(A) Schematic of mouse visual system. Binocular zone (BZ), located between primary (V1) and secondary (V2) visual cortex, receives input from both eyes. Arc mRNA induction was used to map cortical neurons driven by stimulation of one eye (Experimental procedures and (Tagawa et al., 2005)). Below: darkfield autoradiograph of Arc in situ hybridization in a coronal section from a P34 WT (K^bD^b+/+) mouse; 30 minutes of visual stimulation upregulates Arc mRNA in neurons of layers 2-4 and 6 of visual cortex (layer 5 neurons only express very low levels of Arc mRNA). Box indicates region of Arc mRNA upregulation driven by ipsilateral eye stimulation within the BZ; broad induction of Arc mRNA is present throughout V1 and V2 contralateral to the stimulated eye, Scale = 900μm. (B) Ipsilateral eye representation in cortex expands more in K^bD^b-/- than in WT (K^bD^b+/+) mice following monocular enucleation (ME) during the critical period (P22-31). Top: In situ hybridization for Arc mRNA in K^bD^b+/+ (upper) and K^bD^b-/- (lower) visual cortex ipsilateral to the remaining eye; arrows indicate borders of signal in layer 4. Below: cumulative histograms of mean width of Arc induction in layer 4 ± sem for K^bD^b+/+ (upper) and K^bD^b-/- (lower) mice reared with normal vision (open symbols) or mice that received ME (filled symbols). Note increased width of Arc induction following ME in both genotypes. (K^bD^b+/++ME: 1426.3 ± 89.7 μm, n = 18 mice vs. K^bD^b+/+ normal vision: 945 ± 58.3 μm, n = 2 8 mice; P < 0.05; K^bD^b-/-+ME: 2404.6 ± 105.1 μm, n = 25 mice; P = 0.0017). Note also that width of Arc induction in K^bD^b-/- mutant mice reared with normal visual experience (open squares) is slightly larger than that of normally-reared K^bD^b+/+ mice (open circles): K^bD^b-/-: 1111 ± 50.8 μm, n = 25 mice; K^bD^b+/+: 945 ± 58.3 μm n = 2 8 mice. Each symbol represents the average of several scanned sections from a single animal ± sem. Scale = 400μm. (C) Average width of Arc induction in layer 4 for normally reared K^bD^b+/+ or K^bD^b-/- mice (open bar) vs. mice receiving monocular visual deprivation from P25-34 (MD: gray bar, n = 7) or from P22-31 (ME: black bar, n = 25). (D) Plasticity Index (see text) reveals greater OD plasticity in K^bD^b-/- than in K^bD^b+/+ visual cortex by MD and ME, (*) statistical significance determined by one-way ANOVA. Error bars = standard error of mean (sem) in B and C, and root mean square error (RMSE) in D.

(A) RGC projections labeled by intraocular injections of CTB AF594 (red) into the contralateral (contra) eye and CTB AF488 (green) into the ipsilateral (ipsi) eye. Top: Merged fluorescent micrographs of dLGN from K^bD^b+/+ and K^bD^b-/- mice at P34. Middle (green pixels): ipsilateral eye projection pattern (intensity threshold = 60% of maximum). Bottom (yellow pixels): overlapping pixels from ipsilateral and contralateral eye projections each at an intensity threshold 60% of maximum (Figure S3 and Experimental procedures). Note ectopic patches of ipsilateral eye projections not eliminated during development in K^bD^b-/- mice. Scale = 150μm. (B, C) Mean % of dLGN area ± sem of ipsilateral eye projection and mean overlapping pixels in both channels. More ipsilateral territory as well as overlapping pixels are present in mutant dLGN: K^bD^b+/+ = 5 mice, K^bD^b-/- = 5 mice, P< 0.05 (two-tailed t-test).

(A) Schematic of connections in mouse visual system: thalamocortical axon terminals innervate layer 4 of cortex. Below, transneuronal transport of H³–proline following intraocular injection reveals (age P34; Experimental procedures) a broad contralateral signal (left), and smaller ipsilateral patch (right) in layer 4. Scale=1500μm. (B) Higher magnification of representative sections from K^bD^b+/+ (top) and K^bD^b-/- (bottom) mice. Arrows indicate measurement borders used. Scale = 450μm. (C) Population averages for width ± sem of layer 4 label for each genotype after ME. P<0.05; (Mann-Whitney U test).

(A) AT micrographs reconstructed from 25 serial ultrathin sections (each 70nm thick) of P7 LGN showing MHCI immunostaining (green) in relation to known synaptic markers (Syn=synapsin (orange), PSD=postsynaptic density-95 (white), GAD=glutamic acid decarboxylase 65/67 (cyan)), as well as to C1q=complement protein C1q (magenta). DAPI stain of nuclei, blue. Scale = 5μm. (B) Four serial sections of 2 different synapsin positive puncta: Left example is characteristic of an excitatory synapse (close apposition of presynaptic marker synapsin with postsynaptic excitatory synapse marker PSD-95); Right example is characteristic of an inhibitory synapse (overlap of synapsin with GAD and absence of PSD-95). MHCI and C1q are closely associated with both types of synapses. (C) Single ultrathin section, showing colocalization between MHCI puncta and PSD, Synapsin, GAD and C1q. Bottom right, zoomed in view of puncta numbered on left, showing immunofluoresence signal in separate channels, Scale = 2μm. Note colocalization of signal for MHCI, PSD and C1q at puncta #1 and 2. (D) Cross correlations showing pairwise comparisons of degree of spatial overlap between puncta immunostained for the various markers (Experimental procedures and Figure S4 online). Synapsin vs. PSD95 shows strongest correlation, and GAD vs. vGluT2 the weakest. MHCI is more correlated with C1q than with other markers. Si/St = Cr, the correlation ratio between two channels as a multiple of their baseline correlation. Cr = 1 indicates no correlation, Cr ≫ 1 indicates high correlation, Cr < 1 indicates negative correlation.