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.

Very broad peri-centromeric regions containg mostly repeats and confining the genes in the subtelomeric regions.

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.

Hi-C profiles tend to show centromeric clustering in cells that lack condensin II or have very long chromosomes, because they are in “Rabl” conformation.

“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.

Nanopore ultra-long reads barcoded with singly unique nucleotide k-mers (SUNKs) of length 20 and assembled. Sequence was then corrected with HiFi PacBio reads bearing the same k-mer barcodes. The centromere was assembled with 11 ultra-long reads. 5 different evolutionary strates were found.

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.

Fluorescence in situ hybridization (FISH) using chromosome enumeration DNA probes (CEPs) labeling centromeric regions. The intensity of the staining increases as the cell progresses in the cell cycle. On the published pictures, it is rare to be able to resolve the centromeric regions of the sister chromatids.

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.

“debris” fragments wrongly identified by 3D-DNA were added back to the assembly. Centromere of chrY different from the one of chrX.

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.

Chromosome arms do not interact much with each other. Large and highly repetitive pericentric regions in which it is hard to map the Hi-C reads.

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

HA epitope introduced into centromeric histone H3 (Cse4) using CRISPR-Cas9 editing. ChIP-seq then identified centromeres. “The species C. parapsilosis is therefore polymorphic for centromere location on two chromosomes. The centromere relocations are associated with a transition from a structured (IR) format to a format with no obvious structure or sequence dependence, within a single species. On Chromosome 5, it is likely that the centromeres on both copies of this chromosome have moved to a new location. It is possible that C. parapsilosis 90-137 is heterozygous at CEN1, with Cse4 at the expected location on one copy of Chromosome 1 and at a new location on the other copy.” “The C. parapsilosis neocentromeres are formed at regions that are transcribed, and transcription is known to facilitate centromere activity in S. cerevisiae”

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.

Hi-C contacts between telomeres and between centromeres. Few contacts between arms of the same chromosome.

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.

Hypothetises that AT-richness at centromeres can trigger breaks, and structural changes. Centromeres detected by ChIP-seq on GFP-Mtw1 in M. sympodialis. ”PhyloGibbs-MP predicted a 12 bp long AT-rich 239 motif common to all of the centromere sequences.” “In each chromosome, the centromere region shows between 7 and 13 motif matches, while no other 500 bp window shows more than 3 matches.” “In the absence of any centromere exclusive DNA sequence, the unique and distinguishing features of centromere regions in M. sympodialis are an AT-rich core region of <1 kb [...] enriched with the 12 bp motif in a kinetochore protein-bound region of 3 to 5 kb [containing] a reduced level of histone H3.” “Syntenic regions of all 8 M. sympodialis centromeres are present in the genomes of M. globosa and M. slooffiae [(each carries 9 chromosomes)].” “In the case of M. restricta, 7 putative centromeres are completely syntenic with M. sympodialis centromeres and one centromere retained partial gene synteny.” “No gene synteny conservation was observed at the centromeres of Chr2 in M. globosa, Chr5 in M. slooffiae, or Chr8 in M. restricta, indicative of loss of a centromere during the transition from the 9-chromosome state to the 8-302 chromosome state.”

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.

Components of the constitutive centromere-associated network (CCAN) at the inner kinetochore seem to be missing in the genome. H3T3p and H3S28p mark inner centromeric regions (single spots) and H3T11p mark outer centromeric regions (pairs of spots). Fluorescent microscopy pictures supporting a 2 × 3 karyotype.

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.

Brute-force analysis assuming that the most abundant tandem repeat is a centromere. Sequence conservation is limited to close species. Similarity can be lost quickly (~10 MY) or can be kept for as long as ~50 MY. High order repeat structures could be detected. Discussees that “centromere DNA and CENH3 differences could introduce reproductive barriers, causing speciation”.

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.

Comparison of centromere sequences between interfertile medaka strains that separated 18~25 My ago. Also, within a species, homologous pairs of centromeres (derived from the same ancestral pre-teleost (350 My ago) chromosome) were conserved, and acrocentric ones were shown to evolve slower.