Genomic–anatomic evidence for distinct functional
domains in hippocampal field CA1
Hong-Wei Donga,1, Larry W. Swansonb, Lin Chenc, Michael S. Fanselowd, and Arthur W. Togaa
aLaboratory of Neuro Imaging and Department of Neurology, School of Medicine, University of California, Los Angeles, CA 90095-7334;bDepartment
of Biological Sciences, University of Southern California, Los Angeles, CA 90089;cDepartment of Genomic Science, University of Washington,
Seattle, WA 98195; anddDepartment of Psychology and Brain Institute, University of California, Los Angeles, CA 90095-1563
Edited by Edward G. Jones, University of California, Davis, CA, and approved May 8, 2009 (received for review December 15, 2008)
Functional heterogeneity has been investigated for decades in the
hippocampal region of the mammalian cerebral cortex, and evi-
ing. Direct evidence that hippocampal field CA1 displays clear
regional, laminar, and pyramidal neuron differentiation is pre-
sented here, based on a systematic high-resolution analysis of a
publicly accessible, genome-wide expression digital library (Allen
Brain Atlas) [Lein et al. (2007) Genome-wide atlas of gene expres-
sion in the adult mouse brain. Nature 445:168–176]. First, genetic
markers reveal distinct spatial expression domains and subdo-
mains along the longitudinal (dorsal/septal/posterior to ventral/
temporal/anterior) axis of field CA1. Second, genetic markers
divide field CA1 pyramidal neurons into multiple subtypes with
characteristic laminar distributions. And third, subcortical brain
regions receiving axonal projections from molecularly distinct
patterns, suggesting that field CA1 spatial domains may be genet-
ically wired independently to form distinct functional networks
related to cognition and emotion. Insights emerging from this
genomic–anatomic approach provide a starting point for a de-
tailed analysis of differential hippocampal structure–function
genetics ? genomics ? hippocampus ? learning and memory ?
Lorente de No ´ (2), who named field CA3 (with large pyramidal
neurons and mossy fibers), field CA2 (with large pyramids but no
mossy fibers), and field CA1 (with small pyramids). The hippocam-
pus and other interconnected medial temporal lobe cortical areas
have been known for some time to be critical for learning and
functions are subserved as well (4–6). Overall, the evidence sug-
is involved in navigation and related spatial memory, whereas in
contrast the ‘‘ventral’’ (temporal or in humans anterior) hippocam-
pus influences stress responses and motivated or emotional behav-
iors. Experimental neuroanatomical work has established in rats
and primates that different transverse levels along the dorsoventral
differentiated and topographic way (7–11). Nevertheless, the exact
until now, been clearly established. Here, we directly parcel field
CA1 into multiple, spatially distinct molecular domains and sub-
domains using robust gene markers selected from a comprehensive
digital gene expression library (Allen Brain Atlas [ABA], www.
brain-map.org) (12) combined with hippocampal cytoarchitectonic
cortical area but instead displays clear regional and laminar spec-
ificity. These basic structural insights immediately suggest genetic,
physiological, and behavioral experiments to clarify exactly how
these molecular expression domains are differentially involved in
he basic outlines of hippocampal architecture were established
by the pioneering work of Ramo ´n y Cajal (1) and his student
two of the most complex cerebral functions—cognition and
More than 4,000 genes are expressed in the hippocampal for-
mation, based on data on the ABA web site. We first screened
expression patterns of ?2,000 genes in the hippocampal region,
based on expression level, expression density, and gene cluster-
ing. From this, we carefully analyzed expression patterns of 48
genes when we interrogated points in dorsal, intermediate,
ventral, and ventral tip parts of field CA1 (Fig. 1 A–C). Although
these genes display very heterogeneous expression patterns, we
found that many display consistent regional specificities in field
CA1. Using these genes as molecular spatial markers, we have
divided field CA1 into three distinct domains along the dorso-
ventral or longitudinal axis (Fig. 1D and Fig. S1): dorsal (CA1d),
intermediate (CA1i), and ventral (CA1v) domains. They are
visualized simultaneously in transverse mouse brain levels be-
tween 2.7 and 2.9 mm caudal to bregma where the maximal
dorsoventral extent of field CA1 is displayed (Fig. 1 D–F and Fig.
