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issn:1567-133
1.  Expression of LIM-homeodomain transcription factors in the developing and mature mouse retina 
LIM-homeodomain (LIM-HD) transcription factors have been extensively studied for their role in the development of the central nervous system. Their function is key to several developmental events like cell proliferation, differentiation and subtype specification. However, their roles in retinal neurogenesis remain largely unknown. Here we report a detailed expression study of LIM-HD transcription factors LHX9 and LHX2, LHX3 and LHX4, and LHX6 in the developing and mature mouse retina using immunohistochemistry and in situ hybridization techniques. We show that LHX9 is expressed during the early stages of development in the retinal ganglion cell layer and the inner nuclear layer. We also show that LHX9 is expressed in a subset of amacrine cells in the adult retina. LHX2 is known to be expressed in retinal progenitor cells during development and in Müller glial cells and a subset of amacrine cells in the adult retina. We found that the LHX2 subset of amacrine cells is not cholinergic and that a very few of LHX2 amacrine cells express calretinin. LHX3 and LHX4 are expressed in a subset of bipolar cells in the adult retina. LHX6 is expressed in cells in the ganglion cell layer and the neuroblast layer starting at embryonic stage 13.5 (E13.5) and continues to be expressed in cells in the ganglion cell layer and inner nuclear layer, postnatally, suggesting its likely expression in amacrine cells or a subset thereof. Taken together, our comprehensive assay of expression patterns of LIM-HD transcription factors during mouse retinal development will help further studies elucidating their biological functions in the differentiation of retinal cell subtypes.
doi:10.1016/j.gep.2013.12.001
PMCID: PMC3921069  PMID: 24333658
LIM-homeodomain; Lhx genes; retinogenesis; retinal development; transcription factors
2.  Expression of CXCL12 and CXCL14 during eye development in Chick and Mouse 
Gene expression patterns : GEP  2013;13(8):10.1016/j.gep.2013.05.006.
Vertebrate eye development is a complex multistep process coordinated by signals from the lens, optic cup and periocular mesenchyme. Although chemokines are increasingly being recognized as key players in cell migration, proliferation, and differentiation during embryonic development, their potential role during eye development has not been examined. In this study, we demonstrate by section in situ hybridization that CXCL12 and CXCL14 are expressed during ocular development. CXCL12 is expressed in the periocular mesenchyme, ocular blood vessels, retina, and eyelid mesenchyme, and its expression pattern is conserved between chick and mouse in most tissues. Expression of CXCL14 is localized in the ocular ectoderm, limbal epithelium, scleral papillae, eyelid mesenchyme, corneal keratocytes, hair follicles, and retina, and it was only conserved in the upper eyelid ectoderm of chick and mouse. The unique and non-overlapping patterns of CXCL12 and CXCL14 expression in ocular tissues suggest that these two chemokines may interact and have important functions in cell proliferation, differentiation and migration during eye development.
doi:10.1016/j.gep.2013.05.006
PMCID: PMC3797226  PMID: 23727298
Cornea; limbal epithelium; eyelid; nictitating membrane; scleral ossicles; retina
3.  Catalog of mRNA expression patterns for DNA methylating and demethylating genes in developing mouse lower urinary tract 
Gene expression patterns : GEP  2013;13(8):10.1016/j.gep.2013.07.008.
The mouse prostate develops from a component of the lower urinary tract (LUT) known as the urogenital sinus (UGS). This process requires androgens and signaling between mesenchyme and epithelium. Little is known about DNA methylation during prostate development, including which factors are expressed, whether their expression changes over time, and if DNA methylation contributes to androgen signaling or influences signaling between mesenchyme and epithelium. We used in situ hybridization to evaluate the spatial and temporal expression pattern of mRNAs which encode proteins responsible for establishing, maintaining or remodeling DNA methylation. These include DNA methyltrasferases, DNA deaminases, DNA glycosylases, base excision repair and mismatch repair pathway members. The mRNA expression patterns were compared between male and female LUT prior to prostatic bud formation (14.5 days post coitus (dpc)), during prostatic bud formation (17.5 dpc) and during prostatic branching morphogenesis (postnatal day (P) 5). We found dramatic changes in the patterns of these mRNAs over the course of prostate development and identified examples of sexually dimorphic mRNA expression. Future investigation into how DNA methylation patterns are established, maintained and remodeled during the course of embryonic prostatic bud formation may provide insight into prostate morphogenesis and disease.
doi:10.1016/j.gep.2013.07.008
PMCID: PMC3825751  PMID: 23920106
urogenital sinus; lower urinary tract; prostate; epigenetics; DNA methylation; DNA demethylation
4.  The expression analysis of Sfrs10 and Celf4 during mouse retinal development 
Gene expression patterns : GEP  2013;13(8):10.1016/j.gep.2013.07.009.
