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1. Ipsilateral restriction of chromosome movement along a centrosome, and apical- basal axis during the cell cycle

   Cai, Pingping; Casas, Christian J; Plancarte, Gabriel Quintero; Mikawa, Takashi; Hua, Lisa L (January 2025, Chromosome research)

   Sullivan, Beth A (Ed.)

   Little is known about how distance between homologous chromosomes are controlled during the cell cycle. Here, we show that the distribution of centromere components display two discrete clusters placed to either side of the centrosome and apical/basal axis from prophase to G1 interphase. 4- Dimensional live cell imaging analysis of centromere and centrosome tracking reveals that centromeres oscillate largely within one cluster, but do not cross over to the other cluster. We propose a model of an axis-dependent ipsilateral restriction of chromosome oscillations throughout mitosis. 

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2. The Interaction of NF-κB Transcription Factor with Centromeric Chromatin

   https://doi.org/10.1021/acs.jpcb.3c08388  

   Filliaux, Shaun; Bertelsen, Chloe; Baughman, Hannah; Komives, Elizabeth; Lyubchenko, Yuri (June 2024, The Journal of Physical Chemistry B)

   Centromeric chromatin is a subset of chromatin structure and governs chromosome segregation. The centromere is composed of both CENP-A nucleosomes (CENP-A(nuc)) and H3 nucleosomes (H3(nuc)) and is enriched with alpha-satellite (alpha-sat) DNA repeats. These CENP-A(nuc) have a different structure than H3(nuc), decreasing the base pairs (bp) of wrapped DNA from 147 bp for H3(nuc) to 121 bp for CENP-A(nuc). All these factors can contribute to centromere function. We investigated the interaction of H3(nuc) and CENP-A(nuc) with NF-kappaB, a crucial transcription factor in regulating immune response and inflammation. We utilized atomic force microscopy (AFM) to characterize complexes of both types of nucleosomes with NF-kappaB. We found that NF-kappaB unravels H3(nuc), removing more than 20 bp of DNA, and that NF-kappaB binds to the nucleosomal core. Similar results were obtained for the truncated variant of NF-kappaB comprised only of the Rel homology domain and missing the transcription activation domain (TAD), suggesting that RelA(TAD) is not critical in unraveling H3(nuc). By contrast, NF-kappaB did not bind to or unravel CENP-A(nuc). These findings with different affinities for two types of nucleosomes to NF-kappaB may have implications for understanding the mechanisms of gene expression in bulk and centromere chromatin. 

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3. The Role of Human Centromeric RNA in Chromosome Stability

   https://doi.org/10.3389/fmolb.2021.642732  

   Leclerc, Simon; Kitagawa, Katsumi (March 2021, Frontiers in Molecular Biosciences)

   Chromosome instability is a hallmark of cancer and is caused by inaccurate segregation of chromosomes. One cellular structure used to avoid this fate is the kinetochore, which binds to the centromere on the chromosome. Human centromeres are poorly understood, since sequencing and analyzing repeated alpha-satellite DNA regions, which can span a few megabases at the centromere, are particularly difficult. However, recent analyses revealed that these regions are actively transcribed and that transcription levels are tightly regulated, unveiling a possible role of RNA at the centromere. In this short review, we focus on the recent discovery of the function of human centromeric RNA in the regulation and structure of the centromere, and discuss the consequences of dysregulation of centromeric RNA in cancer. 

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4. Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila

   https://doi.org/10.1371/journal.pbio.3002911  

   Courret, Cécile; Hemmer, Lucas W; Wei, Xiaolu; Patel, Prachi D; Chabot, Bryce J; Fuda, Nicholas J; Geng, Xuewen; Chang, Ching-Ho; Mellone, Barbara G; Larracuente, Amanda M (November 2024, PLOS Biology)

   Kelleher, Erin S (Ed.)

   Centromeres reside in rapidly evolving, repeat-rich genomic regions, despite their essential function in chromosome segregation. Across organisms, centromeres are rich in selfish genetic elements such as transposable elements and satellite DNAs that can bias their transmission through meiosis. However, these elements still need to cooperate at some level and contribute to, or avoid interfering with, centromere function. To gain insight into the balance between conflict and cooperation at centromeric DNA, we take advantage of the close evolutionary relationships within theDrosophila simulansclade—D.simulans,D.sechellia, andD.mauritiana—and their relative,D.melanogaster. Using chromatin profiling combined with high-resolution fluorescence in situ hybridization on stretched chromatin fibers, we characterize all centromeres across these species. We discovered dramatic centromere reorganization involving recurrent shifts between retroelements and satellite DNAs over short evolutionary timescales. We also reveal the recent origin (<240 Kya) of telocentric chromosomes inD.sechellia, where the X and fourth centromeres now sit on telomere-specific retroelements. Finally, the Y chromosome centromeres, which are the only chromosomes that do not experience female meiosis, do not show dynamic cycling between satDNA and TEs. The patterns of rapid centromere turnover in these species are consistent with genetic conflicts in the female germline and have implications for centromeric DNA function and karyotype evolution. Regardless of the evolutionary forces driving this turnover, the rapid reorganization of centromeric sequences over short evolutionary timescales highlights their potential as hotspots for evolutionary innovation. 

