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issn:1567-133
26.  The cis- Regulatory Dynamics of the Drosophila CNS Determinant castor are Controlled by Multiple Sub-Pattern Enhancers 
Gene expression patterns : GEP  2012;12(7-8):261-272.
In the developing CNS, unique functional identities among neurons and glia are, in part, established as a result of successive transitions in gene expression programs within neural precursor cells. One of the temporal-identity windows within Drosophila CNS neural precursor cells or neuroblasts (NBs) is marked by the expression of a zinc-finger transcription factor (TF) gene, castor (cas). Our analysis of cis-regulatory DNA within a cas loss-of-function rescue fragment has identified seven enhancers that independently activate reporter transgene expression in specific sub-patterns of the wild-type embryonic cas gene expression domain. Most of these enhancers also regulate different aspects of cas expression within the larval and adult CNS. Phylogenetic footprinting reveals that each enhancer is made up of clusters of highly conserved DNA sequence blocks that are flanked by less-conserved inter-cluster spacer sequences. Comparative analysis of the conserved DNA also reveals that cas enhancers share different combinations of sequence elements and many of these shared elements contain core DNA-binding recognition motifs for characterized temporal-identity TFs. Intra-species alignments show that two of the sub-pattern enhancers originated from an inverted duplication and that this repeat is unique to the cas locus in all sequenced Drosophila species. Finally we show that three of the enhancers differentially require cas function for their wild-type regulatory behavior. Cas limits the expression of one enhancer while two others require cas function for full expression. These studies represent a starting point for the further analysis of cas gene expression and the TFs that regulate it.
doi:10.1016/j.gep.2012.05.004
PMCID: PMC3436978  PMID: 22691242
Drosophila CNS development; cis-regulatory DNA; sub-pattern enhancers; DNA sequence conservation; castor gene regulation
27.  Rb1 mRNA expression in developing mouse teeth 
Gene expression patterns : GEP  2012;10.1016/j.gep.2012.01.004.
Rb1 is a tumor suppressor gene that regulates cell cycle progression through interactions with E2F transcription factors. In recent years, new roles for Rb1 in regulating cellular differentiation have also emerged. For example, it has been shown that Rb1 regulates osteoblast differentiation in a cell cycle independent manner, by binding to the transcription factor Runx2, and facilitating the up-regulation of late bone differentiation markers. Based on the facts that Runx2 also functions in tooth development, and that little is known about potential roles for Rb1 in mammalian tooth development, here we evaluated the expression of Rb1 mRNA in developmentally staged mouse teeth. Our data show that Rb1 mRNA is expressed in both dental epithelial and dental mesenchymal progenitor cells. In addition, Rb1 mRNA appears upregulated in differentiating ameloblasts and odontoblasts, suggesting roles for Rb1 in tooth differentiation.
doi:10.1016/j.gep.2012.01.004
PMCID: PMC3442146  PMID: 22300525
Rb1; tooth development; dental epithelium; dental mesenchyme; cell-cell signaling
28.  Segment - and Cell- Specific Expression of D-type Cyclins in the Postnatal Mouse Epididymis 
Gene expression patterns : GEP  2012;10.1016/j.gep.2012.01.003.
Sperm transport, maturation and storage are the essential functions of the epididymis. The epididymis in the mouse is structurally characterized by regional and segmental organization including caput, corpus and cauda epididymis that are comprised of ten segments. Although several growth factor signaling pathways have been discovered in the epididymis, how these converge onto the cell cycle components is unknown. To begin to elucidate the growth factor control of cell cycle events in the epididymis, we analyzed the expression of D-type cyclins at different postnatal ages. At 7d, cyclin D1 was mainly expressed in the cauda epithelium, by 14d its expression occurred in the epithelium of caput, corpus and cauda that persisted up to 21d. By 42d, cyclin D1 was mostly detectable in the principal cells of the caput and corpus (segments 1–7) but not in the cauda epididymis. Expression of cyclin D2, unlike that of cyclin D1, was evident only at 42d but not earlier, and was mostly confined to corpus and cauda epithelium. In contrast to both cyclin D1 and D2, cyclin D3 was expressed primarily in the interstitium at 7d and by 21d its expression was localized to the epithelium of the corpus and cauda epididymis. By 42d, expression of cyclin D3 peaked in segments 6–10 and confined to basal and principal cells of the corpus and apical cells of the cauda epithelium. Ki67 immunoreactivity confirmed absence of cell proliferation despite continued expression of D-type cyclins in the adult epididymis. Collectively, on the basis of our immunophenotyping and protein expression data, we conclude that the D-type cyclins are expressed in a development -, segment-, and cell- specific manner in the postnatal mouse epididymis.
doi:10.1016/j.gep.2012.01.003
PMCID: PMC3376213  PMID: 22289519
Epididymis; Cyclin D1; Cyclin D2; Cyclin D3; Ki67
29.  Mustn1 is essential for craniofacial chondrogenesis during Xenopus development 
Gene expression patterns : GEP  2012;10.1016/j.gep.2012.01.002.
