Variation and Evolution of Human Centromeres: A Field Guide and Perspective

We are entering a new era in genomics where entire centromeric regions are accurately represented in human reference assemblies. Access to these high-resolution maps will enable new surveys of sequence and epigenetic variation in the population and offer new insight into satellite array genomics and centromere function. Here, we focus on the sequence organization and evolution of alpha satellites, which are credited as the genetic and genomic definition of human centromeres due to their interaction with inner kinetochore proteins and their importance in the development of human artificial chromosome assays. We provide an overview of alpha satellite repeat structure and array organization in the context of these high-quality reference data sets; discuss the emergence of variation-based surveys; and provide perspective on the role of this new source of genetic and epigenetic variation in the context of chromosome biology, genome instability, and human disease.

Construction of stable mouse artificial chromosome from native mouse chromosome 10 for generation of transchromosomic mice

Mammalian artificial chromosomes derived from native chromosomes have been applied to biomedical research and development by generating cell sources and transchromosomic (Tc) animals. Human artificial chromosome (HAC) is a precedent chromosomal vector which achieved generation of valuable humanized animal models for fully human antibody production and human pharmacokinetics. While humanized Tc animals created by HAC vector have attained significant contributions, there was a potential issue to be addressed regarding stability in mouse tissues, especially highly proliferating hematopoietic cells. Mouse artificial chromosome (MAC) vectors derived from native mouse chromosome 11 demonstrated improved stability, and they were utilized for humanized Tc mouse production as a standard vector. In mouse, however, stability of MAC vector derived from native mouse chromosome other than mouse chromosome 11 remains to be evaluated. To clarify the potential of mouse centromeres in the additional chromosomes, we constructed a new MAC vector from native mouse chromosome 10 to evaluate the stability in Tc mice. The new MAC vector was transmitted through germline and stably maintained in the mouse tissues without any apparent abnormalities. Through this study, the potential of additional mouse centromere was demonstrated for Tc mouse production, and new MAC is expected to be used for various applications.

Construction of Stable Mouse Artificial Chromosome from Native Mouse Chromosome 10 for Generation of Transchromosomic Mice

Mammalian artificial chromosomes derived from native chromosomes have been applied to biomedical research and development by generating cell sources and transchromosomic (Tc) animals. Human artificial chromosome (HAC) is a precedent chromosomal vector which achieved generation of valuable humanized animal models for fully human antibody production and human pharmacokinetics. While humanized Tc animals created by HAC vector have attained significant contributions, there was a potential issue to be addressed regarding stability in mouse tissues, especially highly proliferating hematopoietic cells. Mouse artificial chromosome (MAC) vectors derived from native mouse chromosome 11 demonstrated improved stability, and they were utilized for humanized Tc mouse production as a standard vector. In mouse, however, stability of MAC vector derived from native mouse chromosome other than mouse chromosome 11 remains to be evaluated. To clarify the potential of mouse centromeres in the additional chromosomes, we constructed a new MAC vector from native mouse chromosome 10 to evaluate the stability in Tc mice. The new MAC vector was transmitted through germline and stably maintained in the mouse tissues without any apparent abnormalities. Through this study, the potential of additional mouse centromere was demonstrated for Tc mouse production, and new MAC is expected to be used for various applications.

Implementing the human artificial chromosome gene therapy platform remains challenging, but continuous animal model research will advance the platform closer to clinical trials

A normal degree of ectopic gene expression, infinite retention in target cells without chromosomal integration, minimal risk of cell or neoplastic transformation, and minimal or no immunogenicity are all critical characteristics for vectors employed in gene therapy. HACs were produced and used as autonomous vectors to compensate for genetic defects in mouse and human cell cultures. Bottom-up human artificial chromosomes (HACs) were studied for functional transgene expression in vitro and in vivo mice models. The primary advantages of synthesized alphoid-HACs over top-down HACs are their defined and documented structure, as well as their relative simplicity of modification in adding numerous Cre-lox-type transgen loading sites. The HAC transfer method's efficacy has greatly increased in recent years. Despite significant progress in developing alphoid-HAC-based gene therapy models, the technology still has a number of drawbacks, including low HAC efficiency, complex repeated HAC alphoid-DNA structure, large DNA fragmentation difficulties outside eukaryotic cells, inefficient transfer of chromosomes to target cells, and variable mitotic stability. The quantity and quality of PSC-derived or reversibly immortalized stem/precursor cells that can transplant specific tissues are also critical determinants in the effectiveness of HAC-based tissue replacement therapies. Translating the HAC-based gene therapy platform remains difficult, but ongoing animal model research will move the HAC platform closer to clinical trials.

