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Sequential de novo centromere formation and inactivation on a chromosomal fragment in maize

Significance The centromere is the part of the chromosome that is involved with movement in mitosis and meiosis. The activity of the centromere is epigenetic in that the underlying DNA sequences do not necessarily determine function. In the present study, a chromosomal fragment was followed in which a sequential de novo formation and inactivation occurred for the position of the active centromere. The results suggest that de novo centromere formation occurs regularly. However, when coupled with previous findings that larger centromeres can inactivate smaller ones when present together, it is hypothesized that such frequent de novo centromere formations are cleared from normal chromosomes by inactivation, but can persist on structurally acentric fragments and be inherited. The ability of centromeres to alternate between active and inactive states indicates significant epigenetic aspects controlling centromere assembly and function. In maize (Zea mays), misdivision of the B chromosome centromere on a translocation with the short arm of chromosome 9 (TB-9Sb) can produce many variants with varying centromere sizes and centromeric DNA sequences. In such derivatives of TB-9Sb, we found a de novo centromere on chromosome derivative 3-3, which has no canonical centromeric repeat sequences. This centromere is derived from a 288-kb region on the short arm of chromosome 9, and is 19 megabases (Mb) removed from the translocation breakpoint of chromosome 9 in TB-9Sb. The functional B centromere in progenitor telo2-2 is deleted from derivative 3-3, but some B-repeat sequences remain. The de novo centromere of derivative 3-3 becomes inactive in three further derivatives with new centromeres being formed elsewhere on each chromosome. Our results suggest that de novo centromere initiation is quite common and can persist on chromosomal fragments without a canonical centromere. However, we hypothesize that when de novo centromeres are initiated in opposition to a larger normal centromere, they are cleared from the chromosome by inactivation, thus maintaining karyotype integrity.