Mustn1 is a vertebrate-specific protein that, in vitro, was showed to be essential for prechondrocyte function and thus it has the potential to regulate chondrogenesis during embryonic development. We use Xenopus laevis as a model to examine Mustn1 involvement in chondrogenesis. Previous work suggests that Mustn1 is necessary but not sufficient for chondrogenic proliferation and differentiation, as well as myogenic differentiation in vitro. Mustn1 was quantified and localized in developing Xenopus embryos using RT-PCR and whole mount in situ hybridization. Xenopus embryos were injected with either control morpholinos (Co-MO) or one designed against Mustn1 (Mustn1-MO) at the 4 cell stage. Embryos were scored for morphological defects and Sox9 was visualized via in situ hybridization. Finally, Mustn1-MO-injected embryos were co-injected with Mustn1-MO resistant mRNA to confirm the specificity of the observed phenotype. Mustn1 is expressed from the mid-neurula stage to the swimming tadpole stages, predominantly in anterior structures including the pharyngeal arches and associated craniofacial tissues, and the developing somites. Targeted knockdown of Mustn1 in craniofacial and dorsal axial tissues resulted in phenotypes characterized by small or absent eye(s), a shortened body axis, and tail kinks. Further, Mustn1 knockdown reduced cranial Sox9 mRNA expression and resulted in the loss of differentiated cartilaginous head structures (e.g. ceratohyal and pharyngeal arches). Reintroduction of MO-resistant Mustn1 mRNA rescued these effects. We conclude that Mustn1 is necessary for normal craniofacial cartilage development in vivo, although the exact molecular mechanism remains unknown.
doi:10.1016/j.gep.2012.01.002
PMCID: PMC3348343  PMID: 22281807
Xenopus; Mustn1; chondrogenesis; Sox9; morpholino; knockdown; craniofacial; somite
30.  Expression of Zfhep/δEF1 protein in palate, neural progenitors, and differentiated neurons 
Gene expression patterns : GEP  2003;3(6):709-717.
Zfhep/δEF1 is essential for embryonic development. We have investigated the expression pattern of Zfhep protein during mouse embryogenesis. We show expression of Zfhep in the mesenchyme of the palatal shelves, establishing concordance of expression with the reported cleft palate of the δEF1-null mice. Zfhep protein is strongly expressed in proliferating progenitors of the nervous system. In most regions of the brain, post-mitotic cells stop expressing Zfhep when they migrate out of the ventricular zone and differentiate. However, in the hindbrain, Zfhep protein is also highly expressed in post-mitotic migratory neuronal cells of the precerebellar extramural stream that arise from the neuroepithelium adjacent to the lower rhombic lip. Also, Zfhep is expressed as cells migrate from a narrow region of the pons ventricular zone towards the trigeminal nucleus. Co-expression with Islet1 shows that Zfhep is expressed in motor neurons of the trigeminal nucleus of the pons, but not in the inferior olive motor neurons at E12.5. Therefore, Zfhep is strongly expressed in a tightly regulated pattern in proliferating neural stem cells and a subset of neurons. Zfhep protein is also strongly expressed in trigeminal ganglia, and is moderately expressed in other cranial ganglia. In vitro studies have implicated Zfhep as a repressor of myogenesis, however, we find that Zfhep protein expression increases during muscle differentiation.
PMCID: PMC3682426  PMID: 14643678
AREB6; brain nuclei; cleft; cleft palate; cranial ganglia; delta EF-1; ganglion; heart; hindbrain; medulla; muscle; myogenesis; migration; neurogenesis; neurogenin; pons; pontine nucleus; precerebellar; rhombic lip; trigeminal; ventricular zone; ZEB; Zfhx1a
31.  Spatiotemporal expression pattern of KIF21A during normal embryonic development and in congenital fibrosis of the extraocular muscles type 1 (CFEOM1) 
Gene Expression Patterns  2012;12(5-6):180-188.
