Charged multivesicular body protein 1A (CHMP1A; also known as chromatin-modifying protein 1A) is a member of the ESCRT-III (endosomal sorting complex required for transport-III) complex1,2 but is also suggested to localize to the nuclear matrix and regulate chromatin structure3. Here, we show that loss-of-function mutations in human CHMP1A cause reduced cerebellar size (pontocerebellar hypoplasia) and reduced cerebral cortical size (microcephaly). CHMP1A-mutant cells show impaired proliferation, with increased expression of INK4A, a negative regulator of stem cell proliferation. Chromatin immunoprecipitation suggests loss of the normal INK4A repression by BMI in these cells. Morpholino-based knockdown of zebrafish chmp1a resulted in brain defects resembling those seen after bmi1a and bmi1b knockdown, which were partially rescued by INK4A ortholog knockdown, further supporting links between CHMP1A and BMI1-mediated regulation of INK4A. Our results suggest that CHMP1A serves as a critical link between cytoplasmic signals and BMI1-mediated chromatin modifications that regulate proliferation of central nervous system progenitor cells.


As part of ongoing studies of human disorders affecting neural progenitor proliferation, we identified three families characterized by underdevelopment of the cerebellum, pons and cerebral cortex (Fig. 1a–d). In a consanguineous pedigree of Peruvian origin, three children in two branches were affected (Fig. 1e, family 1). Two additional pedigrees from Puerto Rico showed similar pontocerebellar hypoplasia and microcephaly (Fig. 1e, families 2 and 3). Brain magnetic resonance imaging (MRI) of affected individuals from all families showed severe reduction of the cerebellar vermis and hemispheres relative to normal individuals. Notably, the cerebellar folds (folia) were relatively preserved, despite the extremely small cerebellar size (Fig. 1a–d and Supplementary Videos 1 and 2). All affected individuals had severe pontocerebellar hypoplasia, although affected individuals in family 1 showed better motor and cognitive function than those in families 2 and 3 (Supplementary Note).

Figure 1: Brain MRI and linkage mapping of pontocerebellar hypoplasia with microcephaly.
Figure 1

(ad) T1-weighted sagittal brain MRIs of a neurologically normal individual (a) and affected individuals CH3102 (b), CH2402 (c) and CH2701 (d). Compared to control, affected individuals show mild reduction in cortical volume, thinning of the corpus callosum and severe hypoplasia of the pons, cerebellar vermis and cerebellar hemispheres. (e) Family 1 is a consanguineous pedigree from Peru in which three children from two branches are affected. Families 2 and 3 are both from Puerto Rico. Affymetrix 250K Sty SNP data for each child in families 1 and 2 are shown below (red or blue, homozygous SNP call; yellow, heterozygous SNP call), showing a region of homozygosity (dashed box) shared by all affected individuals in distal chromosome 16q. The graph aligned with the SNP genotyping data shows multipoint LOD scores calculated from microsatellite maker analysis of family 1 (Supplementary Fig. 1). Genes in the region of LOD of >3 are indicated to the right of the graph.

Genome-wide linkage analysis of families 1 and 2 using SNP microarrays implicated only one region on chromosome 16q as linked and homozygous in all six affected individuals (Fig. 1e and Supplementary Fig. 1), with a maximum multipoint logarithm of odds (LOD) score of 3.68 (Fig. 1e). Although families 2 and 3 are not highly informative for linkage analysis, their shared homozygosity provides additional support for the involvement of this locus. Furthermore, families 2 and 3 shared the same haplotype (Supplementary Fig. 1), suggesting a founder effect. Sequencing of 42 genes within the candidate interval at 16q24.3 revealed homozygous variants predicted to be deleterious only in the CHMP1A gene. CHMP1A (NM_002768) consists of seven exons encoding a 196-amino-acid protein (Supplementary Note). Affected individuals in families 2 and 3 had a homozygous nonsense variant in exon 3 predicted to prematurely terminate translation (c.88C>T, p.Gln30*; Fig. 2a,b). Family 1 showed a homozygous variant in intron 2 of CHMP1A (c.28–13G>A; Fig. 2a,b) predicted to create an aberrant splice acceptor site leading to an 11-bp insertion in the spliced mRNA product (Supplementary Fig. 2a). The two mutations were absent from dbSNP, 281 neurologically normal European control DNA samples (562 chromosomes), the 1000 Genomes Project database4 and approximately 5,000 control exomes from the National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We sequenced CHMP1A in 64 individuals with other cerebellar anomalies without finding additional mutations, but none of these affected individuals shared the rare and distinctive pattern of hypoplasia seen in the individuals with CHMP1A mutations.

