Centromeres are essential to genome inheritance, serving as the site of kinetochore assembly and coordinating chromosome segregation during cell division. Abnormal centromere function is associated with birth defects, infertility, and cancer. Most human centromeres are consistently formed at regions containing highly repetitive alpha satellite DNA. However, in cancer cells, new, ectopic centromeres (neocentromeres) frequently arise on intact chromosomes or small supernumerary marker chromosomes (sSMCs) at genomic regions that lack alpha satellite DNA. Studies in model organisms (Drosophila, yeast, chicken cells) have suggested that certain regions of the genome, including pericentromeres, heterochromatin, and regions of open chromatin or high transcription, are particularly amenable to neocentromere activation. Little is known about the mechanisms of human neocentromere formation or the role of neocentromeres in neoplasia. This is largely due to the lack of experimental systems to study ectopic centromere formation in human cells. In this proposal, we propose to establish CRISPR-based assays to induce neocentromeres on specific human chromosomes, compare their (epi)genomic organization and functional efficiency, and define DNA and chromatin features at sites of formation.
In Aim 1, we will use CRISPR-based approaches to independently trigger neocentromere formation on individual human chromosomes after removal or suppression of the native centromere. Our rationale is that by removing or incapacitating the largest concentration of CENP-A, neocentromeres will arise at ectopic sites that harbor low concentrations of CENP-A and/or are vulnerable to CENP-A invasion.
In Aim 2, we will define the functional consequences of neocentromere formation by mapping chromatin structure at ectopic centromere regions and measuring the effect of neocentromere formation on gene expression and the surrounding chromatin environment. The technological and intellectual outcomes of this study will fundamentally transform our ability to create and study human chromosome abnormalities and expand our view of genome function and plasticity. Our proposed experiments will establish new methods to induce ectopic centromere assembly on specific human chromosomes to better understand the clinical consequences of neocentromere formation.

Public Health Relevance

Centromeres are chromosomal regions required for genome stability. In humans, the centromere is built on highly repetitive alpha satellite DNA found at a single locus on each chromosome. However, in cancer cells, new, ectopic centromeres (neocentromeres) frequently arise on intact chromosomes or on small supernumerary marker chromosomes (sSMCs) at genomic sites that lack alpha satellite DNA. This research proposal will focus on spontaneous centromere formation in normal and cancer cells in humans. Using CRISPR-based approaches to induce ectopic human centromeres, we will systematically identify chromosomal regions that are amenable to neocentromere formation following loss or suppression of the natural centromere. These pioneering studies hold the promise of fundamentally transforming our ability to create and study human chromosome abnormalities and to expand our view of genome function and plasticity, particularly in cancer and other diseases.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Exploratory/Developmental Grants (R21)
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Genomics, Computational Biology and Technology Study Section (GCAT)
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Li, Jerry
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Duke University
Schools of Medicine
United States
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