Congenital fibrosis of the extraocular muscles type 1 (CFEOM1) is a rare inherited strabismus syndrome characterized by non-progressive ophthalmoplegia. We previously identified that CFEOM1 results from heterozygous missense mutations in KIF21A, which encodes a kinesin motor protein. Here we evaluate the expression pattern of KIF21A in human brain and muscles of control and CFEOM1 patients, and during human and mouse embryonic development. KIF21A is expressed in the cell bodies, axons, and dendrites of many neuronal populations including those in the hippocampus, cerebral cortex, cerebellum, striatum, and motor neurons of the oculomotor, trochlear, and abducens nuclei from early development into maturity, and its spatial distribution is not altered in the CFEOM1 tissues available for study. Multiple splice isoforms of KIF21A are identified in human fetal brain, but none of the reported CFEOM1 mutations are located in or near the alternatively spliced exons. KIF21A immunoreactivity is also observed in extraocular and skeletal muscle biopsies of control and CFEOM1 patients, where it co-localizes with triadin, a marker of the excitation-contractile coupling system. The diffuse and widespread expression of KIF21A in the developing human and mouse central and peripheral nervous system as well as in extraocular muscle does not account for the restricted ocular phenotype observed in CFEOM1, nor does it permit the formal exclusion of a myogenic etiology based on expression patterns alone.
doi:10.1016/j.gep.2012.03.003
PMCID: PMC3358471  PMID: 22465342
32.  Expression of Wnt9, TCTP, and Bmp1/Tll in sea cucumber visceral regeneration 
Gene Expression Patterns  2011;12(1-2):24-35.
We employ non-radioactive in situ hybridization techniques, which combine good tissue morphology preservation with high sensitivity of transcript detection, to map gene expression in the regenerating digestive tube of the sea cucumber Holothuria glaberrima. We investigated localization of transcripts of Wnt9, TCTP, Bmp1/Tll, the genes that have been previously known to be implicated in embryogenesis and cancer. The choice was determined by our long-term goal of trying to understand how the developmental regulatory pathways known to be involved in tumor development can be activated in post-traumatic regeneration without leading to malignant growth. The gene expression data combined with the available morphological information highlight the gut mesothelium (the outer layer of the digestive tube) as a highly dynamic tissue, whose cells undergo remarkable changes in their phenotype and gene expression in response to injury. This reversible transition of the gut mesothelium from a complex specialized tissue to a simple epithelium composed of rapidly proliferating multipotent cells seems to depend on the expression of genes from multiple developmental/cancer-related pathways.
doi:10.1016/j.gep.2011.10.003
PMCID: PMC3272084  PMID: 22079950
33.  Identification of hunchback cis-regulatory DNA conferring temporal expression in neuroblasts and neurons 
Gene Expression Patterns  2011;12(1-2):11-17.
The specification of temporal identity within single progenitor lineages is essential to generate functional neuronal diversity in Drosophila and mammals. In Drosophila, four transcription factors are sequentially expressed in neural progenitors (neuroblasts) and each regulates the temporal identity of the progeny produced during its expression window. The first temporal identity is established by the Ikaros-family zinc finger transcription factor Hunchback (Hb). Hb is detected in young (newly-formed) neuroblasts for about an hour and is maintained in the early-born neurons produced during this interval. Hb is necessary and sufficient to specify early-born neuronal or glial identity in multiple neuroblast lineages. The timing of hb expression in neuroblasts is regulated at the transcriptional level. Here we identify the cis-regulatory elements that confer proper hb expression in “young” neuroblasts and early-born neurons. We show that the neuroblast element contains clusters of predicted binding sites for the Seven-up transcription factor, which is known to limit hb neuroblast expression. We identify highly conserved sequences in the neuronal element that are good candidates for maintaining Hb transcription in neurons. Our results provide the necessary foundation for identifying trans-acting factors that establish the Hb early temporal expression domain.
doi:10.1016/j.gep.2011.10.001
PMCID: PMC3272097  PMID: 22033538
34.  Expression pattern of polyketide synthase-2 during sea urchin development 
Gene Expression Patterns  2011;12(1-2):7-10.
doi:10.1016/j.gep.2011.09.004
PMCID: PMC3272118  PMID: 22001775
35.  Dynamic expression of Tbx2 and Tbx3 in developing mouse pancreas 
Gene expression patterns : GEP  2011;11(8):476-483.
Tbx2 and Tbx3 are closely related members of the T-box family of transcription factors that are important regulators during normal development as well as major contributors to human developmental syndromes when mutated. Although there is evidence for the involvement of Tbx2 and Tbx3 in pancreatic cancer, so far there are no reports characterizing the normal expression pattern of these genes in the pancreas. In this study, we examined spatial and temporal expression of Tbx2 and Tbx3 in mouse pancreas during development and in the adult using in situ hybridization and immunohistochemistry. Our results show that Tbx2 and Tbx3 are both expressed in the pancreatic mesenchyme throughout development beginning at embryonic day (E) 9.5. In addition, Tbx2 is expressed in pancreatic vasculature during development and in epithelial-derived endocrine and ductal cells during late fetal stages, postnatal development and in adult pancreas. In contrast, Tbx3 is expressed in exocrine tissue in the postnatal and adult pancreas. Further our results demonstrate that Tbx2 and Tbx3 are expressed in tumor-derived endocrine and exocrine cell lines, respectively. These dynamic changes in the expression pattern of these transcription factors lay the foundation for investigation of potential roles in pancreas development.
doi:10.1016/j.gep.2011.08.003
PMCID: PMC3200443  PMID: 21867776
Tbx2; Tbx3; T-box; Pancreas; Islets
36.  Molecular and Functional Analysis of Drosophila single-minded Larval Central Brain Expression 
Gene expression patterns : GEP  2011;11(8):533-546.