Figure 2: Loss-of-function mutations in CHMP1A and dysregulation of INK4A in cell lines from affected individuals.
Figure 2

(a) Chromatograms showing homozygous mutations (red, indicated by arrows) in intron 2 (CH3101; c.28–13G>A; white background) and in exon 3 (CH2401; c.88C>T; black background) of CHMP1A. (b) Schematic of full-length wild-type (WT) CHMP1A. The mutation in CH2401 leads to premature termination of translation. The intronic mutation in CH3101 creates a novel splice acceptor site, and usage of this novel acceptor site causes a frameshift after exon 2, resulting in termination of translation after 36 amino acids. (c) Protein blotting of lysates from lymphoblastoid cell lines from CH2401 and CH3101 showing a complete loss of the 24-kDa band detected by antibody to CHMP1A in control lysate. Lysate from a cell line generated from CH3103 (the mother of CH3101) show 50% of the protein amount relative to the control. Protein amounts were normalized to the 40-kDa β-actin loading control bands. (d) Lymphoblastoid cell lines from CH2401 and CH3101 proliferate at a much lower rate than eight control cell lines. (e) qPCR analysis of CDKN2A-derived cDNA levels in human lymphoblastoid cell lines from CH2401 and CH3101 (normalized to GAPDH levels) shows nearly twofold higher expression of INK4A in these cells relative to four unrelated, neurologically normal control cell lines. The other transcribed isoform at the locus, ARF, shows no significant difference in expression in cells from affected individuals and control cells. (f) ChIP-qPCR in lymphoblastoid cell lines using an antibody to BMI1 shows an approximately eightfold enrichment of INK4A promoter DNA relative to a probe targeted 7-kb upstream of the locus in a control cell line. Enrichment is nearly half of this in cell lines derived from CH2401 with a homozygous mutation in CHMP1A. Enrichment at the ARF promoter is not significantly different from that observed in the control cell line. Error bars in df, s.e.m.

RT-PCR analysis of CHMP1A in lymphoblastoid cells from affected individuals from family 1 (CH3101 and CH3105) identified the predicted aberrant transcript with the 11-bp insertion and a second aberrant transcript with a 21-bp insertion but no normal CHMP1A transcript (Supplementary Fig. 2b). In the parents of affected children from family 1 and in unaffected control samples, only the normal transcript was detected, suggesting that the abnormal splice products are unstable. Protein blot analysis revealed a single 24-kDa band in a normal control individual, but no corresponding band was detected in affected individuals from families 1 and 2 (CH3101 and CH2401, respectively; Fig. 2c). In the parent (CH3103), the amount of CHMP1A was 50% relative to the amount detected in control lysate. Hence, this genetic study establishes CHMP1A null mutations as the cause of pontocerebellar hypoplasia and microcephaly in these pedigrees.

CHMP1A has been assigned two distinct putative functions as both a chromatin-modifying protein and a charged multivesicular body protein1,3. CHMP1A was originally identified as a binding partner of the Polycomb group protein Pcl (Polycomblike)3. In the nucleus, it has been suggested to recruit the Polycomb group transcriptional repressor BMI1 to heterochromatin, and overexpressed CHMP1A has been shown to arrest cells in S phase3. In the cytoplasm, CHMP1A is part of the ESCRT-III complex1,2. The ESCRT-III complex localizes to endosomes and interacts with VPS4A and VPS4B5 to assist in the trafficking of ubiquitinated cargo proteins to the lysosome for degradation6.

We investigated the potential effects of CHMP1A on Polycomb function by analysis of cell lines from two affected individuals harboring different CHMP1A mutations (CH3101 from family 1 and CH2401 from family 2), which show severely impaired doubling times compared to control cell lines, suggesting essential roles for CHMP1A in regulating cell proliferation (Fig. 2d). To examine BMI1 function in these cells, we performed quantitative PCR (qPCR) analysis of expression of the BMI1 target locus CDKN2A, which encodes alternative transcripts INK4A (also known as p16INK4A; NM_000077) and ARF (also known as p14ARF; NM_058195) in humans. This analysis revealed abnormally high expression of INK4A, the isoform implicated in cerebellar development, but not of ARF (Fig. 2e), suggesting derepression of INK4A. Chromatin immunoprecipitation (ChIP) with an antibody to BMI1 in control cell lines showed an approximately eightfold enrichment of BMI1 binding at INK4A promoter DNA relative to a control region 7 kb upstream, whereas cells from an affected individual (CH2401) showed only approximately half this enrichment in BMI1 binding (Fig. 2f). Enrichment of BMI1 at the ARF promoter was not substantial in this assay and was similar in both control cells and cell lines from affected individuals, consistent with the specificity of regulation of the INK4A isoform by BMI1 (Fig. 2f). Bmi1 has been shown to suppress the Cdkn2a locus and be required for neural stem cell self-renewal7. Our evidence suggests a role for CHMP1A in mediating BMI1-directed epigenetic silencing at the INK4A promoter but not at the ARF promoter.

We further explored the relationship between CHMP1A and BMI1 using morpholino-based knockdown experiments in zebrafish. Knockdown of the zebrafish CHMP1A ortholog (chmp1a; NM_200563) resulted in reduced cerebellum and forebrain volume compared to control, uninjected zebrafish, similar to the effects of human CHMP1A mutations and knockdown in zebrafish of BMI1 orthologs (bmi1a, NM_194366, and bmi1b, NM_001080751; Fig. 3a–e and Supplementary Figs. 3 and 4). A second morpholino targeting chmp1a led to a similar phenotype, and both morpholinos were partially rescued by the introduction of human CHMP1A mRNA, confirming morpholino specificity (Supplementary Fig. 4). The cerebellum consists of five major cell types, with the principal cell, known as the Purkinje cell, deriving from the ventricular epithelium, whereas granule cells derive from a separate progenitor pool known as the rhombic lip. Granule cell precursors then migrate over the outer surface of the cerebellum and form the external germinal layer (EGL) before migrating radially past the Purkinje cells to settle in the internal granule layer (IGL)8. Within the chmp1a-morphant cerebellum, the internal granule and molecular layers were severely affected (Fig. 3a,b), which is consistent with the relatively preserved folia pattern of the human cerebellum (thought to primarily be established by Purkinje cells) and severely reduced volume (which is determined mainly by granule cell quantity).

Figure 3: Genetic links between CHMP1A and BMI1 in zebrafish and mice.
Figure 3

(a,b) In parasagittal sections at 5 days post-fertilization (d.p.f.), zebrafish injected with chmp1a morpholino (MO) (b) show reduction in cerebellum and forebrain volume relative to control, uninjected zebrafish (a). Insets, images of the cerebellum highlighting loss of molecular and internal granular layers in the morphant (arrowheads). (cf) Compared to control, uninjected zebrafish (c), embryos with MO-based knockdown of chmp1a (d) show reduced head size, with the hindbrain more markedly reduced in thickness (asterisks). This effect is similar to that seen with knockdown of the zebrafish orthologs of BMI1, bmi1a and bmi1b (e). When the cdkn2a MO is co-injected with the chmp1a MO, the chmp1a knockdown phenotype is partially rescued (f). (g) Control or morphant embryos were classified 28 hours post-fertilization (h.p.f.) as normal, disrupted or severely disrupted (Online Methods). The number above each bar is the total number of embryos examined. *P < 0.001, two-tailed Pearson's χ-squared test. (h,i) In sagittal cross-sectional areas from the mouse cerebellum at P25, Bmi1−/− mice (i) have markedly reduced cerebellum size relative to Bmi1+/− mice (h), although foliation and the structure of the lobules (indicated by roman numerals) are generally preserved. Representative scale bars, 200 μm in a,c; 500 μm in h.

We then tested genetic interactions between chmp1a and the zebrafish ortholog of INK4A (cdkn2a; XM_002660468). Knockdown of cdkn2a alone did not result in noticeable abnormalities, and double knockdown of chmp1a and cdkn2a resulted in partial rescue of the brain morphology defects seen with chmp1a knockdown (Fig. 3f,g). This rescue was analogous to the rescue of the Bmi1-knockout mouse cerebellar phenotype in Bmi1- and Cdkn2a-double knockout mice9. Of note, there were also parallels in brain morphology between individuals with CHMP1A mutations and Bmi1-deficient mice, which show cerebellar hypoplasia10,11 (Fig. 3h,i). In Bmi1-null mice, the cerebellar architecture was generally preserved, but the thickness of the granular and molecular layers was markedly reduced10, and Bmi1-deficient mice show a modest reduction in cerebral volume10,12, similar to individuals with CHMP1A mutations (Supplementary Note).

Subcellular localization of CHMP1A seems to vary depending on the cell type. Confocal images of NIH 3T3 cells showed prominent exclusion of Chmp1a from the nucleus (mouse Chmp1a, NM_145606), where Bmi1 was detected (Fig. 4a). In contrast, confocal images of HEK 293T cells, although also showing predominantly cytoplasmic localization of CHMP1A, showed some nuclear immunoreactivity as well (Fig. 4b). Primary cultures of cerebellar granule cells from mice also showed predominantly cytoplasmic localization of Chmp1a, along with a speckled nuclear pattern (Fig. 4c). Overexpression of HA-tagged mouse Chmp1a in cultured granule cells resulted in abundant nuclear Chmp1a with a punctate expression pattern, confirming the speckled nuclear localization of endogenous Chmp1a (Fig. 4d) and consistent with earlier reports that CHMP1A can be present in the nucleus3. Even with Chmp1a overexpression, Chmp1a and Bmi1 do not prominently colocalize within the nucleus, which is also in agreement with previous data3.

Figure 4: CHMP1A and BMI1 expression in cultured cells and the developing mouse brain.
Figure 4

(a,b) Immunocytochemical analysis of NIH 3T3 cells (a) and HEK 293T cells (b). (c,d) Immunocytochemical analysis of mouse dissociated cerebellar granule cells (Cb GC) (c) and of these cells transfected with an expression construct encoding HA-tagged Chmp1a (d). Arrowheads indicate nuclear punctate staining for HA-Chmp1a. (e,f) Immunocytochemical analysis in mice of the developing cerebellum at P2 (P2 Cb) (e), P2 EGL cells (f) and the developing cerebral cortex at E13.5 (E13.5 Ctx) (g). EGL, external germinal layer; PC, Purkinje cells; IGL, internal granule layer; SVZ, subventricular zone; VZ, ventricular zone; CP, cortical plate. Scale bars, 20 μm in ae,g; 5 μm in f.

Immunohistochemical studies of the developing cerebellum and cerebral cortex in mice revealed widespread expression of Chmp1a in dividing and postmitotic cells. Chmp1a immunoreactivity was seen in the nucleus and cytoplasm of EGL, Purkinje and IGL cells at postnatal day (P) 2 (Fig. 4e,f and Supplementary Fig. 5). In the nucleus of these cells, Chmp1a immunoreactivity was seen in a speckled pattern. These speckles may be seen adjacent to Bmi1 signals, but they usually did not colocalize (Fig. 4f and Supplementary Fig. 5). At later stages of cerebellar development (P4, P10 and P29), Chmp1a expression persisted in Purkinje and granule cells (Supplementary Fig. 6). Embryonic day (E) 13.5 cerebral cortex showed widespread Chmp1a expression in the neuroepithelial cells (Fig. 4g). In the postnatal cerebral cortex (at P4, P10 and P29), Chmp1a expression in postmitotic neurons of the cortical plate gradually decreased and became almost undetectable by P29 (Supplementary Fig. 6). These expression studies confirm that Bmi1 and Chmp1a are often expressed in the same cells. However, the absence of widespread subcellular colocalization of Bmi1 and Chmp1a suggests that the regulation of Bmi1 by Chmp1a is perhaps not mediated by direct physical interaction.

Our data implicate CHMP1A as an essential central nervous system regulator of BMI1, which in turn is a key regulator of stem cell self-renewal. The dual cytoplasmic and nuclear localization of CHMP1A and its connection to the ESCRT-III complex position CHMP1A as a potentially crucial link between cytoplasmic signals and the global regulation of stem cells via the Polycomb complex.



Genetic screening.

The genetic study was approved by the Institutional Review Boards of Boston Children's Hospital and the University of Chicago. Appropriate informed consent was obtained from all involved human subjects.

The affected individuals and their parents from family 1 and the affected individuals from family 2 were subjected to genome-wide SNP screening with the Affymetrix GeneChip Human Mapping 250K Sty Array, performed at the Microarray Core of the Dana-Farber Cancer Institute. Microsatellite markers for fine mapping were identified using the UCSC Human Genome Browser13 and were synthesized with fluorescent labels (Sigma-Genosys). Two-point and multipoint LOD scores were calculated using Allegro14, assuming recessive inheritance with full penetrance and a disease allele frequency of 0.001. Sequencing primers were designed using Primer3 (ref. 15), and genomic DNA was sequenced using standard Sanger technology. Control DNA samples from neurologically normal individuals of European descent were obtained from the Coriell Cell Repositories (Coriell Institute for Medical Research). All nucleotide numbers are in reference to CHMP1A isoform 2 cDNA (NM_002768, with A of the ATG start site corresponding to +1) from the UCSC Genome Browser.

Analysis of CHMP1A splicing.

Splice prediction software NetGene2 (ref. 16) was used to determine the effect of the family 1 allele on CHMP1A splicing. Epstein-Barr virus (EBV)-transformed lymphocytes were grown in RPMI-1640 (Gibco) with 15% FBS (Gibco) and 1% penicillin/streptomycin in (Lonza) a humidified incubator at 37 °C in 5% CO2. RNA was isolated using the RNeasy Mini kit (Qiagen). Total RNA (5 μg) was used for first-strand synthesis with oligo(dT) primers and SuperScript III First-Strand Synthesis SuperMix (Invitrogen), and 1 μl of the product was used for the subsequent PCR reaction, with primers mapping from the 5′ UTR to exon 6 of CHMP1A (NM_002768). Primer sequences are listed in Supplementary Table 1.

Proliferation assay of lymphoblastoid cell lines.

EBV-transformed lymphoblastoid cell lines from eight control subjects and two affected individuals (CH2401 and CH3101) were grown. For each cell line, 2 × 107 cells were grown, and 1 × 106 cells were aliquoted into 4 sets of 5 T25 flasks filled with 10 ml of medium. Each set was allowed to grow for 24, 48, 72 and 96 h. Cell densities were estimated using a hemocytometer.


EBV-transformed lymphoblastoid cell lines were grown, and cDNA was generated. INK4A and ARF levels were quantified using the StepOnePlus Real-Time PCR System (Applied Biosystems) with GAPDH as a control. Primer sequences are listed in Supplementary Table 1.

ChIP assays.

ChIP was assays were performed as previously described17 with some modifications. For a single experiment, 2 × 107 EBV-transformed lymphoblastoid cells and 4 μg of the antibody to BMI1 (Abcam, ab14389) were used. qPCR reactions were performed using SYBR Green reagents (Applied Biosystems) and the StepOnePlus Real-Time PCR System. Primers were assessed for specificity by analysis of their melt curves, and a standard curve was determined using four tenfold serial dilutions for each primer using the input DNA samples. The standard curve from the input DNA was determined using 3 μl from each serial dilution as a template. Fold enrichment for each ChIP sample was determined by using 3 μl from each sample as a template and comparing the resultant amplification to the standard curve for that primer pair. Primer sequences are listed in Supplementary Table 1.

Zebrafish morpholino experiments.

ATG-targeting morpholinos were designed against chmp1a (chmp1a MO 1), bmi1a, bmi1b and the INK4A zebrafish ortholog (cdkn2a) (Gene Tools). In all experiments where bmi1 morpholinos were used, bmi1a and bmi1b were injected together. Injections were performed at the one-cell stage. Optimal doses for the chmp1a MO 1, bmi1a and bmi1b, and cdkn2a morpholinos were 4.5, 1.2 and 4.0 ng, respectively. At 28 h.p.f., the embryos were visualized using a stereo microscope (Zeiss). To confirm the specificity of the effects of the chmp1a MO 1 morpholino, a second ATG-targeting chmp1a morpholino (chmp1a MO 2) was designed. For this experiment, the dosages of injected chmp1a MO 1 and chmp1a MO 2 were 6.0 and 3.0 ng, respectively. Morpholino sequences are listed in Supplementary Table 1.

For the rescue experiment, morphants were screened at 28 h.p.f. and scored for the presence of a defect in the angle of the head to the tail (measured at the otic vesicle) or a deviation in the straightness of the tail18. Human CHMP1A cDNA was PCR amplified from control human lymphoblastoid cell total RNA. Primer sequences are listed in Supplementary Table 1. The PCR product was subcloned into the pCS2+ vector, and 5′-capped mRNA was synthesized in vitro using the mMESSAGE kit (Ambion). mRNA was diluted in 0.1 M KCl and was titrated for the rescue experiments.

For histological preparation, morphants were grown at 28 °C for 5 d, fixed overnight at 4 °C in paraformaldehyde (PFA) and embedded in 3% low-melt agarose blocks (in PBS), which were fixed again in 4% PFA in PBS overnight. The fixed agarose blocks were embedded in paraffin and sectioned at 5-μm thickness in the sagittal plane. Sections were stained by standard techniques with hematoxylin and eosin and were visualized using a bright field microscope (Nikon).

For protein blotting, zebrafish embryos were harvested at 48 h.p.f. They were dechorionated and deyolked as described19 and treated with lysis buffer (10% SDS and 0.5 M EDTA in 1× PBS) containing Complete Mini Protease Inhibitor Cocktail (Roche). Lysates were mixed with 2× Laemmli sample buffer, loaded onto a NuPage 4–12% Bis-Tris gel (Invitrogen) and run at 100 V for 2 h. Proteins were wet transferred onto Immobilon-P transfer membrane (Millipore) at 300 mA for 1.5 h at 4 °C. The membrane was blocked with Odyssey Blocking Buffer (LI-COR) and was incubated first with antibodies against Chmp1a (1:100 dilution; Abcam, ab104103) and β-actin (1:10,000 dilution; Abcam, ab6276) and then with IRDye secondary antibodies (LI-COR, 926-32212 and 926-68023). The LI-COR Imaging System was used for imaging and quantification.

Immunocytochemistry and immunohistochemistry.

NIH 3T3 and HEK 293T cells were grown in DMEM with 10% FBS and 1% penicillin/streptomycin and were fixed and stained with antibodies against Chmp1a (1:200 dilution; Abcam, ab36679) and Bmi1 (1:250 dilution; Abcam, ab14389) using standard techniques. Staining was visualized on a confocal microscope (Nikon).

All animal work was approved by Harvard Medical School, Beth Israel Deaconess Medical School and Boston Children's Hospital Institutional Animal Care and Use Committees.

Cerebellar granule neuron cultures from euthanized, P5 mouse pups were prepared as described20. After dissociation, cell density was measured using a hemocytometer, and 1 × 106 cells were plated on each poly-L-ornithine–coated coverslip with 500 μl of plating medium in a 24-well plate. After 1 d in vitro (d.i.v.) in a 37 °C incubator, 20 μl of 250 μM AraC (cytosine-1-β-D-arabinofuranoside) was added to each well to arrest mitosis of non-neurons. At 2 d.i.v., conditioned medium was collected from each well, and the wells were washed with DMEM. Cells were then transfected with the HA-Chmp1a mammalian expression construct (GeneCopoeia, EX-Mm15805-M06). Transfection solution (87.6 μl of HBSS and 4.4 μl of 2.5 M calcium chloride with 1.5 μg of plasmid DNA) was prepared at room temperature, and 35 μl of the transfection solution was added to a total of 400 μl of conditioned medium and then added to each well. After an additional 36 h (4 d.i.v.), cells were fixed with 4% PFA for 20 min at room temperature, washed with PBS and stained with antibodies against HA (1:100 dilution; Abcam, ab9110) and Bmi1 (1:250 dilution; Abcam, ab14389). Untransfected cells were processed similarly and were stained with antibodies against Chmp1a (1:200 dilution; Abcam, ab36679) and Bmi1.

Tissues were perfused with 4% PFA, dissected and fixed overnight in 4% PFA and were then embedded in paraffin and sectioned at 5- or 8-μm thickness. After rehydration of the slides in serial washes with xylene, 50% xylene in ethanol, 100% ethanol, 70% ethanol, 50% ethanol, 30% ethanol and finally in PBS, the slides were boiled in antigen-retrieval solution (Retrievagen A, BD Biosciences) for 8 min in the autoclave. Slides were blocked with PBS with 0.1% Triton X-100 supplemented with 1% donkey serum for 1 h at room temperature, and antibodies against Bmi1 (1:400 dilution; Millipore, clone F6), Chmp1a (1:300 dilution; Abcam, ab36679 and ab104103) or calbindin (Swant, CB300) were added in the blocking solution for overnight incubation at 4 °C. Slides were washed three times for 5 min per wash in PBS and were developed with secondary antibodies conjugated to Alexa-Fluor dyes (Invitrogen) for 1.5 h at room temperature. Slides were again washed three times for 5 min per wash in PBS and were mounted with Fluoromount-G (Southern Biotech) containing DAPI (1:1,000 dilution) and visualized on a confocal microscope (Nikon) or fluorescence microscope (Zeiss). For E13.5 and P2 cerebral cortex, frozen section specimens were used. For frozen sections, heads of E13.5 mouse embryos were directly fixed in 4% PFA, and P2 pups were perfused with 2 ml of 1× PBS and then with 4 ml of 4% PFA in PBS, followed by overnight fixation in 4% PFA. They were then placed in gradually increasing sucrose solutions (10%, 15% and 30%), each overnight, for cryopreservation and were then embedded in optimum cutting temperature (OCT) compound (Sakura Finetek) and sectioned at 20-μm thickness. The same antigen retrieval and staining procedure was used as for the paraffin-embedded sections.



  1. 1.

    , , & CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins. J. Cell Sci. 114, 2395–2404 (2001).

  2. 2.

    et al. A systematic analysis of human CHMP protein interactions: additional MIT domain–containing proteins bind to multiple components of the human ESCRT III complex. Genomics 88, 333–346 (2006).

  3. 3.

    , , & CHMP1 is a novel nuclear matrix protein affecting chromatin structure and cell-cycle progression. J. Cell Sci. 114, 2383–2393 (2001).

  4. 4.

    1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).

  5. 5.

    et al. ESCRT-III recognition by VPS4 ATPases. Nature 449, 740–744 (2007).

  6. 6.

    & The endocytic matrix. Nature 463, 464–473 (2010).

  7. 7.

    et al. Bmi-1 dependence distinguishes neural stem cell self-renewal from progenitor proliferation. Nature 425, 962–967 (2003).

  8. 8.

    , & The fetal cerebellum: development and common malformations. J. Child Neurol. 26, 1483–1492 (2011).

  9. 9.

    , , , & The oncogene and Polycomb-group gene bmi-1 regulates cell proliferation and senescence through the ink4a locus. Nature 397, 164–168 (1999).

  10. 10.

    et al. Bmi1 is essential for cerebellar development and is overexpressed in human medulloblastomas. Nature 428, 337–341 (2004).

  11. 11.

    et al. Posterior transformation, neurological abnormalities, and severe hematopoietic defects in mice with a targeted deletion of the bmi-1 proto-oncogene. Genes Dev. 8, 757–769 (1994).

  12. 12.

    et al. Bmi1 loss produces an increase in astroglial cells and a decrease in neural stem cell population and proliferation. J. Neurosci. 25, 5774–5783 (2005).

  13. 13.

    et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).

  14. 14.

    , , & Allegro, a new computer program for multipoint linkage analysis. Nat. Genet. 25, 12–13 (2000).

  15. 15.

    & Primer3 on the WWW for general users and for biologist programmers. in Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds. Krawetz, S. & Misener, S.) 365–386 (Humana Press, Totowa, New Jersey, 2000).

  16. 16.

    , & Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol. 220, 49–65 (1991).

  17. 17.

    et al. Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity–dependent polyadenylation site selection. Neuron 60, 1022–1038 (2008).

  18. 18.

    , , , & Stages of embryonic development of the zebrafish. Dev. Dyn. 203, 253–310 (1995).

  19. 19.

    , & Proteomics of early zebrafish embryos. BMC Dev. Biol. 6, 1 (2006).

  20. 20.

    & Cultures of cerebellar granule neurons. CSH Protoc. 2008, pdb prot5107 (2008).

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We thank the individuals and their families reported herein for their participation in this research. We thank M. van Lohuizen (Netherlands Cancer Institute) for providing the Bmi1-knockout mice, A. Wagers for help with breeding the Bmi1-knockout mice and P. Baas for sharing human DNA samples. This research was supported by grants from the US National Institute of Neurological Disorders and Stroke (NINDS; R01NS035129) and the Fogarty International Center (R21TW008223) to C.A.W., the Dubai Harvard Foundation for Medical Research, the Simons Foundation and the Manton Center for Orphan Disease Research. G.H.M. was supported by the Young Investigator Award of the National Alliance for Research on Schizophrenia and Depression (NARSAD) as a NARSAD Lieber Investigator. V.S.G. is supported by the Medical Scientist Training Program of Harvard Medical School, with financial support from the US National institute of General Medical Sciences (NIGMS). C.A.W. and L.I.Z. are investigators of the Howard Hughes Medical Institute. Microscopy and image analyses were performed with support from the Cellular Imaging Core of the Boston Children's Hospital Intellectual and Developmental Disabilities Research Center.

Author information

Author notes

    • Ganeshwaran H Mochida
    •  & Vijay S Ganesh

    These authors contributed equally to the work.


  1. Department of Medicine, Division of Genetics, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Ganeshwaran H Mochida
    • , Vijay S Ganesh
    • , Kutay D Atabay
    • , R Sean Hill
    • , Jillian M Felie
    • , Daniel Rakiec
    • , Danielle Gleason
    • , Brenda J Barry
    • , Jennifer N Partlow
    • , Wen-Hann Tan
    •  & Christopher A Walsh
  2. Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Ganeshwaran H Mochida
    • , Vijay S Ganesh
    • , Kutay D Atabay
    • , R Sean Hill
    • , Jillian M Felie
    • , Daniel Rakiec
    • , Danielle Gleason
    • , Brenda J Barry
    • , Jennifer N Partlow
    •  & Christopher A Walsh
  3. Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Ganeshwaran H Mochida
    • , Vijay S Ganesh
    • , Kutay D Atabay
    • , Katie L Kathrein
    • , Hsuan-Ting Huang
    • , R Sean Hill
    • , Jillian M Felie
    • , Daniel Rakiec
    • , Danielle Gleason
    • , Brenda J Barry
    • , Jennifer N Partlow
    • , Leonard I Zon
    •  & Christopher A Walsh
  4. Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.

    • Ganeshwaran H Mochida
    • , Wen-Hann Tan
    • , Laurie J Glader
    • , Leonard I Zon
    •  & Christopher A Walsh
  5. Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA.

    • Ganeshwaran H Mochida
  6. Harvard–Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, Massachusetts, USA.

    • Vijay S Ganesh
    •  & Athar N Malik
  7. Department of Morphologic Sciences, Cayetano Heredia University, Lima, Peru.

    • Maria I de Michelena
  8. Institute for Child Development–ARIE, Lima, Peru.

    • Hugo Dias
  9. Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Katie L Kathrein
    • , Hsuan-Ting Huang
    •  & Leonard I Zon
  10. Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Katie L Kathrein
    • , Hsuan-Ting Huang
    •  & Leonard I Zon
  11. Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Katie L Kathrein
    • , Hsuan-Ting Huang
    •  & Leonard I Zon
  12. Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Anthony D Hill
  13. Complex Care Service, Division of General Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Laurie J Glader
  14. Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA.

    • A James Barkovich
  15. Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA.

    • William B Dobyns
  16. Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.

    • Leonard I Zon
  17. Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.

    • Christopher A Walsh


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G.H.M. designed the study, interpreted clinical information and brain MRIs, identified the disease locus, helped sequence candidate genes, analyzed the sequencing data to identify CHMP1A mutations, helped analyze the functional data and wrote the manuscript. V.S.G. performed RT-PCR, protein blots, mouse histology and immunohistochemistry, qPCR, ChIP and zebrafish morpholino experiments and wrote the manuscript. M.I.d.M. and H.D. ascertained family 1 and provided clinical information. K.D.A. performed zebrafish protein blots and mouse immunohistochemistry. K.L.K. performed the morpholino injections. H.-T.H. and L.I.Z. assisted with the morpholino experiments. R.S.H. helped organize genetic data and calculate LOD scores. J.M.F. and D.G. organized human samples and helped perform sequencing experiments. D.R. organized human samples and helped perform microsatellite analysis. A.D.H. assisted in immunohistochemical studies and imaging. A.N.M. assisted in ChIP. B.J.B. and J.N.P. organized clinical information and human samples. W.-H.T. and L.J.G. provided clinical information for family 3. A.J.B. interpreted the brain MRIs of the affected individuals. W.B.D. ascertained family 2 and provided clinical information. C.A.W. directed the overall research and wrote the manuscript.

Competing interests

L.I.Z. is a founder and stockholder of Fate Therapeutics, Inc., and a scientific advisor for Stemgent.

Corresponding author

Correspondence to Christopher A Walsh.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–6, Supplementary Table 1 and Supplementary Note


  1. 1.

    Supplementary Video 1

    Brain MRI of CH2402. T1-weighted sagittal sequence reveals a very small cerebellum (vermis and hemispheres) and pons. There is no malformation of the cerebral cortex but the cerebral white matter volume is severely reduced with a fully formed but thin corpus callosum.

  2. 2.

    Supplementary Video 2

    Brain MRI of CH3102. T1-weighted saggital sequence shows a very small cerebellum (vermis and hemispheres), and pons. There is no malformation of the cerebral cortex but the cerebral white matter is moderately diminished in volume with a fully formed but thin corpus callosum.

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