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5. Complete genomic and epigenetic maps of human centromeres

   https://doi.org/10.1126/science.abl4178  

   Altemose, Nicolas; Logsdon, Glennis A.; Bzikadze, Andrey V.; Sidhwani, Pragya; Langley, Sasha A.; Caldas, Gina V.; Hoyt, Savannah J.; Uralsky, Lev; Ryabov, Fedor D.; Shew, Colin J.; et al (April 2022, Science)

   INTRODUCTION To faithfully distribute genetic material to daughter cells during cell division, spindle fibers must couple to DNA by means of a structure called the kinetochore, which assembles at each chromosome’s centromere. Human centromeres are located within large arrays of tandemly repeated DNA sequences known as alpha satellite (αSat), which often span millions of base pairs on each chromosome. Arrays of αSat are frequently surrounded by other types of tandem satellite repeats, which have poorly understood functions, along with nonrepetitive sequences, including transcribed genes. Previous genome sequencing efforts have been unable to generate complete assemblies of satellite-rich regions because of their scale and repetitive nature, limiting the ability to study their organization, variation, and function. RATIONALE Pericentromeric and centromeric (peri/centromeric) satellite DNA sequences have remained almost entirely missing from the assembled human reference genome for the past 20 years. Using a complete, telomere-to-telomere (T2T) assembly of a human genome, we developed and deployed tailored computational approaches to reveal the organization and evolutionary patterns of these satellite arrays at both large and small length scales. We also performed experiments to map precisely which αSat repeats interact with kinetochore proteins. Last, we compared peri/centromeric regions among multiple individuals to understand how these sequences vary across diverse genetic backgrounds. RESULTS Satellite repeats constitute 6.2% of the T2T-CHM13 genome assembly, with αSat representing the single largest component (2.8% of the genome). By studying the sequence relationships of αSat repeats in detail across each centromere, we found genome-wide evidence that human centromeres evolve through “layered expansions.” Specifically, distinct repetitive variants arise within each centromeric region and expand through mechanisms that resemble successive tandem duplications, whereas older flanking sequences shrink and diverge over time. We also revealed that the most recently expanded repeats within each αSat array are more likely to interact with the inner kinetochore protein Centromere Protein A (CENP-A), which coincides with regions of reduced CpG methylation. This suggests a strong relationship between local satellite repeat expansion, kinetochore positioning, and DNA hypomethylation. Furthermore, we uncovered large and unexpected structural rearrangements that affect multiple satellite repeat types, including active centromeric αSat arrays. Last, by comparing sequence information from nearly 1600 individuals’ X chromosomes, we observed that individuals with recent African ancestry possess the greatest genetic diversity in the region surrounding the centromere, which sometimes contains a predominantly African αSat sequence variant. CONCLUSION The genetic and epigenetic properties of centromeres are closely interwoven through evolution. These findings raise important questions about the specific molecular mechanisms responsible for the relationship between inner kinetochore proteins, DNA hypomethylation, and layered αSat expansions. Even more questions remain about the function and evolution of non-αSat repeats. To begin answering these questions, we have produced a comprehensive encyclopedia of peri/centromeric sequences in a human genome, and we demonstrated how these regions can be studied with modern genomic tools. Our work also illuminates the rich genetic variation hidden within these formerly missing regions of the genome, which may contribute to health and disease. This unexplored variation underlines the need for more T2T human genome assemblies from genetically diverse individuals. Gapless assemblies illuminate centromere evolution. ( Top ) The organization of peri/centromeric satellite repeats. ( Bottom left ) A schematic portraying (i) evidence for centromere evolution through layered expansions and (ii) the localization of inner-kinetochore proteins in the youngest, most recently expanded repeats, which coincide with a region of DNA hypomethylation. ( Bottom right ) An illustration of the global distribution of chrX centromere haplotypes, showing increased diversity in populations with recent African ancestry. 

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