Developmental regulatory proteins are commonly utilized in multiple cell types throughout development. The Drosophila single-minded (sim) gene acts as master regulator of embryonic CNS midline cell development and transcription. However, it is also expressed in the brain during larval development. In this paper, we demonstrate that sim is expressed in 3 clusters of anterior central brain neurons: DAMv1/2, BAmas1/2, and TRdm and in 3 clusters of posterior central brain neurons: a subset of DPM neurons, and two previously unidentified clusters, which we term PLSC and PSC. In addition, sim is expressed in the lamina and medulla of the optic lobes. MARCM studies confirm that sim is expressed at high levels in neurons but is low or absent in neuroblasts (NBs) and ganglion mother cell (GMC) precursors. In the anterior brain, sim+ neurons are detected in 1st and 2nd instar larvae but rapidly increase in number during the 3rd instar stage. To understand the regulation of sim brain transcription, 12 fragments encompassing 5’-flanking, intronic, and 3’-flanking regions were tested for the presence of enhancers that drive brain expression of a reporter gene. Three of these fragments drove expression in sim+ brain cells, including all sim+ neuronal clusters in the central brain and optic lobes. One fragment upstream of sim is autoregulatory and is expressed in all sim+ brain cells. One intronic fragment drives expression in only the PSC and laminar neurons. Another downstream intronic fragment drives expression in all sim+ brain neurons, except the PSC and lamina. Thus, together these two enhancers drive expression in all sim+ brain neurons. Sequence analysis of existing sim mutant alleles identified 3 likely null alleles to utilize in MARCM experiments to examine sim brain function. Mutant clones of DAMv1/2 neurons revealed a consistent axonal fasciculation defect. Thus, unlike the embryonic roles of sim that control CNS midline neuron and glial formation and differentiation, postembryonic sim, instead, controls aspects of axon guidance in the brain. This resembles the roles of vertebrate Sim that have an early role in neuronal migration and a later role in axonogenesis.
doi:10.1016/j.gep.2011.09.002
PMCID: PMC3200459  PMID: 21945234
Autoregulation; Axon guidance; Brain; Drosophila; Enhancer; Optic lobes; single-minded
37.  A zebrafish SKIV2L2-enhancer trap line provides a useful tool for the study of peripheral sensory circuit development 
Gene expression patterns : GEP  2011;11(7):409-414.
The zebrafish is an ideal model for elucidating the cellular and molecular mechanisms that underlie development of the peripheral nervous system. A transgenic line that selectively labels all the sensory circuits would be a valuable tool for such investigations. In this study, we describe such a line: the enhancer trap zebrafish line Tg(SKIV2L2:gfp)j1775 which expresses green fluorescent protein (gfp) in the peripheral sensory ganglia. We show that this transgene marks all peripheral ganglia and sensory nerves, beginning at the time when the neurons are first extending their processes, but does not label the efferent nerves. The trapped reporter is inserted just upstream of a previously poorly described gene: lhfpl4 on LG6. The expression pattern of this gene by in situ hybridization reveals a different, but overlapping, pattern of expression compared to that of the transgene. This pattern also does not mimic that of the gene (skiv2l2), which provided the promoter element in the construct. These findings indicate that reporter expression is not dictated by an endogenous enhancer element, but instead arises through an unknown mechanism. Regardless, this reporter line should prove to be a valuable tool in the investigation of peripheral nervous system formation in the zebrafish.
doi:10.1016/j.gep.2011.06.002
PMCID: PMC3163734  PMID: 21742057
38.  A BAC transgenic Hes1-EGFP reporter reveals novel expression domains in mouse embryos 
Gene expression patterns : GEP  2011;11(7):415-426.
Expression of the basic helix-loop-helix factor Hairy and Enhancer of Split-1 (Hes1) is required for normal development of a number of tissues during embryonic development. Depending on context, Hes1 may act as a Notch signalling effector which promotes the undifferentiated and proliferative state of progenitor cells, but increasing evidence also points to Notch independent regulation of Hes1 expression. Here we use high resolution confocal scanning of EGFP in a novel BAC transgenic mouse reporter line, Tg(Hes1-EGFP)1Hri, to analyse Hes1 expression from embryonic day 7.0 (e7.0). Our data recapitulates some previous observations on Hes1 expression and suggests new, hitherto unrecognised expression domains including expression in the definitive endoderm at early somite stages before gut tube closure and thus preceding organogenesis. This mouse line will be a valuable tool for studies addressing the role of Hes1 in a number of different research areas including organ specification, development and regeneration.
doi:10.1016/j.gep.2011.06.004
PMCID: PMC3163761  PMID: 21745596
39.  Live imaging of endogenous Collapsin response mediator protein-1 expression at subcellular resolution during zebrafish nervous system development 
Gene expression patterns : GEP  2011;11(7):395-400.
