Complete genomic and epigenetic maps of human centromeres

Science, Journal Year: 2022, Volume and Issue: 376(6588)

Published: March 31, 2022

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric centromeric repeats, constitute 6.2% the (189.9 megabases). Detailed maps these regions revealed multimegabase structural rearrangements, including in active repeat arrays. Analysis centromere-associated uncovered strong relationship between position centromere evolution surrounding DNA through layered expansions. Furthermore, comparisons X centromeres across diverse panel individuals illuminated high degrees structural, epigenetic, sequence variation complex rapidly evolving regions.

Language: Английский

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From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Science, Journal Year: 2022, Volume and Issue: 376(6588)

Published: March 31, 2022

Mobile elements and repetitive genomic regions are sources of lineage-specific innovation uniquely fingerprint individual genomes. Comprehensive analyses such repeat elements, including those found in more complex the genome, require a complete, linear genome assembly. We present de novo discovery annotation T2T-CHM13 human reference genome. identified previously unknown satellite arrays, expanded catalog variants families for repeats mobile characterized classes composite repeats, located retroelement transduction events. detected nascent transcription delineated CpG methylation profiles to define structure transcriptionally active retroelements humans, centromeres. These data expand our insight into diversity, distribution, evolution that have shaped

Language: Английский

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The complete sequence of a human Y chromosome

Nature, Journal Year: 2023, Volume and Issue: 621(7978), P. 344 - 354

Published: Aug. 23, 2023

Language: Английский

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Telomere-to-telomere assembly of diploid chromosomes with Verkko

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(10), P. 1474 - 1482

Published: Feb. 16, 2023

Language: Английский

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Cycles of satellite and transposon evolution in Arabidopsis centromeres

Nature, Journal Year: 2023, Volume and Issue: 618(7965), P. 557 - 565

Published: May 17, 2023

Language: Английский

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Evolutionary analysis of a complete chicken genome

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(8)

Published: Feb. 13, 2023

Microchromosomes are prevalent in nonmammalian vertebrates [P. D. Waters et al. , Proc. Natl. Acad. Sci. U.S.A. 118 (2021)], but a few of them missing bird genome assemblies. Here, we present new chicken reference containing all autosomes, Z and W chromosome, with gaps closed except for the W. We identified ten small microchromosomes (termed dot chromosomes) distinct sequence epigenetic features, among which six were newly assembled. Those chromosomes exhibit extremely high GC content level DNA methylation enriched housekeeping genes. The pericentromeric heterochromatin is disproportionately large continues to expand proliferation satellite testis-expressed Our analyses revealed that 41-bp CNM repeat frequently forms higher-order repeats (HORs) at centromeres acrocentric chromosomes. centromere core regions where kinetochore attaches often encompass telomeric (TTAGGG)n, one chromosomes, recruits an endogenous retrovirus (ERV). further demonstrate chromosome shares some common features having arrays hypermethylated tandem repeats. Finally, using complete models, reconstructed fine picture chordate karyotype evolution, revealing frequent chromosomal fusions before after vertebrate whole-genome duplications. characterization shed insights into understanding evolution biology.

Language: Английский

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The variation and evolution of complete human centromeres

Nature, Journal Year: 2024, Volume and Issue: 629(8010), P. 136 - 145

Published: April 3, 2024

Abstract Human centromeres have been traditionally very difficult to sequence and assemble owing their repetitive nature large size 1 . As a result, patterns of human centromeric variation models for evolution function remain incomplete, despite being among the most rapidly mutating regions 2,3 Here, using long-read sequencing, we completely sequenced assembled all from second genome compared it finished reference 4,5 We find that two sets show at least 4.1-fold increase in single-nucleotide when with unique flanks vary up 3-fold size. Moreover, 45.8% cannot be reliably aligned standard methods emergence new α-satellite higher-order repeats (HORs). DNA methylation CENP-A chromatin immunoprecipitation experiments 26% differ kinetochore position by >500 kb. To understand evolutionary change, selected six chromosomes 31 orthologous common chimpanzee, orangutan macaque genomes. Comparative analyses reveal nearly complete turnover HORs, characteristic idiosyncratic changes HORs each species. Phylogenetic reconstruction haplotypes supports limited no recombination between short (p) long (q) arms across reveals novel share monophyletic origin, providing strategy estimate rate saltatory amplification mutation DNA.

Language: Английский

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Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Nature, Journal Year: 2023, Volume and Issue: 621(7978), P. 355 - 364

Published: Aug. 23, 2023

Language: Английский

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The complete sequence and comparative analysis of ape sex chromosomes

Nature, Journal Year: 2024, Volume and Issue: 630(8016), P. 401 - 411

Published: May 29, 2024

Abstract Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males females. The crucial for male reproduction, with deletions being linked to infertility 1 . vital reproduction cognition 2 Variation mating patterns brain function among apes suggests corresponding differences their chromosomes. However, owing repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using methodology developed telomere-to-telomere (T2T) human genome, we produced gapless assemblies of five great (bonobo ( Pan paniscus ), chimpanzee troglodytes western lowland gorilla Gorilla Bornean orangutan Pongo pygmaeus ) Sumatran abelii )) a lesser (the siamang gibbon Symphalangus syndactylus )), untangled intricacies evolution. Compared chromosomes, vary greatly size low alignability high levels structural rearrangements—owing accumulation lineage-specific ampliconic regions, palindromes, transposable elements satellites. Many genes expand multi-copy families some evolve under purifying selection. Thus, exhibits dynamic evolution, whereas more stable. Mapping short-read sequencing data these revealed diversity selection on than 100 individual apes. These are expected inform evolution conservation genetics non-human apes, all endangered species.

Language: Английский

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Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing

Nature Methods, Journal Year: 2023, Volume and Issue: 20(1), P. 12 - 16

Published: Jan. 1, 2023

Language: Английский

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