in

DNA methylation profiling in mummified human remains from the eighteenth-century

[adace-ad id="91168"]
  • 1.

    Orlando, L., Gilbert, M. T. & Willerslev, E. Reconstructing ancient genomes and epigenomes. Nat. Rev. Genet. 16, 395–408 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 2.

    Smith, Z. D. & Meissner, A. DNA methylation: Roles in mammalian development. Nat. Rev. Genet. 14, 204–220 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 3.

    Schmidt, M., Maie, T., Dahl, E., Costa, I. G. & Wagner, W. Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites. BMC Biol. 18, 178 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 4.

    Moss, J. et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat. Commun. 9, 5068 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 5.

    Shen, H. & Laird, P. W. Interplay between the cancer genome and epigenome. Cell 153, 38–55 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 6.

    Koch, C. M. & Wagner, W. Epigenetic-aging-signature to determine age in different tissues. Aging (Albany N.Y.) 3, 1018–1027 (2011).

    CAS 

    Google Scholar 

  • 7.

    Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 14, R115 (2013).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 8.

    Weidner, C. I. et al. Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol. 15, R24 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 9.

    Dabney, J., Meyer, M. & Paabo, S. Ancient DNA damage. Cold Spring Harb. Perspect Biol. 5, a012567 (2013).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 10.

    Gokhman, D. et al. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science 344, 523–527 (2014).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 11.

    Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 12.

    Bibikova, M. et al. High density DNA methylation array with single CpG site resolution. Genomics 98, 288–295 (2011).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 13.

    Pap, I., Susa, E. & Joszsa, L. Mummies from the 18–19th century Domanical Church of Vác, Hungary. Acta Biol. Szegediensis 42, 107–112 (1997).

    Google Scholar 

  • 14.

    Donoghue, H. D., Pap, I., Szikossy, I. & Spigelman, M. The Vác Mummy Project: Investigation of 265 eighteenth-century mummified remains from the TB pandemic era. In The Handbook of Mummy Studies (eds Shin, D. H. & Bianucci, R.) 1–30 (Springer, 2021).

    Google Scholar 

  • 15.

    Hotz, G. et al. Der rätselhafte Mumienfund aus der Barfüsserkirche in Basel. Ein aussergewöhnliches Beispiel interdisziplinärer Familienforschung. Jahrbuch der Schweizerischen Gesellschaft für Familienforschung 2018, 1–30 (2018).

    Google Scholar 

  • 16.

    Hotz, G. Das Rätsel der Anna Catharina Bischoff. Spektrum der Wissenschaft 3, 76–81 (2018).

    Google Scholar 

  • 17.

    Zhou, W., Triche, T. J. Jr., Laird, P. W. & Shen, H. SeSAMe: Reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. Nucleic Acids Res. 46, e123 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 18.

    Triche, T. J., Weisenberger, D. J., Van Den Berg, D., Laird, P. W. & Siegmund, K. D. low-level processing of illumina infinium DNA methylation beadarrays. Nucleic Acids Res. 41, e90 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 19.

    Ruiz-Hernandez, A. et al. Environmental chemicals and DNA methylation in adults: A systematic review of the epidemiologic evidence. Clin. Epigenet. 7, 55 (2015).

    Article 
    CAS 

    Google Scholar 

  • 20.

    Pedersen, J. S. et al. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. 24, 454–466 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 21.

    Gaudin, M. & Desnues, C. Hybrid capture-based next generation sequencing and its application to human infectious diseases. Front. Microbiol. 9, 2924 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 22.

    Knapp, M. & Hofreiter, M. Next generation sequencing of ancient DNA: Requirements, strategies and perspectives. Genes (Basel) 1, 227–243 (2010).

    CAS 
    Article 

    Google Scholar 

  • 23.

    Koop, B. E. et al. Postmortem age estimation via DNA methylation analysis in buccal swabs from corpses in different stages of decomposition—A “proof of principle” study. Int. J. Legal Med. 135, 167–173 (2021).

    PubMed 
    Article 

    Google Scholar 

  • 24.

    Joehanes, R. et al. Epigenetic signatures of cigarette smoking. Circ. Cardiovasc. Genet. 9, 436–447 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 25.

    Bozic, T. et al. Investigation of measurable residual disease in acute myeloid leukemia by DNA methylation patterns. Leukemia https://doi.org/10.1038/s41375-021-01316-z (2021).

    Article 
    PubMed 

    Google Scholar 

  • 26.

    Pap, I. et al. 18–19th century tuberculosis in naturally mummified individuals (Vác, Hungary). In Tuberculosis Past and Present (eds Pálfi, G. et al.) 421–428 (Golden Books/Tuberculosis Foundation, 1999).

    Google Scholar 

  • 27.

    Kreissl Lonfat, B. M., Kaufmann, I. M. & Ruhli, F. A code of ethics for evidence-based research with ancient human remains. Anat. Rec. (Hoboken) 298, 1175–1181 (2015).

    Article 

    Google Scholar 

  • 28.

    Maixner, F. et al. The Iceman’s last meal consisted of fat, wild meat, and cereals. Curr. Biol. 28, 2348–2355 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 29.

    Tang, J. N. et al. An effective method for isolation of DNA from pig faeces and comparison of five different methods. J. Microbiol. Methods 75, 432–436 (2008).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 30.

    Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 31.

    Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, 5448 (2010).

    Article 

    Google Scholar 

  • 32.

    Rosenbloom, K. R. et al. The UCSC genome browser database: 2015 update. Nucleic Acids Res. 43, D670–D681 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 33.

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 34.

    Peltzer, A. et al. EAGER: Efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 35.

    Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. & Orlando, L. mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 36.

    Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 37.

    Huson, D. H. et al. MEGAN Community edition—Interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12, e1004957 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 38.

    Ondov, B. D., Bergman, N. H. & Phillippy, A. M. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 12, 385 (2011).

    Article 

    Google Scholar 

  • 39.

    Xu, Z., Langie, S. A., De Boever, P., Taylor, J. A. & Niu, L. RELIC: A novel dye-bias correction method for illumina methylation beadchip. BMC Genomics 18, 4 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 40.

    Lee, D. D. & Seung, H. S. Algorithms for non-negative matrix factorization. Adv. Neural. Inf. Process. Syst. 13(13), 556–562 (2001).

    Google Scholar 

  • 41.

    Schmidt, M., Maié, T., Dahl, E., Costa, I. G. & Wagner, W. Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites. BMC Biol. 34, 1969 (2020).

    Google Scholar 

  • 42.

    Frobel, J. et al. Leukocyte counts based on DNA methylation at individual cytosines. Clin. Chem. 64, 566–575 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 


  • Source: Ecology - nature.com

    A new way to detect the SARS-CoV-2 Alpha variant in wastewater

    Inaugural fund supports early-stage collaborations between MIT and Jordan