Collapsin response mediator proteins (CRMPs) are cytosolic phosphoproteins that are functionally important during vertebrate development. We have generated a zebrafish genetrap line that produces fluorescently tagged Crmp1 protein, which can be dynamically tracked in living fish at subcellular resolution. The results show that Crmp1 is expressed in numerous sites in the developing nervous system. Early expression is apparent in the forebrain, epiphysis, optic tectum and the developing spinal cord. In the larval brain, Crmp1 is expressed in several distinct brain regions, such as the telencephalon, habenula and cerebellum. In addition, it is expressed in the spinal cord in a manner that persists in the larva. The results suggest that this Crmp1 protein trap line offers a powerful tool to track selected neuronal populations at high resolution.
doi:10.1016/j.gep.2011.05.002
PMCID: PMC3163798  PMID: 21628002
Crmp1; zebrafish; nervous system; development
40.  Expression of Unconventional Myosin Genes During Neuronal Development in Zebrafish 
Gene expression patterns : GEP  2007;8(3):161-170.
Neuronal migration and growth cone motility are essential aspects of the development and maturation of the nervous system. These cellular events result from dynamic changes in the organization and function of the cytoskeleton, in part due to the activity of cytoskeletal motor proteins such as myosins. Although specific myosins such as Myo2 (conventional or muscle myosin), Myo1, and Myo5 have been well characterized for roles in cell motility, the roles of the majority of unconventional (other than Myo2) myosins in cell motility events have not been investigated. To address this issue, we have undertaken an analysis of unconventional myosins in zebrafish, a premier model for studying cellular and growth cone motility in the vertebrate nervous system. We describe the characterization and expression patterns of several members of the unconventional myosin gene family. Based on available genomic sequence data, we identified 18 unconventional myosin- and 4 Myo2-related genes in the zebrafish genome in addition to previously characterized myosin (-1, -2, -3, -5, -6, -7) genes. Phylogenetic analyses indicate that these genes can be grouped into existing classifications for unconventional myosins from mouse and man. In situ hybridization analyses using EST probes for 18 of the 22 identified genes indicate that 11/18 genes are expressed in a restricted fashion in the zebrafish embryo. Specific myosins are expressed in particular neuronal or neuroepithelial cell types in the developing zebrafish nervous system, spanning the periods of neuronal differentiation and migration, and of growth cone guidance and motility.
doi:10.1016/j.gep.2007.10.010
PMCID: PMC3422748  PMID: 18078791
cytoskeleton; unconventional myosin; neuronal migration; axon guidance; growth cone motility; zebrafish; commissure; spinal cord; motor neuron; neural crest; somite; ear; eye; morphogenesis; in situ hybridization; phylogenetic tree; hindbrain; forebrain; midbrain; cranial muscles
41.  Tissue specific characterisation of Lim-kinase 1 expression during mouse embryogenesis 
Gene expression patterns : GEP  2010;11(3-4):221-232.
The Lim-kinase (LIMK) proteins are important for the regulation of the actin cytoskeleton, in particular the control of actin nucleation and depolymerisation via regulation of cofilin, and hence may control a large number of processes during development, including cell tensegrity, migration, cell cycling, and axon guidance. LIMK1/LIMK2 knockouts disrupt spinal cord morphogenesis and synapse formation but other tissues and developmental processes that require LIMK are yet to be fully determined. To identify tissues and cell-types that may require LIMK, we characterised the pattern of LIMK1 protein during mouse embryogenesis. We showed that LIMK1 displays an expression pattern that is temporally dynamic and tissue-specific. In several tissues LIMK1 is detected in cell-types that also express Wilms’ tumour protein 1 and that undergo transitions between epithelial and mesenchymal states, including the pleura, epicardium, kidney nephrons, and gonads. LIMK1 was also found in a subset of cells in the dorsal retina, and in mesenchymal cells surrounding the peripheral nerves. This detailed study of the spatial and temporal expression of LIMK1 shows that LIMK1 expression is more dynamic than previously reported, in particular at sites of tissue–tissue interactions guiding multiple developmental processes.
doi:10.1016/j.gep.2010.12.003
PMCID: PMC3407955  PMID: 21167960
Limk; Kidney; Heart; Epithelia-to-mesenchyme transition; Mesenchyme-to-epithelia transition; Eye; Testes
42.  Genes expressed in Atoh1 neuronal lineages arising from the r1/isthmus rhombic lip 
Gene expression patterns : GEP  2011;11(5-6):349-359.
