Literature DB >> 35357911

Complete genomic and epigenetic maps of human centromeres.

Glennis A Logsdon1, Andrey V Bzikadze2, Pragya Sidhwani3, Sasha A Langley4, Gina V Caldas4, Nicolas Altemose4, Savannah J Hoyt5,6, Lev Uralsky7,8, Fedor D Ryabov9, Colin J Shew10, Michael E G Sauria11, Matthew Borchers12, Ariel Gershman13, Alla Mikheenko14, Valery A Shepelev8, Tatiana Dvorkina14, Olga Kunyavskaya14, Mitchell R Vollger1, Arang Rhie15, Ann M McCartney15, Mobin Asri16, Ryan Lorig-Roach16, Kishwar Shafin16, Julian K Lucas16, Sergey Aganezov17, Daniel Olson18, Leonardo Gomes de Lima12, Tamara Potapova12, Gabrielle A Hartley5,6, Marina Haukness16, Peter Kerpedjiev19, Fedor Gusev8, Kristof Tigyi16,20, Shelise Brooks21, Alice Young21, Sergey Nurk15, Sergey Koren15, Sofie R Salama16,20, Benedict Paten16,22, Evgeny I Rogaev7,8,23,24, Aaron Streets25,26, Gary H Karpen4,27, Abby F Dernburg4,20,28, Beth A Sullivan29, Aaron F Straight3, Travis J Wheeler18, Jennifer L Gerton12,30, Evan E Eichler1,20, Adam M Phillippy15, Winston Timp13,31, Megan Y Dennis10, Rachel J O'Neill5,6, Justin M Zook32, Michael C Schatz17, Pavel A Pevzner33, Mark Diekhans16, Charles H Langley34, Ivan A Alexandrov8,14,35, Karen H Miga16,22.   

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.

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Mesh：

Year:  2022        PMID： 35357911      PMCID： PMC9233505          DOI： 10.1126/science.abl4178

Source DB:  PubMed          Journal:  Science        ISSN： 0036-8075            Impact factor:   63.714


  86 in total

1.  Chromosome-specific subsets of human alpha satellite DNA: analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat.

Authors:  H F Willard; J S Waye
Journal:  J Mol Evol       Date:  1987       Impact factor: 2.395

2.  Sequence relationships of three human satellite DNAs.

Authors:  J Prosser; M Frommer; C Paul; P C Vincent
Journal:  J Mol Biol       Date:  1986-01-20       Impact factor: 5.469

3.  Chromosomal localization of human satellites 2 and 3 by a FISH method using oligonucleotides as probes.

Authors:  I Tagarro; A M Fernández-Peralta; J J González-Aguilera
Journal:  Hum Genet       Date:  1994-04       Impact factor: 4.132

Review 4.  Alpha satellite DNA biology: finding function in the recesses of the genome.

Authors:  Shannon M McNulty; Beth A Sullivan
Journal:  Chromosome Res       Date:  2018-07-05       Impact factor: 5.239

5.  Segmental duplications and their variation in a complete human genome.

Authors:  Mitchell R Vollger; Xavi Guitart; Philip C Dishuck; Ludovica Mercuri; William T Harvey; Ariel Gershman; Mark Diekhans; Arvis Sulovari; Katherine M Munson; Alexandra P Lewis; Kendra Hoekzema; David Porubsky; Ruiyang Li; Sergey Nurk; Sergey Koren; Karen H Miga; Adam M Phillippy; Winston Timp; Mario Ventura; Evan E Eichler
Journal:  Science       Date:  2022-04-01       Impact factor: 63.714

6.  Human satellite I sequences include a male specific 2.47 kb tandemly repeated unit containing one Alu family member per repeat.

