Abstract

The inability to digest lactose, due to lactase nonpersistence, is a common trait in adult mammals, except in certain human populations that exhibit lactase persistence. It is not known how the lactase gene is dramatically downregulated with age in most individuals but remains active in some individuals. We performed a comprehensive epigenetic study of human and mouse small intestines, by using chromosome-wide DNA-modification profiling and targeted bisulfite sequencing. Epigenetically controlled regulatory elements accounted for the differences in lactase mRNA levels among individuals, intestinal cell types and species. We confirmed the importance of these regulatory elements in modulating lactase mRNA levels by using CRISPR–Cas9-induced deletions. Genetic factors contribute to epigenetic changes occurring with age at the regulatory elements, because lactase-persistence and lactase-nonpersistence DNA haplotypes demonstrated markedly different epigenetic aging. Thus, genetic factors enable a gradual accumulation of epigenetic changes with age, thereby influencing phenotypic outcome.

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Acknowledgements

We thank A. Turinsky and L. Strug for statistical recommendations; T. Karvelis for help with sgRNA construction; M. Susic for technical assistance; A. Patterson, P. Kapranov and D. Swallow for comments on the manuscript; and F. Zhang (Broad Institute of MIT and Harvard University) for pX330 plasmid. This work was supported in part by the Canadian Institutes of Health Research (MOP-199170, MOP-119451 and MOP-77689), the US National Institutes of Health (MH088413 and DK085698), the Krembil Foundation and Brain Canada, to A.P. This work was also supported by the Canadian Centre for Computational Genomics (C3G), part of the Genome Innovation Network (GIN), funded by Genome Canada through Genome Quebec and Ontario Genomics, to M.B. A.P. is supported as the Tapscott Chair in Schizophrenia Studies, University of Toronto, Canada. E.K. was supported by a grant from the Research Council of Lithuania (MIP-045/2013). J.G. and K.K. were funded by a grant (MIP-14032) from the Research Council of Lithuania. V.L. was supported by a Canadian Institutes of Health Research Fellowship (200910MFE-211514-141430).

Author information

Author notes

    • Viviane Labrie
    •  & Orion J Buske

    These authors contributed equally to this work.

Affiliations

  1. Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.

    • Viviane Labrie
    • , Edward Oh
    • , Richie Jeremian
    • , Carolyn Ptak
    • , Akhil Nair
    • , Aiping Zhang
    • , Sasha Ebrahimi
    • , Gabriel Oh
    •  & Arturas Petronis
  2. Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.

    • Viviane Labrie
    •  & Arturas Petronis
  3. Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA.

    • Viviane Labrie
  4. Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

    • Orion J Buske
    •  & Michael Brudno
  5. Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada.

    • Orion J Buske
    •  & Michael Brudno
  6. Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.

    • Giedrius Gasiūnas
    •  & Virginijus Šikšnys
  7. Department of Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania.

    • Almantas Maleckas
  8. Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania.

    • Rūta Petereit
    • , Aida Žvirbliene
    • , Kęstutis Adamonis
    •  & Limas Kupčinskas
  9. Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania.

    • Aida Žvirbliene
    •  & Limas Kupčinskas
  10. Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.

    • Edita Kriukienė
  11. Institute of Mathematics and Informatics, Vilnius University, Vilnius, Lithuania.

    • Karolis Koncevičius
    •  & Juozas Gordevičius

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Contributions

The study was designed by V.L. and A.P., and directed and coordinated by V.L., M.B. and A.P. V.L., E.O., R.J. and C.P. planned and performed the experimental work. O.J.B. coordinated and performed the computational analysis. J.G. and K.K. contributed to the computational analysis of the microarrays. A.M., R.P., A.Ž., K.A. and L.K. collected the human jejunum surgical samples and other human tissues. G.G. and V.Š. prepared the CRISPR–Cas9n cell-line constructs, and R.J. and A.N. contributed to the CRISPR–Cas9n cell-line work. K.K. was involved in the haplotype-dependent epigenetic aging analysis. E.K. consulted on the mTAG approach. S.E., A.Z. and G.O. were involved in bisulfite padlock-probe design and preparation. The manuscript was written by V.L., O.J.B. and A.P., and was commented on by all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Arturas Petronis.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8, Supplementary Tables 1 and 2 and Supplementary Notes 1 and 2

Excel files

  1. 1.

    Supplementary Table 3

    sgRNAs and primer sequences used for the CRISPR-Cas9 deletions in mice and a human intestinal cell line.

  2. 2.

    Supplementary Table 4

    Bisulfite padlock probe sequences and barcode primers used for the high resolution DNA modification analysis at lactase gene region in humans and mice.

  3. 3.

    Supplementary Data Set 1

    Chromosome-wide scan of jejunal enterocytes identifies significant DNA modification differences between infant and adult mice.

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DOI

https://doi.org/10.1038/nsmb.3227

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