Processing of mRNAs including, alternative splicing (AS), mRNA transport and translation regulation are crucial to eukaryotic gene expression. For example, >90% of the gene in the human genome are known to undergo alternative splicing thereby expanding the proteome production capacity of a limited number of genes. Similarly, mRNA export and translation regulation plays a vital role in regulating protein production. Thus, it is important to understand how these RNA binding proteins including alternative splicing factors (ASFs) and mRNA transport and translation factors regulate these processes. Here we report the expression of an ASF, Serine-arginine rich splicing factor 10 (Sfrs10) and a mRNA translation regulation factor, CUGBP, elav like family member 4 (Celf4) in the developing mouse retina. Sfrs10 was expressed throughout postnatal (P) retinal development and was observed progressively in newly differentiating neurons. Immunofluorescence (IF) showed Sfrs10 in retinal ganglion cells (RGCs) at P0, followed by amacrine and bipolar cells, and at P8 it was enriched in red/green cone photoreceptor cells. By P22, Sfrs10 was observed in rod photoreceptors in a peri-nuclear pattern. Like Sfrs10, Celf4 was also observed in the developing retina, but with two distinct retinal isoforms. In situ hybridization (ISH) showed progressive expression of Celf4 in differentiating neurons, which was confirmed by IF that showed a dynamic shift in Celf4 localization. Early in development Celf4 expression was restricted to the nuclei of newly differentiating RGCs and later (E16 onwards) it was observed in the initial segments of RGC axons. Later, during postnatal development, Celf4 was observed in amacrine and bipolar cells, but here it was predominantly cytoplasmic and enriched in the two synaptic layers. Specifically, at P14, Celf4 was observed in the synaptic boutons of rod bipolar cells marked by Pkc-α. Thus, Celf4 might be regulating AS early in development besides its known role of regulating mRNA localization/translation. In all, our data suggests an important role for AS and mRNA localization/translation in retinal neuron differentiation.
doi:10.1016/j.gep.2013.07.009
PMCID: PMC3825781  PMID: 23932931
5.  Expression of Arginine Vasotocin Receptors in the Developing Zebrafish CNS 
Gene expression patterns : GEP  2013;13(8):10.1016/j.gep.2013.06.005.
Vasotocin/vasopressin is a neuropeptide that regulates social and reproductive behaviors in a variety of animals including fish. Arginine vasotocin (AVT) is expressed by cells in the ventral hypothalamic and preoptic areas in the diencephalon during embryogenesis in zebrafish suggesting that vasotocin might mediate other functions within the CNS prior to the development of social and reproductive behaviors. In order to examine potential early roles for vasotocin we cloned two zebrafish vasotocin receptors homologous to AVPR1a. The receptors are expressed primarily in the CNS in similar but generally non-overlapping patterns. Both receptors are expressed in the forebrain, midbrain and hindbrain by larval stage. Of note, AVTR1a-expressing neurons in the hindbrain appear to be contacted by the axons of preoptic neurons in the forebrain that include avt+ neurons and from sensory axons in the lateral longitudinal fasciculus (LLF). Furthermore, AVTR1a-expressing hindbrain neurons extend axons into the medial longitudinal fasciculus (MLF) that contains axons of many neurons thought to be involved in locomotor responses to sensory stimulation. One hypothesis consistent with this anatomy is that AVT signaling mediates or gates sensory input to motor circuits in the hindbrain and spinal cord.
doi:10.1016/j.gep.2013.06.005
PMCID: PMC3825796  PMID: 23830982
6.  Parcellation of the Thalamus into Distinct Nuclei reflects EphA Expression and Function 
Gene expression patterns : GEP  2013;13(8):10.1016/j.gep.2013.08.002.
Intercellular signaling via the Eph receptor tyrosine kinases and their ligands, the ephrins, acts to shape many regions of the developing brain. One intriguing consequence of Eph signaling is the control of mixing between discrete cell populations in the developing hindbrain, contributing to the formation of segregated rhombomeres. Since the thalamus is also a parcellated structure comprised of discrete nuclei, might Eph signaling play a parallel role in cell segregation in this brain structure? Analyses of expression reveal that several Eph family members are expressed in the forming thalamus and that cells expressing particular receptors form cellular groupings as development proceeds. Specifically, expression of receptors EphA4 or EphA7 and ligand ephrin-A5 is localized to distinct thalamic domains. EphA4 and EphA7 are often coexpressed in regions of the forming thalamus, with each receptor marking discrete thalamic domains. In contrast, ephrin-A5 is expressed by a limited group of thalamic cells. Within the ventral thalamus, EphA4 is present broadly, occasionally overlapping with ephrin-A5 expression. EphA7 is more restricted in its expression and is largely nonoverlapping with ephrin-A5. In mutant mice lacking one or both receptors or ephrin-A5, the appearance of the venteroposterolateral (VPL) and venteroposteromedial (VPM) nuclear complex is altered compared to wild type mice. These in vivo results support a role for Eph family members in the definition of the thalamic nuclei. In parallel, in vitro analysis reveals a hierarchy of mixing among cells expressing ephrin-A5 with cells expressing EphA4 alone, EphA4 and EphA7 together, or EphA7 alone. Together, these data support a model in which EphA molecules promote the parcellation of discrete thalamic nuclei by limiting the extent of cell mixing.
doi:10.1016/j.gep.2013.08.002
PMCID: PMC3839050  PMID: 24036135
EphA4; EphA7; Ephrin-A5; Thalamus; Development; Segregation; Nuclei
7.  The tumor suppressor Chd5 is induced during neuronal differentiation in the developing mouse brain 
Gene expression patterns : GEP  2013;13(8):10.1016/j.gep.2013.09.003.