Terpyridine Platinum Compounds Induce Telomere Dysfunction and Chromosome Instability in Cancer Cells

Background Telomerase/telomere-targeting therapy is a potentially promising approach for cancer treatment because even transient telomere dysfunction can induce chromosomal instability (CIN) and may be a barrier to tumor growth. Method: We recently developed a dual-HAC (Human Artificial Chromosome) assay that enables identification and ranking of compounds that induce CIN as a result of telomere dysfunction. This assay is based on the use of two isogenic HT1080 cell lines, one carrying a linear HAC (containing telomeres) and the other carrying a circular HAC (lacking telomeres). Disruption of telomeres in response to drug treatment results in specific destabilization of the linear HAC. Results In this study, we used the dual-HAC assay for the analysis of the platinum-derived G4 ligand Pt-tpy and five of its derivatives: Pt-cpym, Pt-vpym, Pt-ttpy, Pt(PA)-tpy, and Pt-BisQ. Our analysis revealed four compounds, Pt-tpy, Pt-ttpy, Pt-vpym and Pt-cpym, that induce a specific loss of a linear but not a circular HAC. Increased CIN after treatment by these compounds correlates with the induction of double-stranded breaks (DSBs) predominantly localized at telomeres and reflecting telomere-associated DNA damage. Analysis of the mitotic phenotypes induced by these drugs revealed an elevated rate of chromatin bridges (CBs) in late mitosis and cytokinesis. Conclusions These terpyridine platinum-derived G4 ligands are promising compounds for cancer treatment.

First person – Nuno Martins, Fernanda Cisneros-Soberanis and Elisa Pesenti

ABSTRACTFirst Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Nuno Martins, Fernanda Cisneros-Soberani and Elisa Pesenti are co-first authors on ‘H3K9me3 maintenance on a human artificial chromosome is required for segregation but not centromere epigenetic memory’, published in JCS. Nuno conducted the research described in this article while a PhD student in William C. Earnshaw's lab at the Wellcome Trust Centre for Cell Biology, University of Edinburgh, UK. He is now a postdoc in the lab of Ting Wu at Harvard Medical School, Boston, USA, where his research interests lie in the structural and dynamic chromatin regulation of the more mysterious regions of the cell nucleus, such as centromeres, repetitive elements and nucleoli. Fernanda conducted the research described in this article while a postdoc in William C. Earnshaw's lab. She is now an Investigadora en Ciencias Médicas in the lab of Luis Alonso Herrera at Instituto Nacional de Cancerología, México City, México, investigating the transcriptional regulation of microRNAs in breast cancer. Elisa is a postdoc/lab manager in the lab of William C. Earnshaw and is interested in developing human artificial chromosomes (HACs) by applying molecular and synthetic biology techniques to study chromosome segregation and epigenetics in human cells.

CENP-B creates alternative epigenetic chromatin states permissive for CENP-A or heterochromatin assembly

ABSTRACTCENP-B binds to CENP-B boxes on centromeric satellite DNAs (known as alphoid DNA in humans). CENP-B maintains kinetochore function through interactions with CENP-A nucleosomes and CENP-C. CENP-B binding to transfected alphoid DNA can induce de novo CENP-A assembly, functional centromere and kinetochore formation, and subsequent human artificial chromosome (HAC) formation. Furthermore, CENP-B also facilitates H3K9 (histone H3 lysine 9) trimethylation on alphoid DNA, mediated by Suv39h1, at ectopic alphoid DNA integration sites. Excessive heterochromatin invasion into centromere chromatin suppresses CENP-A assembly. It is unclear how CENP-B controls such different chromatin states. Here, we show that the CENP-B acidic domain recruits histone chaperones and many chromatin modifiers, including the H3K36 methylase ASH1L, as well as the heterochromatin components Suv39h1 and HP1 (HP1α, β and γ, also known as CBX5, CBX1 and CBX3, respectively). ASH1L facilitates the formation of open chromatin competent for CENP-A assembly on alphoid DNA. These results indicate that CENP-B is a nexus for histone modifiers that alternatively promote or suppress CENP-A assembly by mutually exclusive mechanisms. Besides the DNA-binding domain, the CENP-B acidic domain also facilitates CENP-A assembly de novo on transfected alphoid DNA. CENP-B therefore balances CENP-A assembly and heterochromatin formation on satellite DNA.

H3K9me3 maintenance on a human artificial chromosome is required for segregation but not centromere epigenetic memory

ABSTRACTMost eukaryotic centromeres are located within heterochromatic regions. Paradoxically, heterochromatin can also antagonize de novo centromere formation, and some centromeres lack it altogether. In order to investigate the importance of heterochromatin at centromeres, we used epigenetic engineering of a synthetic alphoidtetO human artificial chromosome (HAC), to which chimeric proteins can be targeted. By tethering the JMJD2D demethylase (also known as KDM4D), we removed heterochromatin mark H3K9me3 (histone 3 lysine 9 trimethylation) specifically from the HAC centromere. This caused no short-term defects, but long-term tethering reduced HAC centromere protein levels and triggered HAC mis-segregation. However, centromeric CENP-A was maintained at a reduced level. Furthermore, HAC centromere function was compatible with an alternative low-H3K9me3, high-H3K27me3 chromatin signature, as long as residual levels of H3K9me3 remained. When JMJD2D was released from the HAC, H3K9me3 levels recovered over several days back to initial levels along with CENP-A and CENP-C centromere levels, and mitotic segregation fidelity. Our results suggest that a minimal level of heterochromatin is required to stabilize mitotic centromere function but not for maintaining centromere epigenetic memory, and that a homeostatic pathway maintains heterochromatin at centromeres.This article has an associated First Person interview with the first authors of the paper.