A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa (2023)

Villalba de la Peña, M., Summanen, P. A. M., Liukkonen, M., & Kronholm, I. (2023). Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa. Genome Research, 33(4), 599-611. https://doi.org/10.1101/gr.276992.122

JYU-tekijät tai -toimittajat

Julkaisun tiedot

Julkaisun kaikki tekijät tai toimittajat: Villalba de la Peña, Mariana; Summanen, Pauliina A. M.; Liukkonen, Martta; Kronholm, Ilkka

Lehti tai sarja: Genome Research

ISSN: 1088-9051

eISSN: 1549-5469

Julkaisuvuosi: 2023

Ilmestymispäivä: 15.03.2023

Volyymi: 33

Lehden numero: 4

Artikkelin sivunumerot: 599-611

Kustantaja: Cold Spring Harbor Laboratory

Julkaisumaa: Yhdysvallat (USA)

Julkaisun kieli: englanti

DOI: https://doi.org/10.1101/gr.276992.122

Julkaisun avoin saatavuus: Avoimesti saatavilla

Julkaisukanavan avoin saatavuus: Osittain avoin julkaisukanava

Julkaisu on rinnakkaistallennettu (JYX): https://jyx.jyu.fi/handle/123456789/87189

Rinnakkaistallenteen verkko-osoite (pre-print): https://www.biorxiv.org/content/10.1101/2022.03.13.484164v4

Tiivistelmä

While mutation rates have been extensively studied, variation in mutation rates throughout the genome is poorly understood. To understand patterns of genetic variation, it is important to understand how mutation rates vary. Chromatin modifications may be an important factor in determining variation in mutation rates in eukaryotic genomes. To study variation in mutation rates, we performed a mutation accumulation experiment in the filamentous fungus Neurospora crassa, and sequenced the genomes of the 40 MA lines that had been propagated asexually for approximately 1015 [1003, 1026] mitoses. We detected 1322 mutations in total, and observed that the mutation rate was higher in regions of low GC, in domains of H3K9 trimethylation, in centromeric regions, and in domains of H3K27 trimethylation. The rate of single nucleotide mutations in euchromatin was 2.46 [2.19, 2.77] × 10-10. In contrast, the mutation rate in H3K9me3 domains was tenfold higher: 2.43 [2.25, 2.62] × 10-9. We also observed that the spectrum of single nucleotide mutations was different between H3K9me3 and euchromatic domains. Our statistical model of mutation rate variation predicted a moderate amount of extant genetic variation, suggesting that the mutation rate is an important factor in determining levels of natural genetic variation. Furthermore, we characterized mutation rates of structural variants, complex mutations, and the effect of local sequence context on the mutation rate. Our study highlights that chromatin modifications are associated with mutation rates, and accurate evolutionary inferences should take variation in mutation rates across the genome into account.

YSO-asiasanat: epigenetiikka; genomiikka; sienet; perinnöllisyystiede; perimä; mutaatiot

Vapaat asiasanat: fungi; mutation accumulation; genomics; epigenetics; H3K9 trimethylation; H3K27 trimethylation

Liittyvät organisaatiot

Hankkeet, joissa julkaisu on tehty

OKM-raportointi: Kyllä

Raportointivuosi: 2023

Alustava JUFO-taso: 3