S1B). At these levels CA1d, CA1i, and CA1v occupy approxi-
mately the dorsal, intermediate, and ventral thirds of field CA1,
respectively. The CA1d–CA1i border here is parallel to the
ventral edge of the dentate gyrus lateral blade, whereas the
CA1i–CA1v border is approximately level with the dorsal edge
of the rhinal fissure (Fig. 1D and Fig. S1B). Rostral and dorsal
to these transverse levels CA1d extends to the rostral (septal) tip
of field CA1 (Fig. 1E and Fig. S1A), whereas caudally domain
CA1d is gradually replaced by pyramidal neurons of the dorsal
subiculum (Fig. S1 C and D), which is distinguished from domain
CA1d by lack of a stratum oriens. In contrast, domain CA1v
extends rostrally and ventrally for only a short distance (Fig. 1E).
Dorsolaterally domain CA1v is progressively displaced by the
ventral subiculum, until it merges with domain CA1i at the
caudal end of field CA1 (Fig. 1E and Fig. S1 C and D).
The extent of domain CA1d is uniquely defined by strong
expression of Wfs1 (Figs. 1 D–F and 2 and Fig. S1 A–D) and a
number of other gene markers including Nov, Kcnh7, Ndst4, and
2610017I09Rik, whereas domain CA1v is defined by strong and
unique expression of many other gene markers, including Dcn,
Grp, Htr2c, Col5a1, and Gpc3 (Figs. 1 D–F, 2, and 3 and Fig. S1
A–D). (The full names of these genes and image series numbers
of their corresponding full sets of gene expression images in the
ABA are listed in Table S1.) The middle third of field CA1
(CA1i) is characterized most obviously by the absence or much
Author contributions: H.-W.D., L.W.S., M.S.F., and A.W.T. designed research; H.-W.D. and
L.C. performed research; H.-W.D. analyzed data; and H.-W.D., L.W.S., L.C., M.S.F., and
A.W.T. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
1To whom correspondence should be addressed. E-mail: firstname.lastname@example.org.
This article contains supporting information online at www.pnas.org/cgi/content/full/
July 14, 2009 ?
vol. 106 ?
weaker expression of the above markers (Fig. 1 D–F and Fig. S1
A–D). However, many genes have expression patterns that help
to distinguish domain CA1i more directly. For example, Zbtb20
and Gpt2 are expressed in both domains CA1d and CA1i but not
in CA1v, with Zbtb20 expressed more strongly in CA1i than
CA1d (Fig. S1 B–D) and the reverse occurring for Gpt2. Of
fundamental importance, although the expression of many genes
in field CA1 may not be restricted to CA1d, CA1i, or CA1v, the
expression does consistently respect one of the boundaries
between them. Because genes expressed in domain CA1i are
more commonly also expressed in CA1d but not CA1v, CA1i is
possibly simply a subdomain of CA1d.
The concept of subdomains is an important one, especially in
domain CA1v where four are obvious (Figs. 1D and 2 and Fig.
S1B): dorsolateral (CA1vd), intermediodorsal (CA1vid), inter-
medioventral (CA1viv), and ventromedial tip (CA1vv). The tiny
CA1vv is very distinctive because of weak Grp expression (Figs.
1D and 2 and Fig. S1 B–D) and much stronger, localized Htr2c
and Col5a1 expression (Figs. 1 D–F and 2 and Fig. S1 B–D). In
addition, a number of other genes such as Gpr101 (Fig. 2) and
Dlk1are expressed almost exclusively in CA1vv. Genes expressed
in the other three subdomains display more or less overlapping
or gradient-type patterns. For example, Tc1568100 and
Loc432748 are weakly expressed in subdomain CA1vv, are
heavily expressed in CA1viv, and become progressively more
restricted to a single sublayer of pyramidal neurons in CA1vid
and then CA1vd (Fig. 2). Many other genes, including Zdhhc7
and Pole4, are expressed progressively more strongly in CA1vid,
CA1vd, and even CA1i—but not in CA1viv and CA1vv.
The size and shape of field CA1 pyramidal neurons and
differences with field CA3 pyramids are firmly established (1, 2),
and boundaries between these two hippocampal cortical areas
are clearly visualized with molecular markers (13, 14). However,
these pyramidal neuron populations have long been considered
relatively uniform within an area. The expression pattern het-
erogeneity described above next led us to reexamine carefully
field CA1 cytoarchitecture based on high-resolution Nissl-
stained images presented in the Allen Reference Atlas (ARA)
(15). We found that field CA1 cytoarchitecture is clearly heter-
ogeneous both regionally and with respect to pyramidal neuron
layers (Figs. 1D and 3 and Fig. S1 A–D). Following Swanson in
rats (16), we first divided the pyramidal layer into superficial and
deep sublayers. The cytoarchitecture of domain CA1d is char-
acterized by a remarkably darkly stained, densely packed super-
ficial pyramidal layer (CA1d-sps) and a thin deep layer with
many fewer pyramids (CA1d-spd; Fig. 1D1 and Fig. S1 A–D), as
originally described by Lorente de No ´ (2). The CA1d-spd is
considerably thinner rostrally, with mostly only one row of
pyramids (Fig. S1 A and B), but progressively thickens caudally
into 3 or 4 rows of loosely arranged pyramids (Fig. S1 C and D).