Authors:  M Frommer; J Prosser; P C Vincent
Journal:  Nucleic Acids Res       Date:  1984-03-26       Impact factor: 16.971

7.  The structure, function and evolution of a complete human chromosome 8.

Authors:  Glennis A Logsdon; Mitchell R Vollger; PingHsun Hsieh; Yafei Mao; Mikhail A Liskovykh; Sergey Koren; Sergey Nurk; Ludovica Mercuri; Philip C Dishuck; Arang Rhie; Leonardo G de Lima; Tatiana Dvorkina; David Porubsky; William T Harvey; Alla Mikheenko; Andrey V Bzikadze; Milinn Kremitzki; Tina A Graves-Lindsay; Chirag Jain; Kendra Hoekzema; Shwetha C Murali; Katherine M Munson; Carl Baker; Melanie Sorensen; Alexandra M Lewis; Urvashi Surti; Jennifer L Gerton; Vladimir Larionov; Mario Ventura; Karen H Miga; Adam M Phillippy; Evan E Eichler
Journal:  Nature       Date:  2021-04-07       Impact factor: 69.504

8.  The evolutionary origin of man can be traced in the layers of defunct ancestral alpha satellites flanking the active centromeres of human chromosomes.

Authors:  Valery A Shepelev; Alexander A Alexandrov; Yuri B Yurov; Ivan A Alexandrov
Journal:  PLoS Genet       Date:  2009-09-11       Impact factor: 5.917

Review 9.  The cellular mechanisms and consequences of centromere drive.

Authors:  Lisa E Kursel; Harmit S Malik
Journal:  Curr Opin Cell Biol       Date:  2018-02-16       Impact factor: 8.382

10.  The octamer is the major form of CENP-A nucleosomes at human centromeres.

Authors:  Dan Hasson; Tanya Panchenko; Kevan J Salimian; Mishah U Salman; Nikolina Sekulic; Alicia Alonso; Peter E Warburton; Ben E Black
Journal:  Nat Struct Mol Biol       Date:  2013-05-05       Impact factor: 15.369
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  23 in total

1.  The first complete human genome.

Authors:  John T Lovell; Jane Grimwood
Journal:  Nature       Date:  2022-06       Impact factor: 49.962

2.  A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics.

Authors:  Yafei Mao; Guojie Zhang
Journal:  Nat Methods       Date:  2022-06       Impact factor: 28.547

Review 3.  mRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly.

Authors:  Tristan V de Jong; Hao Chen; Wesley A Brashear; Kelli J Kochan; Andrew E Hillhouse; Yaming Zhu; Isha S Dhande; Elizabeth A Hudson; Mary H Sumlut; Melissa L Smith; Theodore S Kalbfleisch; Peter A Doris
Journal:  Physiol Genomics       Date:  2022-05-11       Impact factor: 4.297

Review 4.  Satellite DNAs and human sex chromosome variation.

Authors:  Monika Cechova; Karen H Miga
Journal:  Semin Cell Dev Biol       Date:  2022-05-27       Impact factor: 7.499

5.  Epigenetic patterns in a complete human genome.

Authors:  Ariel Gershman; Michael E G Sauria; Xavi Guitart; Mitchell R Vollger; Paul W Hook; Savannah J Hoyt; Miten Jain; Alaina Shumate; Roham Razaghi; Sergey Koren; Nicolas Altemose; Gina V Caldas; Glennis A Logsdon; Arang Rhie; Evan E Eichler; Michael C Schatz; Rachel J O'Neill; Adam M Phillippy; Karen H Miga; Winston Timp
Journal:  Science       Date:  2022-04-01       Impact factor: 63.714

6.  Enrichment of centromeric DNA from human cells.

Authors:  Riccardo Gamba; Giulia Mazzucco; Therese Wilhelm; Leonid Velikovsky; Catalina Salinas-Luypaert; Florian Chardon; Julien Picotto; Mylène Bohec; Sylvain Baulande; Ylli Doksani; Daniele Fachinetti
Journal:  PLoS Genet       Date:  2022-07-19       Impact factor: 6.020

7.  Epigenetic Signatures of Centrosomes Are Novel Targets in Cancer Diagnosis: Insights from an Analysis of the Cancer Genome Atlas.

