Work in progress
Sequence
- Brute-force analysis to find the most abundant large tandem repeat can find centromeres (Melters and coll., 2013).
- In the three-spine stickleback, the centromere sequence of chrX differs from the one of chrY (Peichel and coll., 2020).
- The pericentromeric regions of Dioscorea alata can comprise most of the chromosome length Bredeson and coll., 2022.
Visualisation
- In Oikopleura (and many others) H3S28p marks mitotic centromeres Fent and coll., 2019.
- Centromeric regions of sister chromatids are rarely resolved in FISH. Instead, the intensity of the spot increases (Amakawa and coll., 2013).
- In Hi-C profiles, centromeric clustering is seen in cells that lack condensin II or have extremely long chromosomes (Hoencamp and coll., 2021).
Evolution
- In medaka, study of homologous pairs of centromeres suggest that the acrocentric ones evolve slower (Ichikawa and coll., 2017).
- Centromere breakage and inactivation in yeast: Sankaranarayanan and coll., 2020.
- Centromere relocation to a transcribed region in yeast, detected by ChIP of centromeric H3 Ola and coll., 2020.
- 5 evolutionary strates were found in human chr8 centromere (Logdson and coll, 2021).
Bredeson JV, Lyons JB, Oniyinde IO, Okereke NR, Kolade O, Nnabue I, Nwadili CO, Hřibová E, Parker M, Nwogha J, Shu S, Carlson J, Kariba R, Muthemba S, Knop K, Barton GJ, Sherwood AV, Lopez-Montes A, Asiedu R, Jamnadass R, Muchugi A, Goodstein D, Egesi CN, Featherston J, Asfaw A, Simpson GG, Doležel J, Hendre PS, Van Deynze A, Kumar PL, Obidiegwu JE, Bhattacharjee R, Rokhsar DS.
Nat Commun. 2022 Apr 14;13(1):2001. doi:10.1038/s41467-022-29114-w
Chromosome evolution and the genetic basis of agronomically important traits in greater yam.
Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD.
Science. 2021 May 28;372(6545):984-989. doi:10.1126/science.abe2218
3D genomics across the tree of life reveals condensin II as a determinant of architecture type.
“In ∆CAP-H2 human cells, centromeres also cluster in or around the nucleolus. However, disrupting nucleolar structure did not affect centromeric clustering. The clustering of centromeres at the human nucleolus is likely because rDNA sequences, which are the genomic component of the nucleolus, often lie near centromeres”
“acute depletion of the condensin I subunit CAP-H did not lead to centromeric clustering”
“we found that the notable increase in chromosome length in the Indian muntjac coincides, as expected, with the appearance of centromeric clustering.”
“We hypothesize that (i) centromeres tend to adhere to one another, a process that is facilitated by proximity during and shortly after mitosis; (ii) the shortening of chromosomes interferes with this adhesion, enabling the centromeres to spread out over the newly formed nuclei; and (iii) chromosome territories emerge as a by-product of the resulting chromosomal separation.”
Nature. 2021 Apr 7. doi:10.1038/s41586-021-03420-7
Logsdon GA, Vollger MR, Hsieh P, Mao Y, Liskovykh MA, Koren S, Nurk S, Mercuri L, Dishuck PC, Rhie A, de Lima LG, Dvorkina T, Porubsky D, Harvey WT, Mikheenko A, Bzikadze AV, Kremitzki M, Graves-Lindsay TA, Jain C, Hoekzema K, Murali SC, Munson KM, Baker C, Sorensen M, Lewis AM, Surti U, Gerton JL, Larionov V, Ventura M, Miga KH, Phillippy AM, Eichler EE.
The structure, function and evolution of a complete human chromosome 8.
Amakawa G, Ikemoto K, Ito H, Furuya T, Sasaki K.
J Histochem Cytochem. 2013 Oct;61(10):699-705. doi:10.1369/0022155413498754
Quantitative analysis of centromeric FISH spots during the cell cycle by image cytometry.
Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA.
Genome Biol. 2020 Jul 19;21(1):177. doi:10.1186/s13059-020-02097-x
Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution.
Bracewell R, Tran A, Chatla K, Bachtrog D.
G3 (Bethesda). 2020 Mar 5;10(3):891-897. doi:10.1534/g3.119.400922
Chromosome-Level Assembly of Drosophila bifasciata Reveals Important Karyotypic Transition of the X Chromosome.
Ola M, O'Brien CE, Coughlan AY, Ma Q, Donovan PD, Wolfe KH, Butler G.
Genome Res. 2020 May;30(5):684-696. doi:10.1101/gr.257816.119.
Polymorphic Centromere Locations in the Pathogenic Yeast Candida parapsilosis
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL.
Science. 2017 Apr 7;356(6333):92-95. doi:10.1126/science.aal3327
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
Sankaranarayanan SR, Ianiri G, Coelho MA, Reza MH, Thimmappa BC, Ganguly P, Vadnala RN, Sun S, Siddharthan R, Tellgren-Roth C, Dawson TL Jnr, Heitman J, Sanyal K.
Elife. 2020 Jan 20;9. pii: e53944. doi: 10.7554/eLife.53944 doi:10.7554/eLife.53944
Loss of centromere function drives karyotype evolution in closely related Malassezia species.
Cell Cycle. 2019 Jul 15:1-20. doi:10.1080/15384101.2019.1634954
Feng H, Raasholm M, Moosmann A, Campsteijn C, Thompson EM.
Switching of INCENP paralogs controls transitions in mitotic chromosomal passenger complex functions.
Genome Biol. 2013 Jan 30;14(1):R10. doi: 10.1186/gb-2013-14-1-r10
Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, Korf I, Chan SW.
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.
Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie N, Takeda H, Morishita S.
Nat Commun. 2017 Nov 28;8(1):1833. doi:10.1038/s41467-017-01982-7
Centromere evolution and CpG methylation during vertebrate speciation.