Cited by 618Chromosomal and Genetic VariationsGenomic variations and chromosomal abnormalitiesGenome Rearrangement Algorithms

Complete genomic and epigenetic maps of human centromeres

Open access
Altemose, Nicolas, Logsdon, Glennis A., Bzikadze, Andrey V., Sidhwani, Pragya, Langley, Sasha A., Caldas, Gina V., Hoyt, Savannah J., Uralsky, Lev +51 more·2022·Science

Published version of a preprint

Abstract

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

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1126/science.abl4178

Cites

164 of 164 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Altemose, N., Logsdon, G. A., Bzikadze, A. V., Sidhwani, P., Langley, S. A., Caldas, G. V., Hoyt, S. J., Uralsky, L., Ryabov, F. D., Shew, C. J., Sauria, M. E. G., Borchers, M., Gershman, A., Mikheenko, A., Shepelev, V. A., Dvorkina, T., Kunyavskaya, O., Vollger, M. R., Rhie, A., McCartney, A. M., Asri, M., Lorig-Roach, R., Shafin, K., Lucas, J. K., Aganezov, S., Olson, D., de Lima, L. G., Potapova, T., Hartley, G. A., Haukness, M., Kerpedjiev, P., Gusev, F., Tigyi, K., Brooks, S., Young, A., Nurk, S., Koren, S., Salama, S. R., Paten, B., Rogaev, E. I., Streets, A., Karpen, G. H., Dernburg, A. F., Sullivan, B. A., Straight, A. F., Wheeler, T. J., Gerton, J. L., Eichler, E. E., Phillippy, A. M., Timp, W., Dennis, M. Y., O’Neill, R. J., Zook, J. M., Schatz, M. C., Pevzner, P. A., Diekhans, M., Langley, C. H., Alexandrov, I. A., & Miga, K. H.
Affiliations
  • University of California, Berkeley (US)
  • University of Washington (US)
  • University of California San Diego (US)
  • Stanford University (US)
  • University of Connecticut (US)
  • Sirius University of Science and Technology (RU)
  • Moscow Polytechnic University (RU)
  • University of California, Davis (US)
  • Johns Hopkins University (US)
  • Stowers Institute for Medical Research (US)
  • St Petersburg University (RU)
  • Vavilov Institute of General Genetics (RU)
  • National Institutes of Health (US)
  • Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • University of California, Santa Cruz (US)
  • University of Montana (US)
  • Stowers Institute for Medical Research, Kansas City, MO, USA.
  • Reservoir Genomics, Oakland, CA.
  • Howard Hughes Medical Institute (US)
  • University of Massachusetts Chan Medical School (US)
  • Chan Zuckerberg Biohub San Francisco (US)
  • Lawrence Berkeley National Laboratory (US)
  • QB3 (US)
  • Duke University (US)
  • Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
  • National Institute of Standards and Technology (US)
  • Russian Academy of Sciences (RU)
Corresponding author
  • Logsdon, Glennis A.
  • Bzikadze, Andrey V.
  • Sidhwani, Pragya
  • Langley, Sasha A.
  • Caldas, Gina V.
  • Alexandrov, Ivan A.
  • Miga, Karen H.
Venue
Science
Published
2022-04
Volume
376
Issue
6588
Pages
eabl4178-eabl4178
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
OpenAlex
W4220937793
Cited by
618
References
164
Citations by year
2026: 127 · 2025: 160 · 2024: 139 · 2023: 119 · 2022: 65 · 2021: 8
FWCI
69.95
Type
journal article
Language
en
Open access
Licence
public-domain
Locations
  • Science (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, public-domain)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
Funders
  • National Science Foundation (1732253, 1627442, 1643825, 1613806, P20GM103546, 1758800)
  • Howard Hughes Medical Institute
  • Damon Runyon Cancer Research Foundation
  • Russian Foundation for Basic Research (18-29-, 18-29-13051)
  • Saint Petersburg State University (51555639, PURE 51555639)
  • Russian Science Foundation (19-75-30039)
  • National Institutes of Health (GM R35, NIH-R01, OT2OD026682, U01 1U01HG010971, DK106766)
  • National Institute of Standards and Technology
  • National Institute on Aging (R01AG054712)
  • National Institute of Mental Health (DP2 OD025824, DP2MH119424)
  • National Human Genome Research Institute (R01HG010329, R01HG010485, R21HG010548, R21 1R21HG010548-01, HG009190, U01HG010971, U41HG007234, R01HG009190, F31HG011205, U01 1U01HG010971, R01HG011274, U01HG010961, U24HG010263, R01HG002385, U24HG011853, U24HG007234, U24HG006620, R01HG010169, R01HG002939, U41HG010972, U24HG010136)
  • National Cancer Institute (R21CA240199, R21CA238758, U01CA253481, R01CA266339)
  • National Institute of General Medical Sciences (GM134558, T32GM007445, R01GM117420, R01GM132600, R01GM123312, R01GM129263, F32GM134558, P20GM103546, R35GM139653, R01GM124041, R01GM074728)
  • National Institute of Diabetes and Digestive and Kidney Diseases (NIH R01, R24DK106766)
  • Division of Biological Infrastructure
  • Division of Integrative Organismal Systems
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
human centromeres, pericentromeric repeats, centromeric repeats, telomere-to-telomere genome assembly, T2T-CHM13, repetitive DNA, structural rearrangement, centromere evolution, centromere position, epigenetic variation, chromosome segregation
MeSH terms
Centromere, Chromosome Mapping, Humans, Repetitive Sequences, Nucleic Acid, Genome, Human, Evolution, Molecular, Genomics, Epigenesis, Genetic

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review