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  • 1.
    Akkuratov, Evgeny E.
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. St Petersburg State Univ, Inst Translat Biomed, St Petersburg, Russia.
    Gelfand, Mikhail S.
    Skolkovo Inst Sci & Technol, Ctr Data Intens Biomed & Biotechnol, Moscow, Russia.;Russian Acad Sci, Inst Informat Transmiss Problems, Moscow, Russia.;Natl Res Univ, Higher Sch Econ, Fac Comp Sci, Moscow, Russia.;MM Lomonosov Moscow State Univ, Dept Bioengn & Bioinformat, Moscow, Russia..
    Khrameeva, Ekaterina E.
    Skolkovo Inst Sci & Technol, Ctr Data Intens Biomed & Biotechnol, Moscow, Russia.;Russian Acad Sci, Inst Informat Transmiss Problems, Moscow, Russia..
    Neanderthal and Denisovan ancestry in Papuans: A functional study2018In: Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, E-ISSN 1757-6334, Vol. 16, no 2, article id 1840011Article in journal (Refereed)
    Abstract [en]

    Sequencing of complete nuclear genomes of Neanderthal and Denisovan stimulated studies about their relationship with modern humans demonstrating, in particular, that DNA alleles from both Neanderthal and Denisovan genomes are present in genomes of modern humans. The Papuan genome is a unique object because it contains both Neanderthal and Denisovan alleles. Here, we have shown that the Papuan genomes contain different gene functional groups inherited from each of the ancient people. The Papuan genomes demonstrate a relative prevalence of Neanderthal alleles in genes responsible for the regulation of transcription and neurogenesis. The enrichment of specific functional groups with Denisovan alleles is less pronounced; these groups are responsible for bone and tissue remodeling. This analysis shows that introgression of alleles from Neanderthals and Denisovans to Papuans occurred independently and retention of these alleles may carry specific adaptive advantages.

  • 2.
    Seplyarskiy, Vladimir B.
    et al.
    Harvard Med Sch, Brigham & Womens Hosp, Div Genet, Boston, MA USA.;Harvard Med Sch, Dept Biomed Informat, Boston, MA USA.;Russian Acad Sci, Inst Informat Transmiss Problems, Kharkevich Inst, Moscow, Russia..
    Akkuratov, Evgeny E.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. St Petersburg State Univ, Inst Translat Biomed, St Petersburg, Russia.;Royal Inst Technol, Dept Appl Phys, Sci Life Lab, Stockholm, Sweden..
    Akkuratova, Natalia
    St Petersburg State Univ, Inst Translat Biomed, St Petersburg, Russia..
    Andrianova, Maria A.
    Skolkovo Inst Sci & Technol, Skolkovo, Russia..
    Nikolaev, Sergey I.
    Univ Paris Saclay, INSERM, U981, Gustave Roussy Canc Campus, Villejuif, France.;Univ Paris 07, St Louis Hosp, Dept Dermatol & Venereol, Paris, France..
    Bazykin, Georgii A.
    Russian Acad Sci, Inst Informat Transmiss Problems, Kharkevich Inst, Moscow, Russia.;Skolkovo Inst Sci & Technol, Skolkovo, Russia..
    Adameyko, Igor
    Karolinska Inst, Dept Physiol & Pharmacol, Stockholm, Sweden.;Med Univ Vienna, Ctr Brain Res, Vienna, Austria..
    Sunyaev, Shamil R.
    Harvard Med Sch, Brigham & Womens Hosp, Div Genet, Boston, MA USA.;Harvard Med Sch, Dept Biomed Informat, Boston, MA USA..
    Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations2019In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 51, no 1, p. 36-+Article in journal (Refereed)
    Abstract [en]

    Studies in experimental systems have identified a multitude of mutational mechanisms including DNA replication infidelity and DNA damage followed by inefficient repair or replicative bypass. However, the relative contributions of these mechanisms to human germline mutation remain unknown. Here, we show that error-prone damage bypass on the lagging strand plays a major role in human mutagenesis. Transcription-coupled DNA repair removes lesions on the transcribed strand; lesions on the non-transcribed strand are preferentially converted into mutations. In human polymorphism we detect a striking similarity between mutation types predominant on the non-transcribed strand and on the strand lagging during replication. Moreover, damage-induced mutations in cancers accumulate asymmetrically with respect to the direction of replication, suggesting that DNA lesions are resolved asymmetrically. We experimentally demonstrate that replication delay greatly attenuates the mutagenic effect of ultraviolet irradiation, confirming that replication converts DNA damage into mutations. We estimate that at least 10% of human mutations arise due to DNA damage.

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