TY - JOUR

T1 - Automated annotation of human centromeres with HORmon

AU - Kunyavskaya, Olga

AU - Dvorkina, Tatiana

AU - Bzikadze, Andrey V

AU - Alexandrov, Ivan A

AU - Pevzner, Pavel A

N1 - © 2022 Kunyavskaya et al.; Published by Cold Spring Harbor Laboratory Press.

PY - 2022/6/1

Y1 - 2022/6/1

N2 - Recent advances in long-read sequencing opened a possibility to address the long-standing questions about the architecture and evolution of human centromeres. They also emphasized the need for centromere annotation (partitioning human centromeres into monomers and higher-order repeats [HORs]). Although there was a half-century-long series of semi-manual studies of centromere architecture, a rigorous centromere annotation algorithm is still lacking. Moreover, an automated centromere annotation is a prerequisite for studies of genetic diseases associated with centromeres and evolutionary studies of centromeres across multiple species. Although the monomer decomposition (transforming a centromere into a monocentromere written in the monomer alphabet) and the HOR decomposition (representing a monocentromere in the alphabet of HORs) are currently viewed as two separate problems, we show that they should be integrated into a single framework in such a way that HOR (monomer) inference affects monomer (HOR) inference. We thus developed the HORmon algorithm that integrates the monomer/HOR inference and automatically generates the human monomers/HORs that are largely consistent with the previous semi-manual inference.

AB - Recent advances in long-read sequencing opened a possibility to address the long-standing questions about the architecture and evolution of human centromeres. They also emphasized the need for centromere annotation (partitioning human centromeres into monomers and higher-order repeats [HORs]). Although there was a half-century-long series of semi-manual studies of centromere architecture, a rigorous centromere annotation algorithm is still lacking. Moreover, an automated centromere annotation is a prerequisite for studies of genetic diseases associated with centromeres and evolutionary studies of centromeres across multiple species. Although the monomer decomposition (transforming a centromere into a monocentromere written in the monomer alphabet) and the HOR decomposition (representing a monocentromere in the alphabet of HORs) are currently viewed as two separate problems, we show that they should be integrated into a single framework in such a way that HOR (monomer) inference affects monomer (HOR) inference. We thus developed the HORmon algorithm that integrates the monomer/HOR inference and automatically generates the human monomers/HORs that are largely consistent with the previous semi-manual inference.

KW - Algorithms

KW - Centromere/genetics

KW - Humans

UR - http://www.scopus.com/inward/record.url?scp=85133102904&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/efd778d5-4d79-3dae-99c4-59e4e4c320e5/

U2 - 10.1101/gr.276362.121

DO - 10.1101/gr.276362.121

M3 - Article

C2 - 35545449

VL - 32

SP - 1137

EP - 1151

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 6

ER -