Nevertheless, expression patterns for most genes (such as Nov
and Ndst4) are very consistent from rostral to caudal in trans-
domains of field CA1. (D) One transverse level of the
field CA1 and its corresponding Nissl-stained histolog-
ical images. Distributions of five marker genes, Wfs1
(blue), Zbtb20 (green), Dcn (purple), Htr2c (red), and
Grp (yellow) are plotted on this level to reveal three
molecular domains of field CA1 (CA1d, CA1i, and
CA1v). (D1, D2, D3) High-resolution Nissl images that
contain CA1d, CA1i, and CA1v, respectively (see text
for details). (E) A three-dimensional model of Am-
mon’s horn (in the context of the whole mouse brain).
The overall shape of CA1 and its molecular domains
revealed by CA1 gene markers Wfs1 (blue), Dcn (pur-
ple), and Htr2c (red) occupy the outside surface of the
C-shaped cylinder of Ammon’s horn, with the dorsal
end (CA1d) extending much more rostral than the
ventral end (CA1v). These two domains merge at the
caudalmost end of CA1. (F) Three-dimensional expres-
sion patterns of 4 representative genes, Wfs1 (blue),
Grp (yellow), Dcn (purple), and Htr2c (red), in one
transverse plane of field CA1. These genes show dis-
CA1i (revealed here by lack of these gene markers).
Three-dimensional images of CA1 were generated in
BrainExplore (http://www.brain-map.org), one three-
dimensional model of the ARA (15, 40). See Fig. S1 for
more detailed mapping of these genes in 4 represen-
tative levels of the ARA. CTX, cerebral cortex; DGlb,
dentate gyrus, lateral blade; ENTl, lateral entorhinal
?m; D1, D2, D3, 212 ?m to match the same magnifi-
cations of the same images on ABA web site.)
(A–C) Overall gene expression ‘‘heat maps’’
Dong et al.PNAS ?
July 14, 2009 ?
vol. 106 ?
no. 28 ?
show much stronger expression in rostral levels of CA1d than in
more caudal levels, and a few others (including Kit) present the
reverse gradient. Wfs1 and Nr4a1 are expressed in both CA1d-
specifically in CA1d-sps, and Ndst4 and Astn2 are expressed
preferentially in CA1d-spd (Fig. 3). Some neurons in the stratum
oriens also express Astn2. Compared with domain CA1d, the
superficial pyramidal layer of CA1i (CA1i-sps) is much less
dense and more lightly stained, whereas the deep layer (CA1i-
spd) is relatively thicker with 3 or 4 rows of pyramids (Fig. 1D2
and Fig. S1B).
CA1v displays even more complex cytoarchitecture. In addi-
tion to superficial (CA1v-sps) and deep (CA1v-spd) pyramidal
layers, a middle sublayer (CA1v-spm) containing smaller pyra-
mids appears to be sandwiched between the other layers in
subdomains CA1vd and CA1vid (Fig. 1D3 and Fig. S1B). In the
progressively more ventral CA1viv, the middle pyramidal sub-
layer disappears, and pyramidal neuron morphology becomes
less distinguishable between the superficial and the deep layers
(Fig. 1 D and D3 and Fig. S1B). On reaching subdomain
CA1vv—the ventral tip of field CA1—pyramids align in an
apparently uniform, evenly stained, thick layer of approximately
7–9 neuronal rows (Fig. 1D and Fig. S1B). This cytoarchitectonic
sublamination pattern in CA1v is substantiated by gene expres-
sion patterns. First, Grp is expressed strongly in both CA1v-sps
and CA1v-spd but weakly in CA1v-spm (Figs. 2 and 3 and Fig.
