Biology subjects

Rogaev, E. I.

Publications and source records attributed to Rogaev, E. I..

3 recordsLinked to original sources

bioRxiv2025

Genetic history of Rus'

The foundation of the first ancient Rus state occurred as a result of the consolidation of diverse communities inhabiting Eastern Europe during the second half of the first millennium CE. Historical sources imply that these communities mostly include East Slavs, whose settlement across a vast territory led to the emergence of the East Slavic/Rus culture within the Rus state. We generated genomic data for 200 medieval individuals from different locations to elucidate the origin and genetic structure of the Rus population during the early stages of the state formation. Our findings reveal a genetic continuum predominantly shaped by two key genetic groups: a broad Slavic-related continuity of different genetic subclusters of Rus occupying the enormous European Plain area, and a Fenno-Ugrian (Uralic)-related component in the Northern Rus region. Importantly, both groups have a shared genetic substrate inherited from preceding ancient Baltic region populations. To scale Scandinavian ("Viking") heritage, we traced minor Scandinavian genetic lineages that did not make up the dominating genetic stratum of the early Rus state. Our study presents the first comprehensive genomic image of the medieval Rus, highlighting the intricate cultural and genetic interactions between Slavic, Fenno-Ugrian, and other groups that formed the first Rus state affecting Europes history.

genomics↗

bioRxiv2021

Complete genomic and epigenetic maps of human centromeres

Existing human genome assemblies have almost entirely excluded highly repetitive sequences within and near centromeres, limiting our understanding of their sequence, evolution, and essential role in chromosome segregation. Here, we present an extensive study of newly assembled peri/centromeric sequences representing 6.2% (189.9 Mb) of the first complete, telomere-to-telomere human genome assembly (T2T-CHM13). We discovered novel patterns of peri/centromeric repeat organization, variation, and evolution at both large and small length scales. We also found that inner kinetochore proteins tend to overlap the most recently duplicated subregions within centromeres. Finally, we compared chromosome X centromeres across a diverse panel of individuals and uncovered structural, epigenetic, and sequence variation at single-base resolution across these regions. In total, this work provides an unprecedented atlas of human centromeres to guide future studies of their complex and critical functions as well as their unique evolutionary dynamics. One-sentence summaryDeep characterization of fully assembled human centromeres reveals their architecture and fine-scale organization, variation, and evolution.

genomics↗

bioRxiv2018

Classification and monomer-by-monomer annotation of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly

In the latest hg38 human genome assembly, centromeric gaps has been filled in by alpha satellite (AS) reference models (RMs) which are statistical representations of homogeneous higher-order repeat (HOR) arrays that make up the bulk of the centromeric regions. We studied these models to compose an atlas of human HORs where each monomer of a HOR could be characterized and represented by a number of its polymorphic sequence variants. We further used these data and HMMER sequence analysis platform to annotate AS HORs in the assembly. This led to discovery and annotation of a new type of low copy number highly divergent HORs which were not represented by RMs. The annotation can be viewed as UCSC Genome Browser custom track (the HOR-track) and used together with our previous annotation of AS SFs in the same assembly where each AS monomer can be viewed in its genomic context together with its classification into one of the 5 major SFs (the SF-track). To catalog the diversity of AS HORs in the human genome we introduced a new naming system. Each HOR received a name which showed its SF, chromosomal location and index number. Here we present the first installment of the HOR-track covering only the 17 HORs that belong to SF1 which forms live functional centromeres in chromosomes 1, 3, 5, 6, 7, 10, 12, 16 and 19 and also a large number of minor dead HOR domains, both homogeneous (pseudo) and divergent (relic). The 4 newly discovered divergent SF1 HORs have provided the missing links in SF1 early evolution and substantiated its partition into 2 generations, archaic and modern, which we reported earlier. Additionally, we demonstrated that monomer-by-monomer HOR annotation was useful for mapping and quantification of various structural variants of AS HORs which would be important for studies of inter-individual polymorphism of AS including centromeric functional epialleles.

bioinformatics↗