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1 Supporting Information Balastik et al /pnas SI Text TRIM2 GT Mice PCR Genotyping. PCR genotyping was based on the known chromosomal localization of Trim2 gene on mouse chromosome 3, area E3 and a simple sequence length polymorphism (SSLP) between mouse strains C57/Bl6 (into which the Trim2 GT mice were back-crossed) and 129/Sv (the origin of the ES cells). The sequence of SSLP PCR markers was obtained from the Whitehead Institute homepage (www-genome.wi.mit-.edu/). Several markers that were localized within 0.1 cm distance from Trim2 locus were tested for PCR polymorphism between the two mouse strains. Primers D3Mit97L (ACTG- CATATGTATGTGTGCATG) and D3Mit97R (AGAACAT- GAAATAACCATGAAAAGC) were selected for genotyping consistently producing SSLP ( 107 bp C57/Bl6 and 101 bp 129/Sv) detectable by 6% agarose gel electrophoresis. Nonradioactive in Situ Hybridization. The sections were fixed in 4% PFA for 15 min at room temperature, washed in PBS, digested with 20 g/ml proteinase K solution at 37 C for 5 min and washed again in 0.2% glycin/pbs buffer. Following the proteinase K digestion, the sections were again fixed in 4% PFA 0.2% glutaraldehyde in PBS and incubated in hybridization buffer (50% formamid; 5x SSC; 1% blocking reagent (Roche); 5 mm EDTA; 0.1% Tween-20; 0.1% CHAPS; 0.1 mg/ml heparin; 1 mg/ml yeast total RNA) in a humidified chamber at 70 C for 2 h. The hybridization with a DIG- labeled probe diluted in hybridization buffer (1 g/ml) was performed overnight at 70 C in a humidified chamber. After the hybridization the sections were rinsed in 2 SSC (ph 4.5) buffer and washed three times for 30 min at 65 C in washing solution [50% formamide/2 SSC (ph 4.5)] and twice 10 min in KTBT buffer (0.05 M Tris-Cl; 0.15 M NaCl; 0.01 M KCl; 1% Triton X-100). Subsequently the slides were incubated in blocking solution (20% sheep serum in KTBT) for2hatroom temperature and overnight at 4 C with anti-dig alkaline phosphatase conjugate antibodies (1:2,000; Roche), washed with KTBT buffer (three times for 5 min. and three times for 30 min) and incubated three times for 5 min in NTMT buffer (100 mm Tris-Cl; 100 mm NaCl; 50 mm MgCl2; 0.05% Tween- 20; 2 mm levamisole). Finally, the color reaction was developed at room temperature in a dark humidified box with NBT-BCIP color substrate (Roche) usually for 2 5 h. The reaction was stopped by washing in 0.1% Triton X-100/PBS, sections were fixed in 4% PFA/PBS (10 min, room temperature), rinsed in PBS, and mounted in Mowiol. Pull-Down Assays of Endogenous NF-L from Brain Lysate. Neuro 2a cells transfected with c-myc tagged Trim2 were lyzed in 300 l of buffer A [50 mm Tris-HCl (ph 7.4); 150 mm NaCl; 0.5% Triton X-100; EDTA-free protease inhibitors, Roche) and spun at 16,000 g for 10 min at 4 C. Meanwhile, one-half of adult mouse cerebellum was homogenized on ice with Polytron (Brinkmann Instruments) in 1 ml of buffer B [50 mm Tris HCl (ph 7.4); 150 mm NaCl; 0.15% SDS; 1% Triton X-100; EDTAfree protease inhibitors (Roche)], sonicated on ice for 20 s and spun at 15,000 g for 15 min at 4 C. N2a cell lysate (150 l)was incubated overnight at 4 C with 150 l of cerebellar lysate and 50 l of anti-c-myc agarose beads (Vector). The beads were washed seven times with washing buffer [50 mm Tris HCl (ph 7.4); 150 mm NaCl; 0.75% Triton X-100] and analyzed by Western blotting. Preembedding Immunocytochemical Electron Microscopy. Freefloating sections were preincubated for 1hin20%normalgoat serum (NGS) diluted in TBS and then incubated for 48 h at 4 C with primary antibodies diluted in TBS-1% NGS. Two different primary antibodies have been used: rabbit polyclonal anti-nf-l raised against purified porcine NF-L (Chemicon) diluted 1:500 and mouse monoclonal anti-nf-l 68 clone NR4 (Sigma) diluted 1:250. Visualization of NF-L antigen antibody complexes was performed using anti-rabbit or anti-mouse affinity purified Fab fragment coupled to 1.4-nm gold particles (1:100, Nanogold; Nanoprobes Inc.). Gold particles were enhanced by silver amplification for 8 10 min using the HQ Silver kit following the manufacturer s instructions (Nanoprobes Inc.). Sections were then routinely processed for EM examination (2% OsO 4 ;1% uranyl acetate) and embedded in Durcupan ACM. Ultrathin sections (70 nm) were collected on pioloform-coated copper slot grids and analyzed in a Philips CM120 electron microscope. Lead citrate contrasting was used for both high-glutaraldehydefixed tissue and ImmunoGold/silver-labeled sections. At least four different blocks of each animal were cut for electron microscopy. 1of11