S1B); Dcn is expressed strongly in CA1v-sps but weakly in
CA1v-spd and CA1v-spm (Fig. 3 and Fig. S1 B–D), whereas
Htr2c and Gpc3 are strongly expressed in CA1vv, but only in the
Fig. S1 B–D). Second, Tc1568100 and Loc432748 are expressed
spm (Fig. 2), whereas Prss23 is expressed specifically in the deep
layer of CA1viv, CA1vid, and CA1vd and in CA1i (Fig. 3). And
third, Prss12 is expressed specifically only in the striatum oriens
of domain CA1v (Fig. 3). Interestingly, some genes display
laminar differences in different domains. For example, Calb1 is
expressed selectively in the superficial layer of CA1d and CA1viv
but is expressed more strongly in the deep layer of CA1i, CA1vd,
and CA1vid (Fig. 3).
Next, we examined global spatial gene expression pattern
correlations between these field CA1 molecular domains and
other brain regions (Fig. 4; all correlation coefficients provided
in Table S2). We found that domain CA1d exhibits a high level
of intrastructural correlation between different transverse
planes of CA1d, but lower correlations with domain CA1v,
confirming their molecular specificities across the dorsoventral
rather than the rostrocaudal axis. As expected from earlier
results (above), domain CA1i expression patterns are correlated
more with those of CA1d than with CA1v. Most interestingly,
probabilistic coexpression correlations of domains CA1d and
CA1v subdomains are labeled: a (CA1vd), b (CA1vid), c (CA1viv), and d (CA1vv). Images in (C) are gene expression heat maps of corresponding images in (B) (for
definition of heat map, see ABA web site, http://www.brain-map.org) that display relative intensities of gene expression signals. All images were downloaded
from the ABA web site. (Gene names and the image series numbers of their original digital images are listed in Table S1.) Overall expression patterns of Wfs1,
Zbtb20, and Grp in the hippocampus are schematically mapped in more detail in Fig. S1. All images in the same panels have the same magnifications. Scale bars
are displayed in the lower right corner of Gpr101 images.
Digital images of six representative genes expressed specifically in three molecular domains of field CA1: CA1d (Wfs1), CA1i (Zbtb20), CA1v (Grp), and
specificities of field CA1 pyramidal neurons. For high-
of pyramidal neuron sublayers, see Fig. 1 and Fig. S1.
CA1v subdomains are labeled: a (CA1vd), b (CA1vid), c
(CA1viv), and d (CA1vv). All digital images were down-
loaded from the ABA gene expression library. (Gene
names and the image series numbers of their original
digital images are listed in Table S1.) Images in the same
rows have the same magnifications.
Gene markers showing regional and laminar
www.pnas.org?cgi?doi?10.1073?pnas.0812608106Dong et al.
CA1v with other brain regions are very distinctive. For example,
although both domains exhibit very high correlation values with
the cortical mantle as a whole, domain CA1v shows higher
correlation values than CA1d with cortical amygdalar areas and
the basolateral amygdalar complex, both of which share direct
bidirectional axonal connections with CA1v (10, 11, 17, 18). In
terms of subcortical regions, CA1v displays strikingly higher
coexpression correlations than CA1d with neuron populations
associated with autonomic, neuroendocrine, and affective be-
haviors, including the central and medial amygdalar nuclei,
intermediate and ventral parts of the lateral septal nucleus, bed
nuclei of the stria terminalis, and hypothalamus—all of which
share massive direct and indirect neuronal connectivity with
CA1v (9, 10, 17–19). These obvious correlations strongly suggest
that CA1d and CA1v are genetically wired independently with
different functional specificities.
Finally, Risold and Swanson (9, 16) proposed the existence of
a series of structure–function domains along the longitudinal
axis of field CA1 and adjacent subiculum that send topograph-
septal nucleus that in turn share bidirectional connections with
hypothalamic structures mediating the expression of different
classes of innate motivated behavior. To explore potential
genetic mechanisms underlying this topographic wiring pattern,
we compared coexpression patterns of CA1 domain-specific
genes with those of the lateral septal nucleus. We found that a
number of CA1 domain-specific genes are also expressed in the
lateral septal nucleus and that their coexpression correlations
respect the topologically ordered dorsal-to-dorsal and ventral-
to-ventral organization of their axonal projection connectivity.
