The Genom of Homo sapiens.pdf

136 HAMILTON ET AL.Figure 6. Diagrammatic example of the potential dramatic effects of zinc-finger motif gain or loss on the DNA sequence recognitionof a hypothetical “code.” (A) Loss of a finger from the middle of the array affects several other fingers on one side of it, causing a“frameshift”-like disruption of any colinear amino acid-nucleotide recognition code and potentially reducing binding affinity for itsoriginal target. Note that a deletion on the ends of the array (not shown) may not have had as much effect on binding this target (butthe remaining fingers may have alternate functions which would be disrupted). (B) The same mutant protein shown with an increasedaffinity for a different target DNA sequence. This is one proposed way in which duplicated zinc-finger genes may find a role that allowsthem to be retained by selection.1997; Laity et al. 2000), so a change in the code of a singlefinger may have wider effects on protein function.However, the gain or loss of whole fingers may havemuch greater potential to drive paralog divergence by alteringarrangement of the KZNF motifs and interruptingthe matched geometries of fingers and nucleotides atbinding sites (Fig. 6). Considering the mode of interactionbetween DNA and KZNF domains, recombinationbetween the adjacent finger-repeat structures may providean unusually rapid path to functional divergence forKZNF proteins, producing more dramatic alterations inDNA-binding structure than could possibly be generatedthrough any other type of single mutational event.How might such changes in finger organization affectthe function of KZNF proteins? Experiments in which differentfingers of specific proteins are mutated using recombinantDNA techniques often produce proteins withaltered DNA-binding specificity (see, e.g., Isalan et al.1997; Ohlsson et al 2001; Hennemann et al. 2003; Mascleet al. 2003). However, several lines of data have suggestedthat all fingers in a polydactyl protein do not contributeequally to DNA binding (Filippova et al. 1996; Obata etal. 1999; Quitschke et al. 2000; Ohlsson et al. 2001;Daniel et al. 2002; Peng et al. 2002; Hennemann et al.2003). Longer or shorter versions of a duplicated KZNFarray in which the core-binding set of fingers is retainedmay potentially bind the same gene targets with alteredstabilities or specificities. Such subtly altered TF proteinsmay be useful in fine-tuning gene regulation; e.g., in differenttissues or at specific times in development. Indeed,one set of rodent-specific KK duplicates has recently beenshown to be involved in regulation of different genes in agender-specific manner in mice (Krebs et al. 2003).The functional impact of deletions or duplications offinger motifs from the middle of a KZNF array has notbeen studied extensively and is therefore a matter of conjecture.The answer may be complex, depending on detailsof structure and function of a particular KZNF domain.Internal rearrangements of finger motifs may havea dramatic effect on DNA binding, analogous to a“frameshift” in the target-recognition code. If such a disruptionoccurs within a core set of fingers, KZNF motifson one side or the other of the change could be mismatchedto the DNA sequence (Fig. 6). However, internalduplications and deletions may also generate novelDNA-binding arrays with affinities for new target sites;by opening new opportunities for gene regulation, evenradical changes in KZNF array structure might sometimesbe adaptive. Finally, not all changes in the physicalcenter of an array need be disruptive; it is possible thatwhen core subsets of fingers at either end of a long or dividedarray bind different targets (Morris et al. 1994), aduplication or deletion between these subsets may be allowedwith little effect.The importance of individual fingers may also shiftover evolutionary time in coordination with mutations inthe target sequence. For example, human and chickenvariants of the highly conserved 11-finger KZNF protein,CTCF, use different (but overlapping) sets of fingersto bind the diverging promoter sequences of the tar-