Barbara McClintock's Unsolved Chromosomal Mysteries: Parallels to Common Rearrangements and Karyotype Evolution

Abstract

Two obscure studies on chromosomal behavior by Barbara McClintock are revisited in light of subsequent studies and evolutionary genomics of chromosome number reduction. The phenomenon of deficiency recovery in which adjacent genetic markers lost in the zygote reappear in later developmental sectors is discussed in light of de novo centromere formation on chromosomal fragments. Second, McClintock described a small chromosome, which she postulated carried an "X component," that fostered specific types of chromosomal rearrangements mainly involving centromere changes and attachments to the termini of chromosomes. These findings are cast in the context of subsequent studies on centromere misdivision, the tendency of broken fragments to join chromosome ends, and the realization from genomic sequences that nested chromosomal insertion and end-to-end chromosomal fusions are common features of karyotype evolution. Together, these results suggest a synthesis that centromere breaks, inactivation, and de novo formation together with telomeres-acting under some circumstances as double-strand DNA breaks that join with others-is the underlying basis of these chromosomal phenomena.

Figure 1.

Deficiency Recovery. The kernel at the right illustrates an apparent spontaneous case of deficiency recovery. The kernel at the left has a recessive genetic marker for anthocyanin production in the endosperm (c1) and is representative of the maternal parent. The center kernel has the dominant allele for the pigment gene (C1) and is representative of the male parent. In the kernel at the right, the dominant marker is missing on most of the endosperm but a small sector with light pigmentation typical of a c1/c1/C1 endosperm is present. The dominant marker must have been delivered to the zygote but is missing in much of the endosperm and recovers only in a sector. (Photo by Zhi Gao.)

Figure 2.

Diagrammatic Representation of Products of Centromere Misdivision. Top, left: Misdivision of the centromere occurs when the kinetochore attaches to the spindle from both poles and fractures the centromere of a univalent (Sears, 1952). The chromosome depicted is a univalent in meiosis I with sister chromatids of a chromosome with arms of different lengths. The different arms are shown in orange and blue. Top, right: The attachment of the chromosome from both poles breaks the chromosome at the centromere and the replicated chromatids of the different arms progress to opposite poles. Molecular studies indicate that centromere misdivision cleaves the underlying DNA sequences (Kaszás and Birchler, 1996, 1998; Jin et al., 2005). Bottom: Products of centromere misdivision include telocentric chromosomes derived from either arm (blue or orange) of the progenitor chromosome, isochromosomes derived from either chromosome arms but that are fused at the site of centromere breakage, and ring chromosomes that join the broken centromere to the end of the same chromosome (Carlson, 1970, 1973a, 1973b; Carlson and Chou, 1981; Kaszás and Birchler, 1996, 1998; Kaszás et al., 2002; Phelps-Durr and Birchler, 2004; Jin et al., 2005).

Figure 3.

Ring Chromosome Showing Centromere-Telomere Fusion. Carlson (1973b) documented that centromere misdivision of the supernumerary B chromosome was correlated with its nondisjunction property. The sister kinetochores apparently attach to the spindle from both poles but the tendency to nondisjoin causes rupture of the centromere. One chromosome recovered from TB-9Sb, a translocation between the B chromosome and the short arm of chromosome 9, was a ring chromosome (Carlson, 1973b). This chromosome is depicted in the pachytene stage of meiosis. On the left is fluorescence in situ hybridization (FISH) with the B-specific repeat that is concentrated at the centromere of the B chromosome in red and knob heterochromatin in green. The short arm of chromosome 9 has a knob at the very terminus of the chromosome. The FISH image reveals that the centromere is annealed to the knob to form the ring indicating that the broken centromere fused with the terminus of the chromosome. The other red signal is the terminal site of the B specific sequence on the 9-B chromosome as the reciprocal portion of the TB-9Sb translocation. Right, gray scale of the same image. Bar = 10 μm.

Figure 4.

Centromere-Centromere Translocation between Wheat and Rye Chromosomes Recovered from Centromere Misdivision. A homozygous translocation (arrows) resulting from centromere misdivision that joins wheat chromosome 1B with rye chromosome 1. In this FISH image, the wheat centromere repeat is depicted in red and the rye centromere repeat is in green. The juxtaposition of the two signals indicates that the breaks were within the centromeric region and were joined together. Bar = 10 μm.

Figure 5.

Diagrammatic Representation of Fragment Attachment to Chromosome Ends. The 9-Bic-1 (9-B inactive centromere-1; a translocation of an inactive B chromosome centromere on the tip of chromosome arm 9S) chromosome has an inactive B centromere present on the tip of the short arm of chromosome 9 (Han et al., 2006). Chromosome 9 is depicted in blue, B chromosomes are depicted in purple, and B centromeres are depicted in red. In the absence of a normal B chromosome, 9-Bic1 disjoins normally (not shown). However, when a normal B chromosome is added to the genotype, it supplies the transacting factors for nondisjunction to itself and to the inactive B centromere on 9S (depicted on the left). The arrows indicate nondisjunction of 9-Bic-1 and the B chromosome. Thus, 9-Bic-1 now undergoes nondisjunction or, more often, is broken in the anaphase of the second pollen mitosis (Han et al., 2007) shown in the center. The B centromere has a specific repeat that allows it to be followed by FISH (depicted in red). In the progeny of crosses of 9-Bic-1 + B chromosomes, broken fragments of 9S with the B centromere were found attached to the ends of other chromosomes (Han et al., 2007; right). Red circles indicate the inactive B centromere attached to chromosome 2, 7, or 8.

Figure 6.

Fragment Attachment to the Terminus of the Short Arm of Chromosome 7. FISH image of 7-Bic-1 in which the inactive B centromere (red) was broken from 9-Bic-1 (see Figure 5) and became attached to the terminus of the short arm of chromosome 7 (arrows). Knob heterochromatin is labeled in green. The chromosome is homozygous viable and thus must not be missing any vital genes. Inset shows the 7-Bic-1 chromosome with the merged image, with the B repeat indicating the inactive B centromere and the knob heterochromatin labels with the gray-scale 4′,6-diamidino-2-phenylindole (DAPI). Bar = 10 μm.

Figure 7.

Diagrammatic Representation of Nested Chromosomal Insertion and End-to-End Fusions: Common Chromosome Number Reduction Events in Evolution. Two of the most common chromosomal rearrangements during karyotype evolution are end-to-end fusions and nested chromosomal insertions (Lysak et al., 2006; Luo et al., 2009, 2017; Murat et al., 2010; Schubert and Lysak, 2011; Wang and Bennetzen, 2012; Wang et al., 2015; Hoang and Schubert, 2017). At the left, two chromosomes are depicted in orange and blue with the centromere depicted as gray ovals. End-to-end fusions result from the joining of the termini of the two chromosomes, which is likely associated with deletion or inactivation of one of the two centromeres such that the result is not functionally dicentric, which would lead to its fracture. Experimentally, centromere inactivation can occur within the span of a cell cycle, or at least a few, and then the inactive state is perpetuated over generations (Han et al., 2009; Gao et al., 2011). Nested chromosomal insertion occurs when one chromosome inserts at or near the centromere of another chromosome. Again, only one centromere would retain function for the integrity of the new chromosome to be maintained.