such as Wfs1 and Matn2, are also strongly expressed in the caudal
end of the caudal and rostral lateral septal nucleus (LSc, LSr),
which are topologically dorsal (Fig. 4D). In contrast, Dlk1 and
Gpr101—the CA1vv (and ventral subicular) marker genes—also
show strong expression patterns in the ventral lateral septal
nucleus (LSv). Genes that show significant expression in more
dorsal subdomains of CA1v are most likely also to coexpress in
ventral levels of the LSr. Thus, Loc432748, a specific marker
gene for CA1viv, presents specific signal only in a specific zone
of the LSr. Gpc3 and Htr2c, which are strongly expressed in
CA1vv and the rest of domain CA1v, are strongly expressed in
7 . 2 - = a
7 . 2 - = a
6 . 1 - = a
0 . 0 = a
maps result from setting seed voxel points in
domain CA1d (A), CA1i (B), and CA1v (C) at
three representative transverse levels of the
mouse brain at approximately bregma ?2.739
(a, b, c), ?1.656 (a?, b?, c?), and 0.029 (a?, b?, c?).
bottom. The coexpression correlation coeffi-
cients of these CA1 molecular domains with
a detailed description of AGEA spatial gene
expression correlation map, see Ng et al. (24).
(D and E) Correlated gene expression patterns
of domain CA1d marker gene Matn2 and CA1v
marker gene Gpc3 in the lateral septal nucleus.
(Scale bars: D and E, 421 ?m.)
Global gene coexpression ‘‘energy’’
Dong et al.PNAS ?
July 14, 2009 ?
vol. 106 ?
no. 28 ?
the LSv and LSr but not in LSc (Fig. 4E). Man1a and Zdhhc7,
which are expressed throughout field CA1 (except in CA1vv),
of the topology and topography of these gene expression cor-
relations with the hippocampal functional domains defined by
Risold and Swanson in rat (9, 16), CA1vv defined here appears
to correspond well to their Domain 5—the ventral tip of field
CA1 and subiculum, which sends projections specifically to the
LSv (9)—one of the primary sources of cerebral inputs to the
hypothalamic neuroendocrine zone and region controlling feed-
ing behavior. The progressively more dorsally located CA1viv,
CA1vid, and CA1vd may correspond to their Domains 2–4.
These CA1v subdomains send topographic projections to
different zones of the LSr, which in turn project to the
hypothalamic medial column that controls two basic classes of
social behavior—reproduction and defense (9). Finally, CA1d
and CA1i together may correspond to their Domain 1, which
theta-rhythm-controlling supramammillary nucleus (8). The dens-
est outputs of dorsal CA1 have been shown to be to the dorsal
subiculum (11)—the major source of the postcommissural fornix
pathway innervating the medial and lateral mammillary nuclei and
anterior thalamic complex. As a matter of fact, this dorsal CA1 to
subiculum projection is the major hippocampal component that
processes spatial memory (20–22).
Many gene markers have been used as reproducible landmarks
for defining nervous system divisions at various stages of devel-
opment (23) and in the adult (15). This is an extension of the
revolutionary chemical neuroanatomy approach that began in
the 1950s with cholinesterase histochemistry, followed by histo-
fluorescence and then immunohistochemistry (see ref. 15). The
resulting chemoarchitectonic data greatly refined classical cyto-
architectonics based on Nissl staining. The present study, com-
bined with two recent reports (24, 25), supply proof-of-principle
examples of how the genomic–neuroanatomic approach can
further refine architectonic maps and identify neuronal pheno-
types amenable to selective experimental genetic manipulation.
Although raw data about these expression patterns (digitized
images) are freely available on the ABA web site and powerful
online informatics tools enable users conveniently to identify
regionally specific gene expression patterns, synthesis and inter-
pretation of this information relative to existing structural,
functional, and behavioral knowledge is still required. Specifi-
cally, we provide here a testable model to guide and stimulate
further analysis of hippocampal structure–function in health and
Our genetic–anatomic analysis and the current axonal con-
nectivity literature (7–11, 17–19, 26) suggest that domains CA1d
and CA1i lie in approximately the dorsal half of the hippocam-
pus, and they display strong global gene expression correlations
primarily with other parts of cerebral cortex and subcortical
regions innervated by dorsal hippocampus and related to theta-
rhythm modulation and navigation. In contrast, domain CA1v
lies in approximately the ventral half of the hippocampus, and
this domain shares strong gene coexpression patterns and pro-
jections with cerebral cortex and subcortical regions mediating
neuroendocrine, autonomic, and goal-oriented or emotional
behavioral responses. The natural boundary between CA1i and
CA1v in mice coincides with the rhinal fissure’s dorsal border, a
boundary shown by certain CA1 domain-specific genes and by
other cortical marker genes, including Col5a1, which is strongly
expressed in isocortical layers 6a and 6b (Fig. 2). The evidence
suggests that the dorsal and ventral halves of field CA1 are
genetically wired independently to support cognitive and emo-
tional responses, respectively (4–6).