During embryogenesis, the rhombic lip of the fourth ventricle is the germinal origin of a diverse collection of neuronal populations that ultimately reside in the brainstem and cerebellum. Rhombic lip neurogenesis requires the bHLH transcription factor Atoh1 (Math1), and commences shortly after neural tube closure (E9.5). Within the rhombomere 1 – isthmus region, the rhombic lip first produces brainstem and deep cerebellar neurons (E9.5-E12), followed by granule cell precursors after E12. While Atoh1 function is essential for all of these populations to be specified, the downstream genetic programs that confer specific properties to early and late born Atoh1 lineages are not well characterized. We have performed a comparative microarray analysis of gene expression within early and later born cohorts of Atoh1 expressing neural precursors purified from E14.5 embryos using a transgenic labeling strategy. We identify novel transcription factors, cell surface molecules, and cell cycle regulators within each pool of Atoh1 lineages that likely contribute to their distinct developmental trajectories and cell fates. In particular, our analysis reveals new insights into the genetic programs that regulate the specification and proliferation of granule cell precursors, the putative cell of origin for the majority of medulloblastomas.
doi:10.1016/j.gep.2011.03.007
PMCID: PMC3095718  PMID: 21440680
rhombic lip; Atoh1; Math1; cerebellum; neurogenesis; rhombomere 1
43.  Dystrobrevin and dystrophin family gene expression in zebrafish 
Dystrophin/dystrobrevin superfamily proteins play structural and signalling roles at the plasma membrane of many cell types. Defects in them or the associated multiprotein complex cause a range of neuromuscular disorders. Members of the dystrophin branch of the family form heterodimers with members of the dystrobrevin branch, mediated by their coiled-coil domains. To determine which combinations of these proteins might interact during embryonic development, we set out to characterise the gene expression pattern of dystrophin and dystrobrevin family members in zebrafish. γ-dystrobrevin (dtng), a novel dystrobrevin recently identified in fish, is the predominant form of dystrobrevin in embryonic development. Dtng and dmd (dystrophin) have similar spatial and temporal expression patterns in muscle, where transcripts are localized to the ends of differentiated fibres at the somite borders. Dtng is expressed in the notochord while dmd is expressed in the chordo-neural hinge and then in floor plate and hypochord. In addition, dtng is dynamically expressed in rhombomeres 2 and 4-6 of the hindbrain and in the ventral midbrain. α-dystrobrevin (dtna) is expressed widely in the brain with particularly strong expression in the hypothalamus and the telencephalon; drp2 is also expressed widely in the brain. Utrophin expression is found in early pronephros and lateral line development and utrophin and dystrophin are both expressed later in the gut. β-dystrobrevin (dtnb) is expressed in the pronephric duct and widely at low levels. In summary, we find clear instances of co-expression of dystrophin and dystrobrevin family members in muscle, brain and pronephric duct development and many examples of strong and specific expression of members of one family but not the other, an intriguing finding given the presumed heterodimeric state of these molecules.
doi:10.1016/j.modgep.2007.10.004
PMCID: PMC3360968  PMID: 18042440
muscle; zebrafish; notochord; midbrain; rhombomere; gene expression; utrophin; dystrophin; dystrobrevin; drp2; dystrotelin
44.  Vestigial-like-2b (VITO-1b) and Tead-3a (Tef-5a) expression in zebrafish skeletal muscle, brain and notochord 
Gene expression patterns : GEP  2007;7(8):827-836.
The vestigial gene has been shown to control skeletal muscle formation in Drosophila and the related Vestigial-like 2 (Vgl-2) protein plays a similar role in mice. Vgl-family proteins are thought to regulate tissue-specific gene expression by binding to members of the broadly expressed Scalloped/Tef/TEAD transcription factor family. Zebrafish have at least four Vgl genes, including two Vgl-2s, and at least three TEAD genes, including two Tead3s. We describe the cloning and expression of one member from each family in the zebrafish. A novel gene, vgl-2b, with closest homology to mouse and human vgl-2, is expressed transiently in nascent notochord and in muscle fibres as they undergo terminal differentiation during somitogenesis. Muscle cells also express a TEAD-3 homologue, a possible partner of Vgl-2b, during myoblast differentiation and early fibre assembly. Tead3a is also expressed in rhombomeres, eye and epiphysis regions.
doi:10.1016/j.modgep.2007.08.001
PMCID: PMC3360971  PMID: 17916448
muscle; adaxial; zebrafish; vestigial-like; transcription enhancer factor; TEAD domain
45.  Specific expression of Kcna10, Pxn and Odf2 in the organ of Corti 
Gene Expression Patterns  2012;12(5-6):172-179.