2 Fig. S1. GT vector integration into the Trim2 gene. (A) PCR and RACE-PCR were used to identify and confirm the insertion site of the GT vector within the Trim2 locus. The RACE-PCR primers were designed from the 5 part of the GT vector and the PCR primers from 5 part of the GT vector and 3 part of the TRIM2 exon 6 sequence. (B and C) Sequences obtained by the 5 RACE-PCR (B) and the PCR amplification of the insertion locus (C). 2of11

3 Fig. S2. Embryonic expression of TRIM2: TRIM2 is expressed in the developing nervous system. -Gal staining of heterozygous E12.5 embryos shows high TRIM2 expression in the spinal cord (arrows), dorsal root ganglia (arrowheads), hindbrain (h), and midbrain (m). 3of11

4 Fig. S3. Cerebellar degeneration in Trim2GT homozygous mice. (A and C) WT mice age-matched to those in B and D. (B and D) HE staining of 2-month-old Trim2GT mutants demonstrates Purkinje cell degeneration as a deficit in Purkinje cell somata. (Scale bars: 100 m.) 4 of 11

5 Fig. S4. Apoptotic degeneration of Purkinje cells. Purkinje cells positive for an apoptotic marker cleaved caspase-3 were present in 2-month-old TRIM2GT homozygous mice (B and D arrows) but not in 1-month-old homozygotes (A and C). (Scale bars: 100 m.) 5 of 11

6 Fig. S5. Degeneration of deep cerebellar neurons ultrastructurally resembles apoptosis. In a few neurons (asterisk) of the deep cerebellar nuclei at P45, we observed initial areas of condensation of the nuclear chromatin (indicated by the arrows) contained within an intact nuclear envelope, which were particularly evident near the nucleolus. These morphological features are suggestive of an early phase of apoptosis. This neuron is adjacent to a healthy presumed astrocyte. ncl, nucleolus. (Scale bar: 2 m.) 6 of 11

7 Fig. S6. Position of smooth endoplasmic reticulum (SR) and distribution of myosin V in Purkinje cells of TRIM2GT mutant mice. Electron micrographs of dendritic spines (s) of Purkinje cells in Trim2GT mutants (arrows, endoplasmic reticulum). (A C) Low- (A) and high- (B and C) magnification of the cerebellar cortex. In B and C, Purkinje cell spines in Trim2GT homozygous mice clearly show the typical stalks (arrows) resembling a spine apparatus. At, axon terminal. (D and E) Myosin V immunostaining of wild-type (D) and Trim2GT mutant (E) Purkinje cells at P30. (Scale bars: 200 nm in A and C; 25 nm in B; and100 m in D and E). 7 of 11

8 Fig. S7. TRIM2 - NF-L interaction in brain lysate and NF-L ubiquitination in vitro.(a) TRIM2 pulldown of NF-L from a cerebellar protein extract in the presence (line 2) or absence (line 4) of c-myc tagged TRIM2. The lower bands in lines 1 and 3 (supernatant) represent a partially degraded NF-L. (B) NF-L is ubiquitinated in an in vitro ubiquitination assay in the presence of UbcH5a E2. (C) NF-L ubiquitination in HeLa cells in the presence of endogenous UbcH5a (line 1), after overexpression of UbcH5a (line 2) and after overexpression of dominant-negative UbcH5a (line 3). 8of11

9 Fig. S8. Cortical NF-L inclusions in the Trim2 GT homozygous mice. NF-L immunostaining of mostly perikaryal NF-L inclusions (B Inset, arrows, counterstained with DAPI) in the frontal cortex (sagittal sections) of the Trim2 GT homozygous mice (B) and WT littermates (A). (Scale bars: 100 m.) 9of11

10 Fig. S9. Ubiquitin does not accumulate in the swollen axons of Purkinje cell in Trim2 GT homozygous mice at P30. CalbindinvD-28k immunostaining (A) detects numerous axonal swellings in the cerebellar white matter of Trim2 GT that do not colocalize (C) with ubiquitin immunostaining (B). (arrows, axonal swellings devoid of ubiquitin). (Scale bars: 50 m.) 10 of 11

11 Movie S1. Two months old Trim2 GT homozygous mice show tremor which is followed by progressive ataxia at around 3 months of age. Movie S1 (MPG) 11 of 11