The model of three major CA1 molecular domains presented
here shows interesting correlations with the 9 even more striking
molecular regions recently reported along the longitudinal axis
of mouse field CA3 (25). The observations of Thompson et al.,
together with our own in fields CA1 and CA3, suggest that field
CA3—and thus Ammon’s horn as a whole—is also divided into
three major molecular domains: (i) a dorsal domain (CA3d)
including their regions 1–3 that is accompanied by domain
CA1d; (ii) an intermediate domain (CA3i) including their re-
gions 4 and 5 that is accompanied by domain CA1i; and (iii) a
ventral domain (CA3v) including their regions 6–7 that is
accompanied by domain CA1v. The domains CA3d and CA3i
(regions 1–5) form approximately the dorsal half of field CA3,
the ventral half.
Ramo ´n y Cajal first noted structural differences along the
hippocampal longitudinal axis, related to what he called the
superior and inferior perforant paths (1) and what would later
be referred to loosely as the dorsal and ventral hippocampus,
respectively (9, 27). Lorente de No ´ (2) vaguely divided the
‘‘Ammonic system’’ into three longitudinal segments based on
now discredited connectional data and also divided field CA3
and field CA1 into three parallel, longitudinally running zones
(a, b, and c for both). Lorente de No ´’s (2) subfields CA3a, CA3b,
and CA3c appear to correspond well with three molecular
regions identified by Thompson et al. (25): region 3 (Mas1
expression) with CA3a, region 2 (Fmo1 expression) with CA3b,
and region 1 (Ttn1 expression) with CA3c. In field CA1, at least
some genes (such as Lct and Kit) were found here to show
differential expression patterns across the topological medial to
lateral (transverse) axis, but correspondences with Lorente de
No’s subfields CA1a, CA1b, and CA1c are not yet clear.
Extensive work since the early 1970s established that intra-
hippocampal circuitry, typified by the classical trisynaptic circuit
from entorhinal area to dentate gyrus to field CA3 to field CA1,
runs transverse to the longitudinal axis and that specific extrinsic
inputs and outputs are associated with specific regions along the
longitudinal axis of the hippocampal formation (8–11, 17–19,
28–33). The dorsal half of field CA1 has a high concentration of
place neurons (e.g., ref. 34) and sends most of its extrinsic
cortical projections, either directly or indirectly via dorsal sub-
iculum, to the cortical retrosplenial area (11, 35), which is
involved in cognitive processing of visual sensory information at
least in part for spatial and contextual memory. The dorsal
massive projections to the mammillary and anterior thalamic
nuclei, two regions containing abundant navigation neurons
(36). These two diencephalic regions in turn project back to the
dorsal hippocampus and retrosplenial area (35). This and other
evidence (see refs. 4–6, 20, and 21) suggest that the dorsal half
of field CA1 (domains CA1d and CA1i) is critically involved in
cognitive spatial memory processing, at least in rodents.
The most distinguishing feature of connectivity associated
with the ventral half of field CA1 (domain CA1v and its 4
subdomains) is dense bidirectional connections with amygdalar
regions implicated in emotional behaviors (10, 11, 17, 18).
Ventral but not dorsal field CA1 also projects directly (19) to the
hypothalamic periventricular region and medial zone, which
integrate neuroendocrine, autonomic, and somatic motor re-
sponses associated with three basic classes of motivated behav-
iors common to all animals: ingestive (feeding and drinking),
reproductive (sexual and parental), and defensive (fight or
dorsal CA1 are reinforced by multiple indirect pathways involv-
ing relays in the ventral subiculum, amygdalar region, lateral
septal nucleus, and bed nuclei of the stria terminalis (9–11,
correlated with those of CA1v as shown here.
www.pnas.org?cgi?doi?10.1073?pnas.0812608106Dong et al.