Highlights
► We studied the expression of Pxn, Kcna10 and Odf2 in the developing mouse inner ear. ► We covered several ages between E14.5 and P5, and also looked at adults. ► Pxn is a focal adhesion protein expressed strongly in pillar cells. ► Kcna10 is a potassium channel expressed in hair cells. ► Odf2 (Cenexin) marks dendrites extending to and contacting hair cells.
The development of the organ of Corti and the highly specialized cells required for hearing involves a multitude of genes, many of which remain unknown. Here we describe the expression pattern of three genes not previously studied in the inner ear in mice at a range of ages both embryonic and early postnatal. Kcna10, a tetrameric Shaker-like potassium channel, is expressed strongly in the hair cells themselves. Odf2, as its centriolar isoform Cenexin, marks the dendrites extending to and contacting hair cells, and Pxn, a focal adhesion scaffold protein, is most strongly expressed in pillar cells during the ages studied. The roles of these genes are yet to be elucidated, but their specific expression patterns imply potential functional significance in the inner ear.
doi:10.1016/j.gep.2012.03.001
PMCID: PMC3368262  PMID: 22446089
Odf2; Cenexin; Pxn; Kcna10; Inner ear
46.  Temporal pattern of the posterior expression of Wingless in Drosophila blastoderm 
Gene expression patterns : GEP  2011;11(7):456-463.
In most animals, the Antero-Posterior (A-P) axis requires a gradient of Wnt signaling. Wnts are expressed posteriorly in many vertebrate and invertebrate embryos, forming a gradient of canonical Wnt/β-Catenin activity that is highest in the posterior and lowest in the anterior. One notable exception to this evolutionary conservation is in the Drosophila embryo, in which the A-P axis is established by early transcription factors of maternal origin. Despite this initial axial establishment, Drosophila still expresses Wingless (Wg), the main Drosophila Wnt homologue, in a strong posterior band early in embryogenesis. Since its discovery 30 years ago this posterior band of Wg has been largely ignored. In this study, we re-examined the onset of expression of the Wg posterior band in relation to the expression of Wg in other segments, and compared the timing of its expression to that of axial regulators such as gap and pair-rule genes. It was found that the posterior band of Wg is first detected in blastoderm at mid nuclear cycle 14, before the segment-polarity stripes of Wg are formed in other segments. The onset of the posterior band of Wg expression was preceded by that of the gap gene products Hunchback (hb) and Krüppel (Kr), and the pair-rule protein Even-skipped (Eve). Although the function of the posterior band of Wg was not analyzed in this study, we note that in temperature-sensitive Wg mutants, in which Wg is not properly secreted, the posterior band of Wg expression is diminished in strength, indicating a positive feedback loop required for Wg robust expression at the cellular blastoderm stage. We propose that this early posterior expression could play a role in the refinement of A-P patterning.
doi:10.1016/j.gep.2011.07.004
PMCID: PMC3200307  PMID: 21821151
Wnt; antero-posterior patterning; gap genes; pair-rule genes; evo-devo
47.  XLMR candidate mouse gene, Zcchc12 (Sizn1) is a novel marker of Cajal-Retzius cells 
Gene expression patterns : GEP  2010;11(3-4):216-220.
Sizn1 (Zcchc12) is a transcriptional co-activator that positively modulates BMP (Bone Morphogenic Protein) signaling through its interaction with Smad family members and CBP. We have demonstrated a role for Sizn1 in basal forebrain cholinergic neuron specific gene expression. Furthermore, mutations in SIZN1 have been associated with X-linked mental retardation. Given the defined role of SIZN1 in mental retardation, knowing its complete forebrain expression pattern is essential to further elucidating its role in cognition. To better define the dynamic expression pattern of Sizn1 during forebrain development, we investigated its expression in mouse brain development from embryonic day 8.0 (E8.0) to adult. We found that Sizn1 is primarily restricted to the ventral forebrain including the medial ganglionic eminence, the septum, amygdala, and striatum. In addition, Sizn1 expression is detected in the cortical hem and Pallial-subpallial boundary (PSB; anti-hem); both sources of Cajal-Retzius cells. Sizn1 expression in the dorsal forebrain is restricted to a subset of cells in the marginal zone that also express Reln, indicative of Cajal-Retzius cells. These data provide novel information on brain regions and cell types that express Sizn1, facilitating further investigations into the function of Sizn1 in both development and the pathogenesis of mental retardation.
doi:10.1016/j.gep.2010.12.005
PMCID: PMC3065530  PMID: 21172456
48.  Expression analysis of the Islet-1 gene in the developing and adult gastrointestinal tract 
Gene expression patterns : GEP  2011;11(3-4):244-254.
