A. A BLAST alignment identifying human KIAA1794 conservation with a portion of the Strongylocentrotus purpuratus (S.p.) ortholog of FANCD2. A star indicates the lysine corresponding to K561 in FANCD2
B. Alignment of FANCI and FANCD2 identifies a conserved lysine K523.
C. Schematic of FANCI and FANCD2. Highlighted are two regions predicted by the SCOP database (Murzin et al., 1995) as ARM repeats which represent alpha-alpha superhelix folds (aa 985–1207 in FANCI and aa 267–1163 in FANCD2) and a lipocalin fold (aa 612–650), which is predicted to bind hydrophobic ligands in its interior. Also shown is putative bipartite NLS (aa 779–795) identified in FANCI. Red stars indicate phosphorylation sites identified in human or mouse proteins (Matsuoka et al., submitted). Black stars indicate the ATR sites in FAND2. The EDGE sequence is also conserved between the proteins. An arrowhead indicates the disease-causing mutation in a cell line of Fanconi anemia complementation group I (see Figure 6).

A. Localization of the endogenous FANCI using BL999 and BL1000 antibodies. U2OS cells treated with 1 μM mitomycin C for 24 hours were triton-extracted before co-staining with anti-FANCI (BL999 or BL1000) and anti-FANCD2 antibodies.
B. Localization of FANCD2 in cells transfected with individual siRNAs against FANCI. U2OS cells were transfected with the indicated individual siRNAs against FANCI and treated with 1 μM mitomycin C. Twenty-four hours later, following triton extraction, the cells were co-stained with an antibody against FANCD2 and H2AX.
C. Western analysis of FANCD2 in U2OS cells transfected with individual siRNAs against FANCI. L is the long (monoubiquitinated) and S is the short form of the proteins. Asterisk indicates cross-reacting band.
D. Interaction of FANCD2 and FANCI. Total protein (0.5 mg) from PD20 fibroblasts expressing indicated constructs was immunoprecipitated with FLAG or control Myc antibodies under non-damaged conditions. The immunoprecipitates were analyzed by western blotting with a rabbit anti-FANCD2 or mouse anti-HA antibody.

A. Complementation of FANCD2 ubiquitination defects in FA-I cells by expression of WT FANCI. Cells stably transduced with empty vector, HA-tagged WT or K523R FANCI, were untreated or treated with 100 nM MMC and collected 24 hours later by lysis in Laemmli buffer. Western analysis with FANCD2, FANCI, and HA antibodies was performed. GM02188 (WT control) cells acted as a control for the presence of long (L, ubiquitinated) forms of FANCD2 and FANCI, which are absent in the uncomplemented BD0952 cells. The transduced form of the protein is identified as T (tagged) since it runs slightly slower than the endogenous (E) form. Also see Supplementary Figure 5B. B. Complementation of MMC sensitivity of BD0952 cells by expression of WT FANCI but not empty vector. Logarithmically growing cells of indicated genotypes were treated in triplicate with different levels of MMC ranging from 0 to 100 nM. They were allowed to grow for 6 days at which time they were harvested and total cell number was counted using a coulter counter. Total cell numbers at each dose were divided by the number of cells in the untreated sample to arrive at percent survival.
C. Sequence analysis of the FANCI genomic locus in BD0952 (FA-I) cells. Sequence of the genomic contig (ref|NT_010274.16|Hs15_10431:4714523–4889523 Homo sapiens chromosome 15 genomic contig, reference assembly), and sequence and sequence traces of genomic DNA from BD0952 cells, shown together with the resulting amino acid sequence deduced from the DNA sequence data.
D. Complementation of FANCD2 ubiquitination by expression of WT FANCI or P55L FANCI, but not R1285Q or P55L, R1285Q FANCI mutants. Cells stably transduced with the indicated alleles of FANCI were left untreated or were treated with 100 nM of MMC and processed 24 hours later as indicated in panel A.
E. Complementation of MMC sensitivity of BD0952 cells by expression of WT FANCI or P55L FANCI, but not R1285Q or P55L, R1285Q FANCI mutants. Experiments were done as indicated in Figure legend 6B.
F. Cytogenetic abnormalities in BD0952 cells cells expressing WT, K523R or R1285Q FANCI alleles. Indicated cells were treated with 0, 20 or 40 ng MMC per ml of media and analyzed for presence of chromosomal aberrations 48 hours later. K523R mutant was not assessed at 20 ng of MMC per ml. Analysis was done only once at 40ng of MMC per ml. 30–50 metaphases were evaluated for each cell line.

A. Western analysis with an antibody raised against a phosphorylated form of SMC3 (SMC3 pS1083) on immunoprecipitates performed with FANCI antibody (BL999) from 293T extracts before and after DNA damage.
B. Schematic of the multicolor competition assay (MCA). See text for details. In this example, the knockdown of a protein of interest caused the gfp cells to become DNA damage sensitive without influencing their proliferative capacity in the absence of damage. The relative resistance to damage of the si-treated cells is 40% of the non-si treated cells.
C. MCA analysis in U2OS cells treated with siRNAs against ATM and ATR and three different siRNAs against FANCI.
D. Cytogenetic abnormalities in IMR90 cells transfected with siRNA against KIAA1794 or LacZ control and treated with 0, 5, or 7.5 ng MMC per ml. Asterisk indicates a statistically significant difference in means as calculated by the t-test. Experiment with 7.5 ng MMC per ml was performed once.