The observation that the dorsal half and ventral half of field
CA1 display distinct global gene expression correlations with
brain structures that they project to either directly or indirectly
is striking. Although the mechanistic significance of this rela-
tionship between CA1 molecular domains and their extrinsic
circuitry is not yet clear, from the above the dorsal and ventral
halves are obviously genetically wired independently for differ-
ent functional specializations. The former is selectively involved
in cognitive aspects of the learning and memory associated with
navigation, exploration, and locomotion, whereas in contrast the
latter is part of the temporal lobe associated most directly with
motivational and emotional aspects of the classic Klu ¨ver–Bucy
Syndrome. In fact, at least two CA1v marker genes, Grp and
Htr2c, have been implicated in psychiatric disorders (38, 39).
of relationships between gene expression patterns and neuronal
networks to clarify genetic contributions to brain structure and
function. However, the detection sensitivity and specificity for
many genes, especially those of low abundance, probably were
compromised in the large-scale, high-throughput process of
ABA data production (12). This would make the list of domain-
specific markers assembled here rather incomplete, and many
genes critical for determining adult brain structure and connec-
tions likely are expressed during development not in the adult
(23). Even for the domain-specific markers listed here (Table
S1), information in Gene Ontology suggests many diverse (and
unknown) functions whose possible role in neuronal develop-
ment and adult structure–function remain to be investigated.
Relative to isocortex, very little is known about laminar and
regional differences in field CA1 pyramidal cell subtypes. Both
Ramo ´n y Cajal (1) and Lorente de No ´ (2) observed deep and
superficial pyramids and noticed that they establish unique
relationships with basket cells. However, the addition of multiple
genetic markers for differentiation of field CA1 pyramids opens
many new possibilities for establishing analytical distinctions.
Materials and Methods
This study was based on a systematic, high-resolution analysis of ?4,000 genes
expressed in the hippocampal formation through a publicly accessible online
patterns of ?2,000 genes under the Anatomic Search tool category ‘‘hippocam-
pal region,’’ based on expression level, expression density, and gene clustering,
pyramidal layer’’ under ‘‘fine structure search.’’ We then used the Gene Finder
tool of the Anatomic Gene Expression Atlas (AGEA) application (Fig. 1 A–C) to
filter candidate genes showing regional specificities. Detailed methodology of
the AGEA has been described in a recent report (24). In brief, because all ABA
image-based, in situ hybridization data are spatially registered to the common
anatomic framework of the ARA (15) with a standard coordinate system and
the mouse brain atlas using the Gene Finder application (24). With this strategy,
we carefully analyzed the expression of ?400 ‘‘return’’ genes when we set seed
voxel points in dorsal, intermediate, and ventral parts of field CA1. AGEA also
With this tool, we have also analyzed gene expression correlations of different
domains of the CA1.
of Health Grants MH083180 (to H.-W.D.), RR013642 (to A.W.T.), NS16686 (to
L.W.S.), and MH62122 (to M.S.F.).
1. Ramo ´nyCajalS(1901–1902)Estudiossobrelacortezacerebralhumana.TrabInstCajal
Invest Biol 1:1–227.
2. LorentedeNo ´ RJ(1934)Studiesonthestructureofthecerebralcortex.II.Continuation
of the study of the ammonic system. J Psychol Neurol 46:113–177.
3. Squire LR (1992) Memory and the hippocampus: A synthesis from findings with rats,
monkeys, and humans. Psychol Rev 99:195–231.
4. Moser MB, Moser EI (1998) Functional differentiation in the hippocampus. Hippocam-
5. Anagnostaras SG, Gale, GD, Fanselow MS (2002) The hippocampus and Pavlovian fear
conditioning: Reply to Bast et al. Hippocampus 12:561–565.
6. Kjelstrup KG, et al. (2002) Reduced fear expression after lesions of the ventral hip-
pocampus. Proc Natl Acad Sci USA 99:10825–10830.
7. Swanson LW, Cowan WM (1975) Hippocampo-hypothalamic connections: Origin in
subicular cortex, not ammon’s horn. Science 189:303–304.
8. Swanson LW, Cowan WM (1977) An autoradiographic study of the organization of the
9. Risold PY, Swanson LW (1996) Structural evidence for functional domains in the rat
hippocampus. Science 272:1484–1486.
10. Witter MP, Amaral DG (2004) Hippocampal formation. The Rat Nervous System, ed
Paxinos G (Elsevier, Amsterdam), pp 637–704.
11. Cenquizca LA, Swanson LW (2007) Spatial organization of direct hippocampal field
CA1 axonal projections to the rest of the cerebral cortex. Brain Res Rev 56:1–26.
12. Lein ES, et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain.
13. Lein ES, Callaway EM, Albright TD, Gage FH (2005) Redefining the boundaries of the
hippocampal CA2 subfield in the mouse using gene expression and 3-dimensional
reconstruction. J Comp Neurol 485:1–18.
14. Lein ES, Zhao X, Gage FH (2004) Defining a molecular atlas of the hippocampus using
DNA microarrays and high-throughput in situ hybridization. J Neurosci 24:3879–3889.