Authors:  Zhou Zhang; Wei Zhang
Journal:  Epigenomes       Date:  2022-06-02

Review 8.  Centromere Identity and the Regulation of Chromosome Segregation.

Authors:  Kousik Sundararajan; Aaron F Straight
Journal:  Front Cell Dev Biol       Date:  2022-06-02

9.  A complete reference genome improves analysis of human genetic variation.

Authors:  Sergey Aganezov; Stephanie M Yan; Daniela C Soto; Melanie Kirsche; Samantha Zarate; Pavel Avdeyev; Dylan J Taylor; Kishwar Shafin; Alaina Shumate; Chunlin Xiao; Justin Wagner; Jennifer McDaniel; Nathan D Olson; Michael E G Sauria; Mitchell R Vollger; Arang Rhie; Melissa Meredith; Skylar Martin; Joyce Lee; Sergey Koren; Jeffrey A Rosenfeld; Benedict Paten; Ryan Layer; Chen-Shan Chin; Fritz J Sedlazeck; Nancy F Hansen; Danny E Miller; Adam M Phillippy; Karen H Miga; Rajiv C McCoy; Megan Y Dennis; Justin M Zook; Michael C Schatz
Journal:  Science       Date:  2022-04-01       Impact factor: 63.714

10.  The complete sequence of a human genome.

Authors:  Sergey Nurk; Sergey Koren; Arang Rhie; Mikko Rautiainen; Andrey V Bzikadze; Alla Mikheenko; Mitchell R Vollger; Nicolas Altemose; Lev Uralsky; Ariel Gershman; Sergey Aganezov; Savannah J Hoyt; Mark Diekhans; Glennis A Logsdon; Michael Alonge; Stylianos E Antonarakis; Matthew Borchers; Gerard G Bouffard; Shelise Y Brooks; Gina V Caldas; Nae-Chyun Chen; Haoyu Cheng; Chen-Shan Chin; William Chow; Leonardo G de Lima; Philip C Dishuck; Richard Durbin; Tatiana Dvorkina; Ian T Fiddes; Giulio Formenti; Robert S Fulton; Arkarachai Fungtammasan; Erik Garrison; Patrick G S Grady; Tina A Graves-Lindsay; Ira M Hall; Nancy F Hansen; Gabrielle A Hartley; Marina Haukness; Kerstin Howe; Michael W Hunkapiller; Chirag Jain; Miten Jain; Erich D Jarvis; Peter Kerpedjiev; Melanie Kirsche; Mikhail Kolmogorov; Jonas Korlach; Milinn Kremitzki; Heng Li; Valerie V Maduro; Tobias Marschall; Ann M McCartney; Jennifer McDaniel; Danny E Miller; James C Mullikin; Eugene W Myers; Nathan D Olson; Benedict Paten; Paul Peluso; Pavel A Pevzner; David Porubsky; Tamara Potapova; Evgeny I Rogaev; Jeffrey A Rosenfeld; Steven L Salzberg; Valerie A Schneider; Fritz J Sedlazeck; Kishwar Shafin; Colin J Shew; Alaina Shumate; Ying Sims; Arian F A Smit; Daniela C Soto; Ivan Sović; Jessica M Storer; Aaron Streets; Beth A Sullivan; Françoise Thibaud-Nissen; James Torrance; Justin Wagner; Brian P Walenz; Aaron Wenger; Jonathan M D Wood; Chunlin Xiao; Stephanie M Yan; Alice C Young; Samantha Zarate; Urvashi Surti; Rajiv C McCoy; Megan Y Dennis; Ivan A Alexandrov; Jennifer L Gerton; Rachel J O'Neill; Winston Timp; Justin M Zook; Michael C Schatz; Evan E Eichler; Karen H Miga; Adam M Phillippy
Journal:  Science       Date:  2022-03-31       Impact factor: 63.714
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