Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, February 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 114-123).A central feature of visual pathway development is its organization into retinotopic maps. The developmental process by which these maps form involves a transition from early patterning cues to arrays of axonal guidance factors allowing the relative order of retinotopic axons to be preserved. Mechanisms linking patterning molecules of early development to topographic wiring and subsequent functional responses are not well understood. In this thesis, I performed a microarray screen comparing gene expression in early visual and auditory regions of the thalamus in order to identify early patterning candidates with a potential role in visual pathway differentiation. Among the candidates enriched in the visual thalamus, the transcription factor, Zic4, was found to be expressed in gradients of the developing retina, lateral geniculate nucleus (LGN) and primary visual cortex (V 1). Mice lacking Zic4 exhibited a deficit in eye-specific patterning to the thalamus that was complementary to the phenotype seen in mice lacking Tenm3, a type II homophilic transmembrane receptor and transcriptional regulator. Using intrinsic signal optical imaging techniques, I characterized the functional properties of primary visual cortical retinotopic maps in Zic4 and Ten_m3 null mice and identified complementary changes in the ipsilateral representation of V1, as well as evidence for eye-specific mismatch in the cortical binocular zone. Additionally, complementary positional shifts in VI were found in these mutants identifying a bidirectional modulation of mapping mechanisms in the visual pathway.(cont.) In order to test whether Zic4 and Ten_m3 interact in serial or parallel pathways, I analyzed the retinogeniculate and cortical maps in the combination mutant. The Ten_m3/Zic4 double null mouse exhibited a partial rescue of retinogeniculate mapping and a complete reversal of the cortical changes found in either mutant alone, suggesting that the two genes interact to modulate common downstream effectors in opposite directions. In sum, this thesis presents a gene microarray screen used to identify Zic4 as a novel visual patterning gene, characterizes its loss-of-function phenotype on retinotopic mapping in the thalamus and cortex, and studies its antagonistic interaction with Ten_m3, another visual pathway patterning gene with a complementary loss-of-function phenotype.by Sam H. Horng.Ph.D.