Male Mouse (Wiley, Hoboken, NJ).
16. Swanson LW (2004) Brain Maps: Structure of the Rat Brain (Elsevier, Amsterdam), 3rd Ed.
17. Pitkanen A, Pikkarainen M, Nurminen N, Ylinen A (2000) Reciprocal connections
between the amygdala and the hippocampal formation, perirhinal cortex, and post-
rhinal cortex in rat. Ann N Y Acad Sci 911:369–391.
18. Petrovich GD, Canteras NS, Swanson LW (2001) Combinatorial amygdalar inputs to
hippocampal domains and hypothalamic behavior systems. Brain Res Rev 38:247–289.
19. Cenquizca LA, Swanson LW (2006) Analysis of direct hippocampal cortical field CA1
axonal projections to diencephalon in the rat. J Comp Neurol 497:101–114.
20. Moser E, Moser MB, Andersen P (1993) Spatial learning impairment parallels the
magnitude of dorsal hippocampal lesions, but is hardly present following ventral
lesions. J Neurosci 13:3916–3925.
21. Hunsaker MR, Fieldsted PM, Rosenberg JS, Kesner RP (2008) Dissociating the roles of
dorsal and ventral CA1 for the temporal processing of spatial locations, visual objects,
and odors. Behav Neurosci 122:643–650.
22. Gigg J (2006) Constraints on hippocampal processing imposed by the connectivity
between CA1, subiculum and subicular targets. Behav Brain Res 174:265–271.
23. Puelles L, Martínez S, Martínez-de-la-Torre M, Rubenstein JLR (2004) Gene maps and
related histogenetic domains in the forebrain and midbrain. The Rat Nervous System,
ed Paxinos G (Elsevier, Amsterdam), pp 3–25.
24. Ng L, et al. (2009) An anatomic gene expression atlas of the adult mouse brain. Nat
25. Thompson CL, et al. (2008) Genomic anatomy of the hippocampus. Neuron 60:1010–
26. Swanson LW (2000) Cerebral hemisphere regulation of motivated behavior. Brain Res
27. Gloor P (1997) The Temporal Lobe and Limbic System (Oxford Univ Press, New York),
28. Witter MP (2000) Anatomical organization of the parahippocampal-hippocampal
network. Ann N Y Acad Sci 911:1–24.
29. Witter MP, Van Hoesen GW, Amaral DG (1989) Topographical organization of the
entorhinal projection to the dentate gyrus of the monkey. J Neurosci 9:216–218.
30. Dolorfo CL, Amaral DG (1998) Entorhinal cortex of the rat: Organization of intrinsic
connections. J Comp Neurol 398:49–82.
31. Van Groen T, Miettinen P, Kadish I (2003) The entorhinal cortex of the mouse: Organiza-
tion of the projection to the hippocampal formation. Hippocampus 13:133–149.
of intrahippocampal association pathways in the rat. J Comp Neurol 181:681–715.
33. Swanson LW, Ko ¨hler C, Bjo ¨rklund A (1987) The limbic region. I: The septohippocam-
pal system. Integrated Systems of the CNS, Part I. Handbook of Chemical Neuro-
anatomy, eds Ho ¨kfelt T, Bjo ¨rklund A, Swanson LW (Elsevier, Amsterdam), Vol 5, pp
34. Jung MW, Wiener SI, McNaughton BL (1994) Comparison of spatial firing characteris-
tics of units in dorsal and ventral hippocampus of the rat. J Neurosci 14:7347–7356.
35. Risold PY, Thompson RH, Swanson LW (1997) The structural organization of connec-
tions between hypothalamus and cerebral cortex. Brain Res Brain Res Rev 24:197–254.
36. Taube JS (2007) The head direction signal: Origins and sensory-motor integration.
Annu Rev Neurosci 30:181–207.
37. Dong H-W, Petrovich GD, Swanson LW (2001) Topography of projections from amyg-
dala to bed nuclei of the stria terminalis. Brain Res Rev 38:192–246.
38. Roesler R, Henriques JA, Schwartsmann G (2006) Gastrin-releasing peptide receptor as
a molecular target for psychiatric and neurological disorders. CNS Neurol Disord Drug
complex disorders. Am J Med Genet B Neuropsychiatr Genet, 10.1002/ajmg.b.30864,
in the adult mouse brain. BMC Bioinformatics 18:9:153.
Dong et al. PNAS ?
July 14, 2009 ?
vol. 106 ?
no. 28 ?