A. Cells depleted for FANCI have checkpoint defects. U2OS cells were treated as shown in the schematic. Two separate fields of cells were examined. The mean and standard deviation from two fields are shown. Average of 1000 cells per siRNA were scored.
B. Effects of FANCI depletion on radio-resistant DNA synthesis. U2OS cells transfected with the indicated combination of three different siRNAs were irradiated with 5Gy or 10Gy of γ-IR depending on an experiment, allowed to recover for 30 minutes and assayed in triplicate for DNA synthesis. The means and standard deviations of four separate experiments are shown. For comparison, IR treatment of the ATM siRNA-transfected cells causes DNA synthesis to be 70–80% of the level found in the untreated cells.
C. Reduction of FANCI causes spontaneous DNA damage. U2OS cells transfected with the indicated combinations of three different siRNAs were collected three days later and the level of γ-H2AX was assayed without inflicting any exogenous damage. Western analysis with Ran antibody acted as a loading control.
D. Flow cytometric analysis of DR U2OS cells uninfected or infected with the AdNgus24i adenovirus carrying I-SceI (I-SceI-Ad) or AdCA36 carrying β-galactosidase (β-gal-Ad). Infections were carried out at an M.O.I. of 5 and analysis for gfp positive cells was performed at 36 hours after infection.
E&F. FANCI is required for homologous recombination. E. DR U2OS cells were transfected with the indicated combination of three different siRNAs and three days later were infected with 10 pfu/cell of adenovirus carrying I-SceI. Flow cytometric analysis of gfp positive cells was carried out 36 hours after infection. Mean and standard deviation of 8 experiments (ATM), 7 experiments (ATR), 4 experiments (Brca2) and 3 experiments (FANCI) are shown. F. DR U2OS cells were transfected with the indicated individual siRNAs, infected with 5 pfu/cell of adenovirus carrying I-SceI (AdNgus24i) and analyzed 24 hours later.

A. Western blot analysis of FANCI in U20S cells. U2OS cells were treated with 1 μM MMC and 24 hour later cells were lysed directly in 2x Laemmlie buffer. Long (L) and short (S) forms of FANCI are shown. The asterisk indicates a cross-reacting band.
B. In vivo ubiquitination of FANCI. Whole cell extracts of 293T cells transiently transfected with HA-tagged ubiquitin or control plasmid carrying dsRed marker were immunoprecipitated using antibodies raised against FANCI and analyzed by western blot with a FANCI antibody (left) and antibody recognizing the HA tag (right).
C. In vivo ubiquitination of FANCI. HeLa cells expressing ubiquitin tagged with His and a biotynylation signal were treated with 2 mM HU for 16 hours, lysed in 8M urea and precipitated using Streptavidin beads under denaturing conditions.
D. Chromatin fractionation of FANCI in U2OS cells. Cells were treated with 1 μM MMC and 24 hours later cells were collected and processed into cellular fractions. Whole cell extract (WCE), cytoplasmic proteins (S1), intact nuclei (P1), soluble nuclear proteins (S2), chromatin-enriched pellet (P2), soluble and insoluble fractions after micrococcal nuclease treatment (S2’ and P2’) are indicated. Orc2 antibody was used to follow the chromatin fraction.
E. Cell cycle analysis of FANCI ubiquitination. After release from nocodazole, cells were collected at indicated times for the western analysis (top panel) and for cell cycle analysis using flow cytometry (lower panel).
F. Analysis of ubiquitination in GM6914 (FA-A) fibroblasts. Cells expressing vector or WT FANCA were stably transduced with empty vector, or HA-tagged WT FANCI. Twenty-four hours after 1 μM MMC treatment cells were collected and western blotting was performed with the indicated antibodies.
G. Analysis of ubiquitination in PD20 (FA-D2) fibroblasts. Cells expressing vector, K561R mutant or WT FANCD2, were treated with 2mM HU and collected 15 hours later. Western blotting was performed with the indicated antibodies including FANCD2 antibody to confirm absence (lane 1 and 2) or presence (lanes 3, 4, 5, and 6) of FANCD2 protein. The asterisk indicates a cross-reacting band.
H. Ubiquitination of FANCD2 and FANCI in HeLa cells transfected with siRNA against USP1 and LacZ control, treated with 2 mM HU and collected 15 hours later. L/S indicates the ratio of the monoubiquitinated to non-ubiquitinated FANCI or FANCD2.
I. Localization of FANCI and FANCD2 in WT and K523R FANCI-expressing U20S cells. Cells stably transduced with the HA-tagged WT or K523R mutant allele of FANCI were treated with 1 μM MMC and processed 24 hours later for immunofluorescence. Note that cells not expressing K523R in the lower panels (K523R - triton) are included as controls for FANCD2 staining. Two FANCD2 positive cells in the lower right panel (+triton) are presumed not to have K523R FANCI expression although that cannot be tested directly since triton removes nucleoplasmic FANCI. Similar results were observed in U2OS cells expressing the K523R mutant treated with HU.

A. Localization of WT, P55L, R1285Q, and P55L, R1285Q mutant proteins in U2OS cells. U20S cells transduced with the indicated alleles of FANCI were treated with 100 nM MMC and 24 hours later were processed for immunofluorescence.
B. Model of Fanconi anemia ID complex regulation and function. The phosphorylation-ubiquitination cascade culminates in chromatin loading of the Fanconi anemia ID complex, which directs downstream repair events.