LIM-Homeodomain genes encode a family of proteins defined by the cysteine-rich protein/protein interacting (Lin-11, Isl-1, and Mec-3) LIM domain and a highly conserved DNA-binding domain. Studies in several organisms have shown that these transcriptional regulators control multiple aspects of embryonic development and are responsible for the pathogenesis of several human diseases. Here we report the expression of Islet-1 (Isl-1) in the gastrointestinal epithelium in developing and adult mice. At embryonic day (E) 9.5–10.5, Isl-1 expression was first detected in the ventral gastric mesenchyme, and expression in the dorsal mesenchyme initiated a few days later. Isl-1 expression was first observed in the gastric epithelium at E13.5 and at E14.5 was restricted to the posterior half of the stomach. In the mature stomach, Isl-1 expression was detected only in subsets of enteroendocrine cells. Furthermore, Isl-1 expression in the intestinal epithelium was first detected at E15.5 and was restricted to subpopulations of enteroendocrine cells in adult mice. These expression analyses suggest that Isl-1 might have an early broad role in stomach and intestinal cells and a secondary role in terminal differentiation and/or maintenance of mature enteroendocrine subtypes in the gastrointestinal epithelium.
doi:10.1016/j.gep.2010.12.007
PMCID: PMC3065958  PMID: 21220053
Islet-1; stomach; intestine; gastrointestinal tract; development; transcriptional control; endocrine cell differentiation; somatostatin; gastrin; ghrelin
49.  Ontological aspects of pluripotency and stemness gene expression pattern in the rhesus monkey 
Gene expression patterns : GEP  2011;11(3-4):285-298.
Two essential aspects of mammalian development are the progressive specialization of cells toward different lineages, and the maintenance of progenitor cells that will give rise to the differentiated components of each tissue and also contribute new cells as older cells die or become injured. The transition from totipotentiality to pluripotentiality, to multipotentiality, to monopotentiality, and then to differentiation is a continuous process during development. The ontological relationship between these different stages is not well understood. We report for the first time an ontological survey of expression of 45 putative “stemness” and “pluripotency” genes in rhesus monkey oocytes and preimplantation stage embryos, and comparison to the expression in the inner cell mass, trophoblast stem cells, and a rhesus monkey (ORMES6) embryonic stem cell line. Our results reveal that some of these genes are not highly expressed in all totipotent or pluripotent cell types. Some are predominantly maternal mRNAs present in oocytes and embryos before transcriptional activation, and diminishing before the blastocyst stage. Others are well expressed in morulae or early blastocysts, but are poorly expressed in later blastocysts or ICMs. Also, some of the genes employed to induce pluripotent stem cells from somatic cells (iPS genes) appear unlikely to play major roles as stemness or pluripotency genes in normal embryos.
doi:10.1016/j.gep.2011.02.001
PMCID: PMC3109727  PMID: 21329766
stem cell; cell lineage; embryo; trophoblast
50.  Expression of Clock Proteins in Developing Tooth 
Gene expression patterns : GEP  2010;11(3-4):202-206.
Morphological and functional changes during ameloblast and odontoblast differentiation suggest that enamel and dentin formation is under circadian control. Circadian rhythms are endogenous self-sustained oscillations with periods of 24 hours that control diverse physiological and metabolic processes. Mammalian clock genes play a key role in synchronizing circadian functions in many organs. However, close to nothing is known on clock genes expression during tooth development. In this work, we investigated the expression of four clock genes during tooth development. Our results showed that circadian clock genes Bmal1, clock, per1, and per2 mRNAs were detected in teeth by RT-PCR. Immunohistochemistry showed that clock protein expression was first detected in teeth at the bell stage (E17), being expressed in EOE and dental papilla cells. At post-natal day four (PN4), all four clock proteins continued to be expressed in teeth but with different intensities, being strongly expressed within the nucleus of ameloblasts and odontoblasts and down-regulated in dental pulp cells. Interestingly, at PN21 incisor, expression of clock proteins was down-regulated in odontoblasts of the crown-analogue side but expression was persisting in root-analogue side odontoblasts. In contrast, both crown and root odontoblasts were strongly stained for all four clock proteins in first molars at PN21. Within the periodontal ligament (PDL) space, epithelial rests of Malassez (ERM) showed the strongest expression among other PDL cells. Our data suggests that clock genes might be involved in the regulation of ameloblast and odontoblast functions, such as enamel and dentin protein secretion and matrix mineralization.
doi:10.1016/j.gep.2010.12.002
PMCID: PMC3073654  PMID: 21156215
Clock genes; Tooth development; Bmal1; Clock; Per1; Per2; expression pattern; immunohistochemistry

Results 26-50 (130)