:457–465

    Article  PubMed  CAS  Google Scholar 

  12. Babak T, Deveale B, Armour C, Raymond C, Cleary MA, van der Kooy D, Johnson JM, Lim LP (2008) Global survey of genomic imprinting by transcriptome sequencing. Curr Biol 18:1735–1741

    Article  PubMed  CAS  Google Scholar 

  13. Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, Dulac C (2010) High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science (New York, NY) 329:643–648

    Article  CAS  Google Scholar 

  14. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG (2008) Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One 3:e3839

    Article  PubMed  Google Scholar 

  15. Babak T, Garrett-Engele P, Armour CD, Raymond CK, Keller MP, Chen R, Rohl CA, Johnson JM, Attie AD, Fraser HB, Schadt EE (2010) Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation. BMC Genomics 11:473

    Article  PubMed  Google Scholar 

  16. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (New York, NY) 320:1344–1349

    Article  CAS  Google Scholar 

  17. Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7:709–715

    Article  PubMed  CAS  Google Scholar 

  18. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37:e123

    Article  PubMed  Google Scholar 

  19. Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, Shah JK, Dey J, Rohl CA, Johnson JM, Raymond CK (2009) Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat Methods 6:647–649

    Article  PubMed  CAS  Google Scholar 

  20. Fontanillas P, Landry CR, Wittkopp PJ, Russ C, Gruber JD, Nusbaum C, Hartl DL (2010) Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Mol Ecol 19(Suppl 1):212–227

    Article  PubMed  Google Scholar 

  21. http://www.novocraft.com/main/index.php

  22. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ (2010) The UCSC Genome Browser database: update. Nucleic Acids Res 38:D613–D619

    Article  PubMed  CAS  Google Scholar 

  23. http://www.sanger.ac.uk/resources/mouse/genomes/

  24. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34:816–834

    Article  PubMed  Google Scholar 

  25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England) 25:2078–2079

    Article  Google Scholar 

  26. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

    Article  PubMed  CAS  Google Scholar 

  27. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19:1124–1132

    Article  PubMed  CAS  Google Scholar 

  28. Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics (Oxford, England) 25:3207–3212

    Article  CAS  Google Scholar 

  29. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England) 25:1754–1760

    Article  CAS  Google Scholar 

  30. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (Oxford, England) 25:1966–1967

    Article  CAS  Google Scholar 

  31. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biology, Stanford University, Stanford, CA, USA

    Tomas Babak

Authors
  1. Tomas Babak
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tomas Babak .

Editor information

Editors and Affiliations

  1. School of Medicine, Fels Institute, Temple University, N. Broad Street 3307, Philadelphia, 19140, Pennsylvania, USA

    Nora Engel

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Babak, T. (2012). Identification of Imprinted Loci by Transcriptome Sequencing. In: Engel, N. (eds) Genomic Imprinting. Methods in Molecular Biology, vol 925. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-011-3_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-011-3_6

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-010-6

  • Online ISBN: 978-1-62703-011-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation