Cell Reports

Report

Mutations in the b-Tubulin Gene TUBB5 Cause

Microcephaly with Structural Brain Abnormalities
Martin Breuss,1,11 Julian Ik-Tsen Heng,2,11 Karine Poirier,3 Guoling Tian,4 Xavier Hubert Jaglin,3 Zhengdong Qu,2
Andreas Braun,1 Thomas Gstrein,1 Linh Ngo,2 Matilda Haas,2 Nadia Bahi-Buisson,3 Marie-Laure Moutard,5
Sandrine Passemard,6,7 Alain Verloes,6,7 Pierre Gressens,6 Yunli Xie,8 Kathryn J.H. Robson,9 Deepa Selvi Rani,10
Kumarasamy Thangaraj,10 Tim Clausen,1 Jamel Chelly,3 Nicholas Justin Cowan,4 and David Anthony Keays1,*
1Institute of Molecular Pathology, Dr Bohr-Gasse, Vienna 1030, Austria
2Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
3Institut Cochin; INSERM Unité 1016; CNRS UMR 8104; Université Paris Descartes, Sorbonne Paris Cité Paris, France
4Department of Biochemistry and Molecular Pharmacology, New York University Medical Center, New York, NY 10016, USA
5Service de Neurologie Pediatrique, AP-HP, Hopital Trousseau, Paris, 75571, France
6INSERM UMR-676, Robert Debré Hospital, Paris, 75019, France
7Paris Diderot University, Department of Génétics, Robert Debré Hospital, Paris, France
8Institute of Molecular Biotechnology, Dr Bohr-Gasse 3, Vienna, Austria
9MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
10Centre for Cellular and Molecular Biology, Habsiguda, Uppal Rd, Hyderabad 500 007, India
11These authors contributed equally to this work

*Correspondence: keays@imp.ac.at
http://dx.doi.org/10.1016/j.celrep.2012.11.017

SUMMARY This sophisticated cellular journey relies on a myriad of intracel-

The formation of the mammalian cortex requires the
generation, migration, and differentiation of neurons.
The vital role that the microtubule cytoskeleton plays
in these cellular processes is reflected by the
discovery that mutations in various tubulin isotypes
cause different neurodevelopmental diseases, in-
cluding lissencephaly (TUBA1A), polymicrogyria
(TUBA1A, TUBB2B, TUBB3), and an ocular motility
disorder (TUBB3). Here, we show that Tubb5 is ex-
pressed in neurogenic progenitors in the mouse
and that its depletion in vivo perturbs the cell cycle
of progenitors and alters the position of migrating
neurons. We report the occurrence of three microce-
phalic patients with structural brain abnormalities
harboring de novo mutations in TUBB5 (M299V,
V353I, and E401K). These mutant proteins, which
affect the chaperone-dependent assembly of tubulin
heterodimers in different ways, disrupt neurogenic
division and/or migration in vivo. Our results provide
insight into the functional repertoire of the tubulin
gene family, specifically implicating TUBB5 in
embryonic neurogenesis and microcephaly.
lular and intercellular signaling factors that converge on the
cytoskeleton (Ayala et al., 2007). The importance of the micro-
tubule cytoskeleton in the sequential steps involved in migra-
tion and differentiation is reflected in the finding that mutations
in various tubulin genes cause a range of structural brain
abnormalities. Mutations in the a-tubulin subunit TUBA1A
have been shown to result in lissencephaly (Keays et al.,
2007); mutations in the b-tubulin subunit TUBB2B cause asym-
metric polymicrogyria (Jaglin et al., 2009); and it has been
shown that mutations in TUBB3 cause an ocular motility
disorder (Tischfield et al., 2010), as well as a broad range of
cortical abnormalities (Poirier et al., 2010). Most recently, the
tubulin genes TUBA1A and TUBB2B have also been implicated
in autism spectrum disorders (Neale et al., 2012; Pinto et al.,
2010). Together, these studies have implicated specific tubulin
isotypes in postmitotic cellular events, but those isotypes that
mediate the generation of neurons, a process that requires
the assembly of microtubules into a highly organized mitotic
spindle, remain unknown (Ohnuma and Harris, 2003). Here,
we set out to identify those tubulin genes required for cortical
neurogenesis. We report that the b-tubulin gene TUBB5 is
highly expressed in the developing cortex and that mutations
in this gene cause microcephaly, with a range of structural
brain abnormalities that include dysmorphic basal ganglia,
dysgenesis of the corpus callosum, brainstem hypoplasia,
and focal polymicrogyria.

INTRODUCTION
The formation of the mammalian cortex, a complex multilay-
ered structure, requires the birth of neurons in the ventricular
and subventricular zones followed by phases of bipolar and
multipolar migration before newly born neurons arrive at their
final destination in the cortical plate (Feng and Walsh, 2001).
RESULTS AND DISCUSSION
Tubb5 Is Expressed at High Levels in the Developing
Brain
We surveyed the expression of all known b-tubulin genes in
the developing mouse (E10.5, E12.5, E14.5, E16.5, P0) and

1554 Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors
human (gestational week [GW] 13, GW22) cortex by quantitative
real-time PCR (Braun et al., 2010). We observed consistently
high expression levels of Tubb2b, Tubb3, and Tubb5, with
Tubb5 the highest expressed isotype in the embryonic mouse
brain (Figures 1A and 1B). We investigated the spatial expres-
sion of Tubb5 by in situ hybridization at embryonic day (E)
12.5, E14.5, and E16.5 (Figures 1C–1H). This revealed robust
expression throughout the developing cortex, particularly in
the subventricular zone (SVZ) at E14.5, which was absent in
sense controls (Figures S1A–S1C). Because there are no vali-
dated antibodies that are specific for Tubb5, we created a trans-
genic mouse line that drives enhanced green fluorescent
protein (EGFP) from the endogenous Tubb5 promoter to deter-
mine which cell types express Tubb5 (Figures S1D–S1Q). This
mouse recapitulated our in situ hybridization results and
demonstrated that Tubb5 is expressed in radial glial cells
(Pax6 positive), intermediate progenitors (Tbr2 positive),
migrating neurons (Dcx positive), and postmitotic neurons (Tuj
positive; Figures 1I–1X).
Depletion of Tubb5 Perturbs the Progenitor Cell Cycle
and the Migration of Neurons
We investigated the effect of Tubb5 depletion on cortical devel-
opment in mice by employing a small hairpin RNA (shRNA) that
targets its 30 UTR. Following validation of this shRNA in Neuro-
2a cells (Figure S2A), we electroporated it into progenitor cells
of the ventricular zone (VZ) at E14.5, together with a GFP ex-
pressing vector (Figure 2A). Quantification of the fraction of
GFP-positive cells that coexpress pH3 (mitotic index) after
36 hr of knockdown revealed an increase in the percentage of
these mitotic cells in the VZ/SVZ when Tubb5 was depleted
(n = 6; p < 0.001). This effect could be rescued by codelivering
a Tubb5 expression construct that lacked the shRNA targeting
sequence (Figures 2B–2D; Figures S2D and S2E; Table S2)
and replicated when employing an alternative shRNA (data not
shown). Because mutations in Tuba1a have been shown to
induce apoptosis, we studied cell survival by staining for cleaved
caspase-3 at E16, following electroporation at E14.5 (Edwards
et al., 2011). This revealed no statistically significant difference
between conditions, but we cannot exclude the possibility of
increased apoptosis following long-term depletion of Tubb5
(Figures S2F–S2O). Next, we investigated the effect of Tubb5
depletion on neuronal migration by electroporating our shRNA
at E14.5 and harvesting embryos 72 hr later (migration index).
In comparison to controls, we observed a significant decrease
in the percentage of GFP-labeled cells in the cortical plate (CP)
when Tubb5 was depleted, concomitant with an accumulation
of cells within the VZ and intermediate zone (IZ) (n R 5; VZ:
p < 0.05; IZ: p < 0.05; CP: p < 0.01; Figures 2E–2G; Figures
S2B and S2C; Table S2). To assess whether Tubb5 depletion
affects the final positioning of neurons, we harvested brains at
postnatal day (P) 17, following electroporation at E14.5. Quanti-
fication of the percentage of GFP positive cells in the six layers of
the P17 cortex showed that Tubb5 knockdown results in a long-
term positioning defect (n = 4; layer VI: p < 0.05; layers II–IV:
p < 0.01) (Figure 2H). We conclude that Tubb5 depletion perturbs
the neurogenic cell cycle and alters the positioning of migrating
neurons.
Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors 1555
Mutations in TUBB5 Cause Microcephaly in Humans
On the basis of these results, we surmised that mutations in
TUBB5 might cause neurodevelopmental disease in humans.
We therefore screened a panel of patients with a range of brain
malformations, resulting in the identification of three unrelated
microcephalic individuals harboring de novo mutations in
TUBB5 (M299V, V353I, and E401K) (Figures S3A–S3C). Each
individual presented with microcephaly (with an orbitofrontal
cortex [OFC] ranging from 2.5 SD to 4 SD), dysmorphic basal
ganglia, corpus callosum abnormalities, and cognitive impair-
ment with motor and language delay (Table 1; Figures 3A–3F;
Figures S3E and S3F). Two of the patients (M299V and V353I)
shared unusual white matter streaks with a radial orientation
through the lenticular nucleus, as well as brainstem hypoplasia
(Figures 3A–3F). The child harboring the V353I mutation origi-
nates from a family with a history of microcephaly (without
mental retardation), raising the prospect that another genetic
factor contributes to his disease. Sequencing of known micro-
cephaly genes (MCPH1, CD5KRAP2, WDR62, ASPM) and the
known disease causing tubulins (TUBA1A, TUBB2B, and
TUBB3) did not identify any pathogenic variants in the patients
described. A search of publicly available genomic databases
showed that the M229V, V353I, and E401K mutations are not
present in the general population. Moreover, screening of ethni-
cally relevant controls (French/Caucasian, 238; Vietnamese,
115; Indian subcontinent, 252) failed to identify these variants.
Homology analysis showed that these residues are highly
conserved in all human b-tubulins and related tubulin isotypes
from yeast to humans (Figure S3D).
Functional Analysis of Disease-Causing Mutations
We mapped the location of the affected residues onto the known
structure of the a/b heterodimer (Figures 3G–3J). M299 lies in
a loop following helix 9, with its side chain protruding into
a deep hydrophobic pocket. V353 lies on the intradimer inter-
face, whereas E401, which precedes helix 12, lies on the surface
of the interdimer interface. This residue is in close proximity to
a loop (aa98–104) that is critical for nucleotide binding (Löwe
et al., 2001) and that may be reoriented by substitution with
a lysine residue. All three mutations have the potential to
compromise either the complex chaperone-dependent reac-
tions that are essential for tubulin heterodimer assembly or the
dynamic behavior of microtubules (Tian et al., 2010). To address
these issues, we monitored the expression and folding of the
mutant proteins kinetically in rabbit reticulocyte lysate. Analysis
of the products under denaturing conditions showed that the
translation efficiency of all three mutants was similar to the
wild-type control (Figure 3K). However, analysis of the same
reaction products under native conditions revealed quantitative
and qualitative differences (Figure 3L). The wild-type protein
and V353I and M299V mutants produced the expected folding
intermediates (CCT/b, TBCD/b, PFD/b, and TBCA/b) (Cowan
and Lewis, 2001) before generating a/b heterodimers when
chased with native bovine tubulin, but with a notable reduction
in yield for the M299V mutation. In the case of the E401K muta-
tion, the assembly pathway was arrested, with a conspicuous
retention of the mutant polypeptide complexed with prefoldin
(PFD) and the cytosolic chaperonin (CCT), and a dearth of native
A 100 B 160
90
140 GW13
80 Tubb1
relative mRNA level

relative mRNA level

GW22
120
70 Tubb2a
60 Tubb2b 100
50 Tubb2c 80
40 Tubb3
60
30 Tubb4
40
20 Tubb5

10 Tubb6 20
0 0
E10.5 E12.5 E14.5 E16.5 E18.5 P0 P6 TUBB1 TUBB2A TUBB2B TUBB2C TUBB3 TUBB4 TUBB5 TUBB6

C D I J K L

PP

IZ
E12.5

SVZ GFP
DCX GFP DCX

VZ M N O P

E F MZ

CP GFP
Tuj1 GFP Tuj1

IZ Q R S T
E14.5

SVZ

VZ GFP
Tbr2 GFP Tbr2
G H MZ
U V W X

CP
E16.5

IZ
GFP
Pax6 GFP Pax6

SVZ
VZ

Figure 1. Tubb5 Is Highly Expressed in the Developing Mouse and Human Brain
(A) Relative expression levels of b-tubulin genes in the developing mouse brain determined by quantitative real-time PCR at E10.5, E12.5, E14.5, E16.5, and E18.5
and postnatal days zero (P0) and six (P6) (n = 3). Note the early onset and consistently high expression of Tubb5.
(B) Relative expression levels of all the human b-tubulin genes in the developing brain at GW13 and GW22.
(C–H) In situ hybridization results obtained with an antisense probe specific for Tubb5 at E12.5 (C and D), E14.5 (E and F), and E16.5 (G and H). (D), (F), and (H)
show higher magnifications of (C), (E), and (G), respectively. Tubb5 is detected throughout the developing cortex with strong expression in the preplate at E12.5,
and in the SVZ at E14.5.
(legend continued on next page)

1556 Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors
a/b heterodimers. We also examined the capacity of the TUBB5
mutants to incorporate into the microtubule network in Neuro-2a
cells (Figures 3M–3X). Whereas the wild-type M299V and V353I
proteins coassembled into interphase microtubules, we found
that the E401K mutant protein failed to do so and was diffusely
distributed throughout the cytoplasm. We conclude that the
V353I and M299V mutations do not affect the ability of the
mutant polypeptides to assemble into heterodimers and incor-
porate into microtubules, although the yield in the case of
M299V may be compromised. In contrast, the E401K mutation
results in a severe ablation of TUBB5 function, as it results in
a massive failure of chaperone-mediated heterodimer assembly
with a consequent inability of the mutant protein to incorporate
into microtubules.
Effects of Human Mutations on Murine Neuronal
Development
To examine the effect of these mutations in vivo, we used in utero
electroporation to overexpress the mutant forms of Tubb5 in the
developing mouse brain. While overexpression of wild-type
Tubb5 had no effect on the mitotic index (n = 5; p > 0.5), we found
a large increase in the percentage of GFP/pH3-colabeled cells in
the VZ and SVZ when expressing the E401K and V353I mutants,
similar to our Tubb5 depletion experiments (n = 5; p < 0.001 for
both mutants; Figures 4A, 4D, and 4E). Electroporation of the
M299V expression construct also resulted in a modest increase
in the mitotic index within the cortical germinal zone (VZ + SVZ),
although this increase was not statistically significant (n = 5;
p > 0.05; Figures 4A and 4C). We also examined the migratory
index following expression of the Tubb5 mutants. In comparison
to controls, we found that expression of all three mutants re-
sulted in a significant increase in the percentage of GFP-positive
cells in the IZ and a corresponding decrease in the CP that was
most severe in the case of the V353I mutant (n = 5; M299V: IZ: p <
0.001; CP: p < 0.01; V353I: VZ: p < 0.01; IZ: p < 0.001; CP: p <
0.001; E401K: IZ: p < 0.001; CP: p < 0.01; Figures 4B and 4G–
4I). These changes were not observed upon overexpression of
wild-type Tubb5 alone (n = 5; p > 0.05; Figure 4F). Analysis of
neurons at P17 following the overexpression of Tubb5 mutants
revealed aberrant clusters of ectopic cells in deep layers of the
cortex (Figure S4). Quantification showed that in comparison to
controls, this results in fewer cells in superficial layers of the
cortex (n R 2; M299V: II–IV: p < 0.05; E401K: II–IV: p < 0.001)
and an accumulation of GFP-positive cells in the deeper layers
(E401K: n = 3; VI: p < 0.01), but this was not significant in the
case of the V353I mutation (n = 3; VI: p > 0.05). This result
demonstrates that the migratory defects described above have
a long-term effect on neuronal position, and consequently on
the structural architecture of the brain. Together, these data
support our conclusion that the mutations are pathogenic, with
an effect on both the generation and subsequent migration of
neurons.
(I–X) Antibody staining for Dcx (I–L), Tuj (M-P), Tbr2 (Q–T), and Pax6 (U–X) performed on coronal sections of the Tg (Tubb5-EGFP) mouse line at E14.5.
Grey scale images of (J), (N), (R), and (V) are shown in (K) and (L), (O) and (P), (S) and (T), and (W) and (X). All markers were found to colocalize with or in
GFP-positive cells.
Scale bars show 500 mm in (C), (E), and (G); 50 mm in (D), (F), and (H); 50 mm in (U); and 10 mm in (V). Error bars in (A) and (B) show SEM. See also Figure S1.
Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors 1557
The three mutations we identified (M299V, V353I, and E401K)
are likely to act by different molecular mechanisms (Walsh
and Engle, 2010). The impairment in heterodimer assembly
observed in the case of the E401K and M299V mutations
suggests that they act by loss-of-function; however, the marked
phenotype that results from heterologous expression of all
mutants in vivo raises the prospect of a dominant-negative
effect. It is conceivable that kinetically trapped E401K and
M299V polypeptides have a deleterious effect on the entire
chaperone-mediated tubulin folding and assembly pathway,
while the V353I mutation may alter the dynamic properties of
microtubules or compromise the binding of one or more essen-
tial microtubule associated proteins (Kumar et al., 2010; Tisch-
field et al., 2010; Walsh and Engle, 2010). The underlying cellular
pathology is likely to be equally as complex. We have shown that
both knockdown of Tubb5 and overexpression of Tubb5
mutants result in a paradoxical increase in pH3 reactivity. There
are a number of explanations for this unexpected result, which
implies an increase in mitotic output. First, it is conceivable
that there is an elongation of M-phase, which delays progression
of the cell cycle and the generation of neurons (Lizarraga et al.,
2010). Second, it is possible that hyperproliferating apical
progenitors result in fewer intermediate progenitors, and conse-
quently an overall reduction in postmitotic neurons (Kim et al.,
2009). Third, M-phase arrest may, at a later point in time, result
in increased apoptosis, accounting for the incongruity between
our in vivo pH3 results and the human phenotype. Further
studies focused on the timing and output of the cell cycle will
be necessary to establish which of the aforementioned mecha-
nisms are responsible.
It is apparent from this study that patients with mutations in
TUBB5 share structural brain abnormalities in common with the
previously described tubulinopathies (TUBA1A, TUBB2B,
TUBB3), including dysmorphic basal ganglia, abnormalities of
the corpus callosum, and brainstem phenotypes (Tischfield
et al., 2011). The distinguishing feature of TUBB5-associated
disease is microcephaly, which we attribute to the high level
of TUBB5 expression in neuronal progenitors. This contrasts
with TUBA1A, TUBB2B, and TUBB3, all of which are largely
restricted in their expression to postmitotic neurons in the devel-
oping brain (Gloster et al., 1999; Jaglin et al., 2009; Liu et al., 2007).
TUBB5 may have a specific function in mitotically active cells, or
alternatively make a critical contribution to the supply of tubulin
heterodimers. In either event, our work provides insight into the
functional repertoire of the tubulin gene family, specifically impli-
cating TUBB5 in embryonic neurogenesis and microcephaly.
EXPERIMENTAL PROCEDURES
Animals
Animals were maintained within the animal research laboratories of the Insti-
tute of Molecular Pathology and Monash University on a 12:12 light:dark
 A B 4 Mitotic Index scrshRNA

% of GFP+ cells that are pH3+

** shRNA
* pCIG2 Tubb5
pCIG2 Tubb5 + shRNA
3

*
2

0
(S)VZ IZ+ Total

C GFP D GFP
pH3 pH3

scrshRNA shRNA

E GFP F GFP G
DAPI DAPI MZ Migration Index
scrshRNA
60
shRNA
pCIG2 Tubb5
CP 50 * pCIG2 Tubb5 + shRNA
% GFP+ cells

40

30 **
IZ
*
20

10

0
VZ
VZ IZ CP MZ
scrshRNA shRNA

Positioning Index
H I J
**
100
scrshRNA
90 shRNA

80

70
% GFP+ cells

60

50

40

30

20
Cux1
10 GFP
0
* scrshRNA DAPI shRNA
VI V II-IV I
Cortex Layer

Figure 2. Tubb5 Depletion Perturbs Progenitor Mitosis and Alters the Positioning of Postmitotic Neurons
(A) Schematic illustrating the three different in utero electroporation experiments. After electroporation at E14.5, embryos were harvested 36 hr later to assess the
mitotic index, harvested 72 hr later to assess the migration index, or harvested at P17 to assess the positioning index.
(B) Quantitation of the mitotic index, showing the relative proportion of GFP positive cells that are also pH3 positive in the VZ and SVZ, IZ, and across all zones
(Total) for the following conditions: scrambled shRNA (scrshRNA); shRNA targeting Tubb5 (shRNA); overexpression of Tubb5 (pCIG2 Tubb5); and the rescue
experiment (pCIG2-Tubb5 + shRNA). Note that Tubb5 depletion results in a significant increase in the mitotic index in comparison to the scrambled control,
overexpression, and rescue experiments (n R 5; VZ and SVZ: p < 0.001; Total: p < 0.05).
(legend continued on next page)

1558 Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors
Table 1. Summary of Clinical, Neurological, Biochemical, Cellular and In Vivo Data Associated with TUBB5 Mutations
M299V V353I E401K
Ethnicity/Origin Caucasian Sri Lanka Vietnam/Caucasian
Sex Male Male Female
Age at last evaluation 2 years 6 months 4 years 10 months 2 years 8 months
OFC at birth 32 cm (3 SD) 31 cm (3 SD) 28.5 cm (4 SD)
OFC at last evaluation 2.5 SD 46.5 cm (4 SD) 42 cm (4 SD)
Cortical dysgenesis Focal polymicrogyria, localized band None apparent None apparent at 4 months
heterotopia
Basal ganglia Dysmorphic Dysmorphic Dysmorphic
White matter streaks White matter streaks
Cerebellum Hypoplastic and dysplastic cerebellar Possible white matter Large 4th ventricle
vermis abnormalities.
Corpus callosum Partial agenesis Thin and short but complete Partial posterior agenesis
Cognitive abilities Severe MR MR (global DQ:48) Mild developmental delay
Verbal abilities Severe language delay Limited language Delayed
Speech delay.
Motor abilities Severe motor delay, ataxia Motor delay. Walked at Motor delay. Walked at 25 months
21 months.
Other Retina dysplasia and micro-ophthalmia None apparent. Prenatal diagnosis of cardiopathy
Family history None Mother’s OFC is 4 SD None
Brother’s OFC is 2 SD
Sister’s OFC is 1 SD
Heterodimer folding Slightly impaired Not affected Severely impaired
Microtubule lattice Not affected Not affected No incorporation
incorporation
Mitotic index n.s. Significantly increased Significantly increased
Migration index Significantly decreased Significantly decreased Significantly decreased
Positioning index Affected n.s. Affected
Ectopic clusters at P17 Yes Yes Yes
OFC, orbitofrontal cortex; MR, mental retardation; DQ, development quotient; n.s., nonsignificant.

cycle with food available ad libitum. All procedures were performed in
accordance with existing animal licenses and guidelines (M58-006093-
2011-13 B).
Generation of Tg(Tubb5-EGFP) Mice
The Red/ET system (K001, Gene Bridges) was employed to replace the endog-
enous Tubb5 (RP24-330C1) with EGFP. Following generation of the construct,
we proceeded with pronuclear injection and PCR screening to confirm germ-
line transmission before immunostaining.
In Situ Hybridization
C57/BL6 embryos were harvested, postfixed in 4% paraformaldehyde
(PFA), dehydrated in a pressure- and temperature-controlled environment,
embedded in paraffin, and sectioned (14 mm). We then proceeded with
in situ hybridization as previously described (Braun et al., 2010).
Real-Time Quantitative PCR
Embryonic, postnatal, and adult tissues (C57/BL6) were dissected and
snap frozen before mRNA extraction and reverse transcription. Quantitative

(C and D) Representative images for the mitotic index experiment. Arrowheads highlight colocalization of GFP-expressing cells (green) with pH3 staining (red).
(E and F) Representative images showing the migration assessment following Tubb5 depletion. Note the conspicuous reduction in the proportion of GFP-positive
cells reaching the CP.
(G) Quantification of the percentage of GFP-positive cells in the VZ, IZ, CP, and marginal zone (MZ) for the migration index following treatment with a scrshRNA; an
shRNA targeting Tubb5 (shRNA); a Tubb5 expression construct (pCIG2 Tubb5); and the rescue experiment (shRNA + pCIG2 Tubb5). Tubb5 depletion results in
a moderate but significant increase in the percentage of GFP-positive cells located in the VZ and IZ and a decrease in the percentage of GFP-positive cells in the
CP (n R 5, VZ: p < 0.05; IZ: p < 0.05; CP: p < 0.01). This phenotype was partially rescued by coexpression of a Tubb5 isotype lacking the shRNA targeting
sequence (pCIG2 Tubb5 + shRNA). Note that overexpression of Tubb5 by itself has no effect on migration (pCIG2 Tubb5).
(H) Quantification of the percentage of GFP-positive cells in the six layers of the P17 cortex following treatment with an scrshRNA and a shRNA targeting
Tubb5. Tubb5 depletion results in a significant increase in the percentage of neurons in layer VI (n = 4; p < 0.05), with a concomitant decrease in layers II–IV (n = 4;
p < 0.01).
(I and J) Representative images for the positioning index in (H). The red channel shows Cux1 staining in layers II–IV.
Scale bars show 50 mm in (D), 100 mm in (F), and 200 mm in (J). Error bars in (B), (G), and (H) show mean ± SEM.*p < 0.05, **p < 0.01, ***p < 0.001. MZ, marginal
zone; scrshRNA , scrambled shRNA. See also Figure S2.

Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors 1559
A B C real-time PCR followed employing exon spanning primers and three internal
D E F (Heng et al., 2008; Pacary et al., 2011). Cell counting was performed blind to
G H I J
K L
M P S V
N Q T W
O R U X
Figure 3. Mutations in TUBB5 Cause Microcephaly and Affect the
Generation of Tubulin Heterodimers in Different Ways
(A–F) Coronal (A and D), sagittal (B and E), and horizontal (C and F) MRIs of
two patients with TUBB5-associated microcephaly (M299V and V353I).
(A–C) The patient with the M299V mutation has microcephaly (OFC of 2.5
SD), focal polymicrogyria (shown with arrowheads in A), severe brainstem
hypoplasia (shown with an arrowhead in B), partial agenesis of the corpus
callosum (shown with an arrow in B), and dysmorphic basal ganglia with
streaks of white matter (highlighted with an arrowhead in C). (D–F) The patient
with the V353I mutation has microcephaly (OFC of 4.0 SD), a hypoplastic
corpus callosum (shown with an arrow in E), and a dysmorphic basal ganglia
with streaks of white matter running through the lenticular nucleus (shown with
an arrowhead in F).
(G) Structural representation of a tubulin heterodimer highlighting the positions
of the mutated residues. The M299 residue is centrally located and is asso-
1560 Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors
control genes. For human studies, fetal brain cDNA was obtained from
Yorkshire Biosciences.
In Utero Electroporation Experiments
Sequence-verified constructs for wild-type and mutant versions of Tubb5
were cloned into pCIG2. shRNAs optimized for specific knockdown of
Tubb5 were cloned into the pSuper vector system. In utero electroporation,
cryosectioning, and immunostaining were performed as previously described
the condition on representative fields of sections of electroporated brains
using ImageJ software.
Biochemical and Cellular Studies
Plasmids encoding the Tubb5 mutants were expressed in rabbit reticulocyte
lysate (Promega) as described (Tian et al., 2010) before analysis on native
polyacrylamide gels. For cellular studies, FLAG-tagged TUBB5 DNA con-
structs were transfected into Neuro-2a cells before immunostaining with
an anti-a-tubulin antibody (Sigma, T6199-200UL) and an anti-FLAG antibody
(Abcam, ab1162).
Human Studies
We obtained DNA and informed consent according to the guidelines of
local institutional review boards at Cochin Hospital and INSERM. TUBB5
was screened in 120 individuals with sporadic structural brain abnormalities
that included lissencephaly, polymicrogyria, microcephaly, and nodular het-
erotopia. These patients had previously been screened for mutations in the
known disease-causing tubulin genes (TUBA1A, TUBB2B, TUBB3), and
(depending on their phenotype) for other pathogenic genes (e.g., DCX,
ciated with a deep hydrophobic pocket. V353 lies on the intradimer interface,
in contrast to E401, which is located at the interdimer interface.
(H–J) Higher-resolution images showing the mutated residues within the three-
dimensional structure of the tubulin heterodimer. (H) The M299 side chain is
surrounded by hydrophobic residues (M267, P305, Y310, F367, shown in
green) that could be disrupted by replacement with valine. (J) E401 lies in
proximity to a loop (98–104, shown in green) that is critical for the binding of
GTP (shown in yellow).
(K) Denaturing gel of in vitro 35S-methionine-labeled transcription/translation
reaction products for wild-type and TUBB5 mutants showing similar trans-
lational efficiencies.
(L) Kinetic analysis on nondenaturing gels of the products of in vitro tran-
scription/translation reactions for wild-type and TUBB5 mutants. Arrows (top
to bottom) denote the migration positions of the chaperonin (CCT)/b-tubulin
binary complex (CCT/b), the TBCD/b-tubulin cocomplex, the prefoldin
(PFD)/b-tubulin binary complex (PFD/b), the native tubulin heterodimer (a/b),
and the TBCA/b-tubulin cocomplex (TBCA/b), each assigned on the basis of
their characteristic electrophoretic mobilities. Note that the V353I mutant
polypeptide behaved similarly to wild-type controls, whereas there was a
diminished heterodimer yield in the case of M299V and little or no detectable
heterodimer in the case of E401K. Note also the absence of TBCA/b-tubulin
and TBCD/b-tubulin cocomplexes and a relatively long persistence of the PFD/
b-tubulin cocomplex in the case of reactions performed with the E401K
mutation. Min. chase indicates that reaction products generated after 90 min
were further chased with added native bovine brain tubulin so as to drive the
generation of tubulin heterodimers for the times shown.
(M–X) Expression of FLAG-tagged wild-type and mutant (M299V, V353I, and
E401K) TUBB5 in cultured Neuro-2a cells. Staining with the anti-FLAG anti-
body is shown in red and the microtubule cytoskeleton visualized using an anti-
a-tubulin antibody (shown in green). Note that wild-type FLAG-tagged TUBB5,
as well as the corresponding M299V and V353I mutants, incorporated into the
microtubule lattice (M–O, P–R, and S–U, respectively). This contrasts with the
E401K protein, which is distributed throughout the cytoplasm and failed to
incorporate into the cytoskeletal network (V–X). Scale bar in (X) is 10 mm.
See also Figure S3.
 A B
Mitotic Index Migration Index
ctrl ctrl
4 70 ** **
** * pCIG2 Tubb5
* * pCIG2 Tubb5
* **
% of GFP+ cells that are pH3+

pCIG2 Tubb5(M299V) 60 ** pCIG2 Tubb5(M299V)

3 pCIG2 Tubb5(V353I) pCIG2 Tubb5(V353I)
50

% GFP+ cells
pCIG2 Tubb5(E401K) pCIG2 Tubb5(E401K)
** 40
2
* **
* ** *
30 **
1
20 **
*
10

0 0
(S)VZ IZ+ Total VZ IZ CP MZ

C GFP D GFP E GFP

pH3 pH3 pH3

M299V V353I E401K

F GFP G GFP H GFP I GFP

DAPI DAPI DAPI DAPI

ctrl M299V V353I E401K

Figure 4. Expression of Disease-Causing Tubb5 Mutations In Vivo

(A) Quantification of the mitotic index for cells electroporated with control vectors (ctrl), a Tubb5 expression vector (pCIG2-Tubb5; note that this control is also
presented in Figure 2B), and the mutants identified (pCIG2-Tubb5(M299V), pCIG2-Tubb5(V353I), pCIG2-Tubb5(E401K)). Tubb5 overexpression resulted in
a mitotic index that was comparable to controls. In contrast, there was a large increase in the percentage of GFP-positive cells that are also pH3 positive in the VZ
and SVZ when expressing the E401K and V353I mutant constructs (n R 5; E401K and V353I: VZ + SVZ: p < 0.001; Total: p < 0.001). This increase in the mitotic
index was also apparent when overexpressing the M299V mutation, although the effect was not statistically significant (n R 5; p > 0.05).
(B) Quantification of the migration index for all five conditions (note that the Tubb5 overexpression control is also presented in Figure 2G). Overexpression of
the mutants results in an accumulation of GFP-positive cells in the IZ with a concomitant decrease in the CP (n = 5; M299V: IZ: p < 0.001; CP: p < 0.01; V353I: VZ:
p < 0.01; IZ: p < 0.001; CP: p < 0.001; E401K: IZ: p < 0.01; CP: p < 0.05) that was not observed when overexpressing Tubb5 alone (n = 5, p > 0.05).
(C–E) Representative images used for mitotic index assessment with arrowheads showing colocalization of GFP-expressing cells (green) with pH3 staining (red).
(F–I) Representative images used for migration assessment. Note the decrease in the relative number of cells reaching the upper layers of the cortex when
expressing the mutant constructs in comparison to controls (*p < 0.05, **p < 0.01, ***p < 0.001).
Scale bars show 50 mm in (E) and 100 mm in (I). (A) and (B) show mean ± SEM. See also Figure S4.

LIS1, FLNA). Following the identification of de novo mutations in TUBB5, Statistics

parental relationships were confirmed using a suite of microsatellite Statistical analysis was performed with the GraphPad Prism 5 software
markers. package. For experiments with two conditions, we performed a Student’s

Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors 1561
t test. For experiments with multiple conditions, we used a one-way ANOVA
followed by Bonferroni multiple comparison test.
For additional details, please see the Extended Experimental Procedures.
SUPPLEMENTAL INFORMATION
Supplemental Information includes Extended Experimental Procedures,
four figures, and two tables and can be found with this article online at
http://dx.doi.org/10.1016/j.celrep.2012.11.017.
LICENSING INFORMATION
This is an open-access article distributed under the terms of the Creative
Commons Attribution-NonCommercial-No Derivative Works License, which
permits non-commercial use, distribution, and reproduction in any medium,
provided the original author and source are credited.
ACKNOWLEDGMENTS
This study was supported by FWF (P21092, P24367) grants to D.A.K,
Fondation pour la Recherche Médicale (Equipe FRM 2007) and ANR
(2010 Blanc 1103 01) grants to J.C., and NIH grants (5R01HD057028 and
5R01GM097376) to N.J.C. J.I.H. is supported by an NH and MRC Career
Development Fellowship (ID:1011505). The Australian Regenerative Medicine
Institute is supported by grants from the State Government of Victoria and the
Australian Government. Thanks to Doug Higgs for access to control DNA
samples. D.A.K coordinated and designed this study with J.C. and N.J.C.
M.B. and A.B. performed the expression studies. J.I.H., M.B., Y.X., M.H.,
and Z.Q. performed the in vivo murine experiments. D.A.K., T.G., and K.P. per-
formed the genetic screening and sequencing. K.J.H.R., D.S.R., K.T., and M.B.
performed the control sequencing. N.B., S.P., M.M., A.V., and P.G. collected
and collated the clinical data. T.C. performed the structural modeling. G.T.,
X.H.J., and N.J.C. undertook the biochemical studies. M.B. conducted the
cellular studies with X.H.J. and L.N. M.B. prepared the figures. D.A.K. and
M.B. wrote the manuscript, and all authors commented on it.
Received: April 27, 2012
Revised: July 18, 2012
Accepted: November 21, 2012
Published: December 13, 2012
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Supplemental Information

EXTENDED EXPERIMENTAL PROCEDURES

Generation and Immunostaining of Tg(Tubb5-EGFP) Mice

A Bacterial Artificial Chromosome (BAC; RP24-330C1) containing the Tubb5 gene was first validated by restriction enzyme (FspI) and
PCR analysis. We employed high fidelity PCR to amplify a GFP-FRT-NEO-FRT cassette flanked by 60 base pair sequences homol-
ogous to the Tubb5 locus (see Table S1), and employed the Red/ET system (K001, Gene Bridges) to replace the endogenous Tubb5
gene. Following excision of the neomycin resistance cassette with a 707-FLPe plasmid (A104, Gene Bridges), we proceeded with
pronuclear injection, and PCR screening for genomic incorporation (see Table S1). Embryos were harvested at E12.5, E14.5 and
E16.5 and fixed in 4% PFA overnight before dehydration in 30% sucrose overnight, embedding and sectioning (12 mm). Sections
were incubated with the primary antibody overnight in 0.1%–0.3% triton/PBS with 2% of the appropriate serum at the following
concentrations: Dcx (1:100, Santa Cruz), Tuj1 (1:1000, Covance), Tbr2 (1:200, Abcam), Pax6 (1:300, Covance). For Tbr2 and Pax6
staining we performed antigen retrieval with citrate buffer (0.01M, pH6.0); slides were heated from room temperature to 90
C in
a water bath and then placed at to room temperature for 20 min prior to incubation with the primary antibody overnight (14-16 hr)
at 4
C. The next day, sections were washed 3 times in PBS (5 min each), before application of a species specific secondary antibody
(Molecular Probes) for 1 hr in 0.1%–0.3% triton/PBS. Sections were then mounted in VectaShield Mounting Medium (hard set with
DAPI). Microscopy was performed on a Zeiss LSM 710, with the exception of the low magnification images of the Tg(Tubb5-EGFP)
embryos that were captured with a Mirax slide scanner (Zeiss).

In Situ Hybridization
C57/BL6 embryos were harvested at E12.5, E14.5 and E16.5, post-fixed in 4% PFA, dehydrated in a pressure and temperature
controlled environment, embedded in paraffin and sectioned (14 mm). Prior to in situ hybridization these sections were de-paraffined
employing standard protocols. A 165 base pair probe for in situ hybridization was amplified by PCR (see Table S1), cloned into
a pCRII-TOPO vector (Invitrogen), the vector linearized and an in vitro transcription reaction conducted with a DIG labeling mix
(Roche). Sections were post-fixed with PFA (4% for 10mins) before pretreatment with proteinase K (1 mg/ml for 10mins), and acet-
ylated (0.1M triethanolamine, 0.25% acetic anhydride, 15mins). Following a prehybridization step (4hrs at RT) in hybridization buffer
(10mM Tris pH7.5, 600mM NaCl, 1mM EDTA, 0.25% SDS, 10% Dextran Sulfate, 1x Denhartdt’s, 200 mg/ml yeast tRNA) the dena-
tured probe was applied, and hybridized overnight at 60
C in a custom-built hybridization chamber. Post hybridization washes and
RNase treatment were performed as previously described (Murtaugh et al., 1999). Staining was visualized by incubating sections with
an alkaline phosphatase conjugated digoxigenin antibody (1:2000, 4
C, overnight), followed by the application of BM-Purple AP.

Real-Time Quantitative PCR

Embryonic (E10.5, E12.5, E14.5, E16.5, E18.5), postnatal (P0, P6) and adult (8 weeks) tissues (C57/BL6) were dissected and snap
frozen, before mRNA extraction employing either an RNeasy lipid tissue kit or an RNeasy fibrous tissue kit. RNA was extracted
from three independent samples at the same developmental time point, brain region or organ, quantified and then pooled for reverse
transcription (SuperScript III First-Strand Synthesis System, Invitrogen, 18080-051). For human studies fetal brain cDNA was ob-
tained from Biochain (C1244051, C1244035). For quantitative real-time PCR we designed intron-spanning primers employing the
Primer3 program, and undertook BLAST searches to confirm their specificity (see Table S1). Following efficiency testing, we did
quantitative real-time PCR with SYBR green on a Bio-Rad Cycler together with negative controls. To maximize the accuracy of
our real-time PCR experiments we used three internal control genes for our mouse (Pgk1, Tfrc, and Hprt) and human studies
(HPRT, PGK1, TBP), and calculated the geometric mean as previously described (Vandesompele et al., 2002).

Generation and Cellular Validation of shRNA Constructs

Short hairpin RNAs for Tubb5 knockdown were cloned into the pSuper vector system according to the manufacturer’s instructions
(VEC-pBS-0002). The efficiency of the short hairpin (see Table S1) was assessed by quantitative real-time PCR 36 and 72 hr post
transfection of the constructs with Lipofectamine 2000 (Invitrogen, 11668-027) into Neuro-2a cells. RNA extraction (Roche, High
Pure RNA Isolation Kit) and cDNA synthesis (Roche, Expand Reverse Transcriptase) were performed in accordance with the manu-
facturers’ protocol. Quantitative real-time PCR utilized the SYBR green dye on a Roche LightCycler. Tubb5 expression levels were
normalized relative to Hprt (see Table S1).

Cellular Studies
Neuro-2a cells were kept under standard cell culture conditions in DMEM supplemented with 10% FBS (Sigma, F7524), 1% L-Glu
(Sigma, G7513) and 1% PenStrep (Sigma, P0781). DNA constructs were transfected with Oligofectamine (Invitrogen, 12252-011) ac-
cording to the manufacturer’s protocol. Immunostaining employing an anti-a-tubulin antibody (Sigma, T6199-200UL) and anti-FLAG
antibody (Abcam, ab1162) was performed as previously described (Keays et al., 2007).

In Utero Electroporation Experiments

Sequence-verified expression constructs for wild-type and mutant versions of Tubb5 were cloned by PCR amplification of the coding
sequence followed by ligation into the EcoRI/XhoI site of pCIG2. In utero electroporation was performed as described previously

Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors S1

(Heng et al., 2008; Pacary et al., 2011). High-quality, low-endotoxin plasmid preparations (QIAGEN) of GFP expression vector (pCIG2)
and shRNA vectors were injected at 1 mg/ml for each plasmid, together with Fast Green (0.05%, Sigma). Electroporation of telence-
phalic vesicles of DNA-injected embryos was achieved using platinum electrodes (Nepagene) connected to an electroporator
(ECM830, BTX) to deliver five pulses of 30 V (50 ms duration) at 1 s intervals. Control electroporations for knockdown experiments
were performed with a scrambled shRNA in the pSuper vector with an empty pCIG2 vector. Control electroporations for Tubb5 over-
expression studies were performed with an empty pCIG2 vector together with an empty pSuper vector. Pregnant dams were sacri-
ficed by cervical dislocation, and the embryonic brains dissected and fixed in 4% PFA in PBS overnight. Following three washes in
PBS, the brains were incubated in 20% sucrose/PBS overnight before embedding in optimal cutting temperature compound. Cry-
osectioning (16 mm) was performed on a freezing microtome (Leica). Fluorescence immunostaining was performed as previously
described (Heng et al., 2008), and images were captured on an epifluorescence microscope (Olympus) equipped with a CCD camera
(SPOT). Subdivisions of the embryonic cortex (VZ, SVZ, IZ, and CP) were identified based on cell density as visualized with DAPI (40 6-
diamidino-2-phenylindole) staining. Cell counting was performed blind to the condition on representative fields of sections of electro-
porated brains using ImageJ software. Immunostaining for activated (cleaved) caspase-3 utilized a rabbit polyclonal antibody
(AB3623, Merck Millipore) at a 1:1,000 dilution.

In Vitro Transcription/Translation Reactions

Plasmids engineered for the T7-driven expression of wild-type, M299V, V353I, and E401K TUBB5 were used to drive expression in
rabbit reticulocyte lysate (Promega) containing 35S-methionine as described (Tian et al., 2010). At various intervals, aliquots were
withdrawn and analyzed on native polyacrylamide gels. In some cases, the reactions were supplemented (to a final concentration
of 0.2 mg/ml) with native bovine brain tubulin after 90 min and the incubation continued for a further 30 or 90 min.

SUPPLEMENTAL REFERENCES

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Genes Dev. 13, 225-237.
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PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3, RESEARCH0034.

S2 Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors

Figure S1. Negative Controls for Figure 1 and Analysis of the Tg(Tubb5-EGFP) Mouse Line
(A–C) Negative controls (sense probe) for the in situ hybridization experiments shown in Figure 1 for the indicated time points (E12.5, E14.5, E16.5).
(D–F) Littermate control of the Tg(Tubb5-EGFP) embryo shown in Figure 1, negative for the GFP transgene. Images were captured employing the same settings as
those shown in (G)-(Q); no background fluorescence can be detected.
(G–Q) Representative coronal (G, I-K, M-O, Q) and sagittal (H, L, P) sections of Tg(Tubb5-EGFP) embryos at the indicated time points (E12.5, E14.5, E16.5). (I) and
(M) show magnifications of the boxed regions shown in (G) and (K). High magnification confocal images of the developing cortex are shown in (J), (N), (Q). Note the
robust expression of EGFP throughout the developing cortex, consistent with our in situ studies. Scale bars show 1000 mm for (A–C), (G), (H), (K), (L), (O) and (P),
500 mm in (F), 50 mm for (J), (N) and (Q). DAPI staining (shown in blue) is visible in (G), (H), (K), (L), (O) and (P).

Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors S3

Figure S2. Supplemental Information to Figure 2 and Assessment of Apoptosis
(A) Relative expression level of Tubb5 mRNA in Neuro2a cells following transfection with a pSuper vector driving expression of a shRNA targeted to the 30 UTR of
this gene. This results in a 62% knockdown (36 hr) and 77% knockdown (72 hr) of Tubb5 mRNA levels. The error bars show the SEM (n = 3 independent
experiments for each time point).
(B and C) Representative images for the assessment of neuronal positioning following electroporation of pCIG2 Tubb5 and pCIG2 Tubb5 + shRNA.
(D and E) Representative images for the mitotic index assessment when electroporating with pCIG2 Tubb5 and pCIG2 Tubb5 + shRNA.
(F–N) Representative image of the apoptosis experiments showing the GFP channel (F-H), activated caspase-3 staining (I-K) and the merged image (L-N). Boxed
regions in F, I and L are shown in the adjacent panels (G, J, M) and (H, K, N). Panels H, K and N highlight the mediodorsal region of the cortex as an internal positive
control for caspase-3 staining. The magnified region in H, K and N show an apoptotic cell positive for caspase-3.
(O) Quantification of GFP+ cells co-localizing with activated capase-3. All conditions show less than 1% of co-localization. An ANOVA followed by a multiple
comparison test revealed no significant difference between the relevant experiments (scrshRNA, shRNA, pCIG2 Tubb5 and pCIG2 Tubb5 + shRNA; ctrl, pCIG2
Tubb5, pCIG2 Tubb5(M299V), pCIG2 Tubb5(V353I) and pCIG2 Tubb5(E401K)).
Scale bars show 50 mm in (C), 100 mm in (E), and 200 mm in (L).

S4 Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors

 A B C
M299V V353I E401K
Patient

Father

Mother

Translation
Parents AAG A A C ATG ATG ACA GCC GTC TGT ACA GGC GAG GGC
Lys Asn Met Met Thr Ala Val Cys Thr Gly Glu Gly

Translation
Patient AAG A A C GT G ATG ACA GCC ATC TGT ACA GGC AA G G G C
Lys Asn Val Met Thr Ala Ile Cys Thr Gly Lys Gly

D
290 300 310
TUBB5 Homo sapiens E L T QQV F DA K NMMA A CDP RHGRY L T
TUBB1 Homo sapiens E L T QQMF DA RNT MA A CDL RRGRY L T
TUBB2A Homo sapiens E L T QQMF DS K NMMA A CDP RHGRY L T
TUBB2B Homo sapiens E L T QQMF DS K NMMA A CDP RHGRY L T
TUBB2C Homo sapiens E L T QQMF DA K NMMA A CDP RHGRY L T
TUBB3 Homo sapiens E L T QQMF DA K NMMA A CDP RHGRY L T
TUBB4 Homo sapiens E L T QQMF DA K NMMA A CDP RHGRY L T
TUBB6 Homo sapiens E L T QQMF DA RNMMA A CDP RHGRY L T
290 300 310
TUBB5 Homo sapiens M299V E L T QQV F DA K NV MA A CDP RHGRY L T
TUBB5 Homo sapiens V353I E L T QQV F DA K NMMA A CDP RHGRY L T
TUBB5 Homo sapiens E401K E L T QQV F DA K NMMA A CDP RHGRY L T
TUBB5 Homo sapiens E L T QQV F DA K NMMA A CDP RHGRY L T
TUBB5 Pan troglodytes E L T QQV F DA K NMMA A CDP RHGRY L T
Tubb5 Mus musculus E L T QQV F DA K NMMA A CDP RHGRY L T
Tubb5 Rattus norvegicus E L T QQV F DA K NMMA A CDP RHGRY L T
TUBB5 Bos tauris E L T QQV F DA K NMMA A CDP RHGRY L T
TUBB5 Sus scrofa E L T QQV F DA K NMMA A CDP RHGRY L T
Tubb5 Danio rerio E L T QQV F DA K NMMA A CDP RHGRY L T
TUB2 S. cerevisiae E L T QQMF DA K NMMA A A DP RNGRY L T
340 350 360 390 400 410
S S Y F V E W I P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S CF V E W I P NNV K V A V CDI P P RGL S MF K RK A F V HW Y T S E GMDI NE F GE A E
S S Y F V E W I P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E W I P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E W I P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E W I P NNV K V A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E W I P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E W I P NNV K V A V CDI P P RGL K MF RRK A F L HW F T GE GMDE ME F T E A E
340 350 360 390 400 410
S S Y F V E WI P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E WI P NNV K T A I CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E WI P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GK GMDE ME F T E A E
S S Y F V E WI P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E WI P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E WI P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E WI P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E WI P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE T E F T E A E
S S Y F V E WI P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S S Y F V E WI P NNV K T A V CDI P P RGL K MF RRK A F L HW Y T GE GMDE ME F T E A E
S DY F V E WI P NNV QT A V CS V A P QGL D MF K RK A F L HW Y T S E GMDE L E F S E A E

E F

E401K E401K

Figure S3. Supplemental Information to Figure 3

(A–C) Sequencing traces for patients and parents showing the mutations in TUBB5 for M299V, V353I, and E401K together with the amino acid conversions. All
mutations are de novo. (D) Protein sequence alignment of b-tubulins present in humans (upper panel). Note the high conservation between the isoforms for all
three loci, with the exception of T299 in TUBB1, the most distinct of the human isoforms. The lower panel shows an alignment of TUBB5 homologs in a variety of
species. Note that the three disease causing residues are conserved from yeast to man. (E and F) Horizontal (E) and sagittal (F) MRI images taken at 4 months of
age for the patient harboring the E401K mutation. This individual presented with microcephaly (4 SD OFC), partial posterior agenesis of the corpus callosum,
and dysmorphic basal ganglia.

Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors S5

 A B C D E
I

II-IV

VI
Cux1
GFP
ctrl DAPI wild type M299V V353I E401K

F G
Positioning Index
100

90
ctrl *
pCIG2 Tubb5
**
80 pCIG2 Tubb5(M299V) * Cux1
pCIG2 Tubb5(V353I) M299V GFP
70 pCIG2 Tubb5(E401K) H
60
% GFP+ cells

50

40

30 V353I

20 ** I
10

0
VI V II-IV I
Cortex Layer

E401K

Figure S4. Positioning Index following Expression of Mutant Tubb5 In Vivo, Related to Figure 4
(A–E) Representative images of P17 mouse brains following in utero electroporation at E14.5 with plasmids expressing: (A) scrambled shRNA; (B) Tubb5 wt; (C)
Tubb5 M299V, (D) Tubb5 V353I, and (E) Tubb5 E401K. The cortical regions analyzed are indicated in A. The red channel shows Cux1 staining in layers II-IV. Note
the increased number of ectopic cells in deep cortical layers when overexpressing the Tubb5 mutants (M299V, V353I, E401K).
(F) Quantification of the percentage of GFP positive cells in layers I-VI of the P17 cortex for all five conditions (note that the control is also presented in Figure 2H;
see also Table S2). Overexpression of the Tubb5 mutants results in fewer cells in superficial layers of the cortex (M299V; II-IV: p < 0.05, E401K; II-IV: p < 0.001),
and an accumulation of GFP positive cells in the deeper layers (E401K; n = 3; VI: p < 0.01), but this was not significant in the case of the V353I mutation (n = 3; p >
0.05). Magnification of the boxed regions in (C), (D), and (E), showing ectopic clusters of GFP positive cells. Note that a number of these cells are also positive for
the post-mitotic marker Cux 1. *p < 0.05, **p < 0.01, ***p < 0.001. Data are mean ± SEM.
Scale bars show 200 mm in (E) and 100 mm in (I).

S6 Cell Reports 2, 1554–1562, December 27, 2012 ª2012 The Authors