Epigenetic regulation of gene expression orchestrates dynamic cellular processes that become perturbed in human disease. An understanding of how subversion of chromatin-mediated events leads to pathologies such as cancer and neurodevelopmental syndromes may offer better treatment options for these pathological conditions. Chromodomain Helicase DNA-binding protein 5 (CHD5) is a dosage-sensitive tumor suppressor that is inactivated in human cancers, including neural-associated malignancies such as neuroblastoma and glioma. Here we report a detailed analysis of the temporal and cell type-specific expression pattern of Chd5 in the mammalian brain. By analyzing endogenous Chd5 protein expression during mouse embryogenesis, in the neonate, and in the adult, we found that Chd5 is expressed broadly in multiple brain regions, that Chd5 sub-cellular localization undergoes a switch from the cytoplasm to the nucleus during mid-gestation, and that Chd5 expression is retained at high levels in differentiated neurons of the adult. These findings may have important implications for defining the role of CHD5-mediated chromatin dynamics in the brain and for elucidating how perturbation of these epigenetic processes leads to neuronal malignancies, neurodegenerative diseases, and neurodevelopmental syndromes.
doi:10.1016/j.gep.2013.09.003
PMCID: PMC3855250  PMID: 24120991
8.  The cone-dominant retina and the inner ear of zebrafish express the ortholog of CLRN1, the causative gene of human Usher syndrome type 3A 
Gene expression patterns : GEP  2013;13(8):473-481.
Clarin-1 (CLRN1) is the causative gene in Usher Syndrome type 3A, an autosomal recessive disorder characterized by progressive vision and hearing loss. CLRN1 encodes Clarin-1, a glycoprotein with homology to the tetraspanin family of proteins. Previous cell culture studies suggest that Clarin-1 localizes to the plasma membrane and interacts with the cytoskeleton. Mouse models demonstrate a role for the protein in mechanosensory hair bundle integrity, but the function of Clarin-1 in hearing remains unclear. Even less is known of its role in vision, because the Clrn1 knockout mouse does not exhibit a retinal phenotype and expression studies in murine retinas have provided conflicting results. Here, we describe cloning and expression analysis of the zebrafish clrn1 gene, and report protein localization of Clarin-1 in auditory and visual cells from embryonic through adult stages. We detect clrn1 transcripts as early as 24 hours post-fertilization, and expression is maintained through adulthood. In situ hybridization experiments show clrn1 transcripts enriched in mechanosensory hair cells and supporting cells of the inner ear and lateral line organ, photoreceptors, and cells of the inner retina. In mechanosensory hair cells, Clarin-1 is polarized to the apical cell body and the synapses. In the retina, Clarin-1 localizes to lateral cell contacts between photoreceptors and is associated with the outer limiting membrane and subapical processes emanating from Müller glial cells. We also find Clarin-1 protein in the outer plexiform, inner nuclear and ganglion cell layers of the retina. Given the importance of Clarin-1 function in the human retina, it is imperative to find an animal model with a comparable requirement. Our data provide a foundation for exploring the role of Clarin-1 in retinal cell function and survival in a diurnal, cone-dominant species.
doi:10.1016/j.gep.2013.09.001
PMCID: PMC3888827  PMID: 24045267
9.  Widespread but tissue-specific patterns of interferon-induced transmembrane protein 3 (IFITM3, FRAGILIS, MIL-1) in the mouse gastrula 
Gene expression patterns : GEP  2013;13(7):225-239.
Interferon-induced transmembrane protein 3 (IFITM3; FRAGILIS; MIL-1) is part of a larger family of important small interferon-induced transmembrane genes and proteins involved in early development, cell adhesion, and cell proliferation, and which also play a major role in response to bacterial and viral infections and, more recently, in pronounced malignancies (Siegrist et al., 2011). IFITM3, together with tissue-nonspecific alkaline phosphatase (TNAP), PRDM1, and STELLA, has been claimed to be a hallmark of segregated primordial germ cells (PGCs) (Saitou et al., 2002). However, whether IFITM3, like STELLA, is part of a broader stem/progenitor pool that builds the posterior region of the mouse conceptus (Mikedis and Downs, 2012), is obscure. To discover the whereabouts of IFITM3 during mouse gastrulation (~E6.5-9.0), systematic immunohistochemical analysis was carried out at closely spaced 2-4-hour intervals. Results revealed diverse, yet consistent, profiles of IFITM3 localization throughout the gastrula. Within the putative PGC trajectory and surrounding posterior tissues, IFITM3 localized as a large cytoplasmic spot with or without staining in the plasma membrane. IFITM3, like STELLA, was also found in the ventral ectodermal ridge (VER), a posterior progenitor pool that builds the tailbud. The large cytoplasmic spot with plasma membrane staining was exclusive to the posterior region; the visceral yolk sac, non-posterior tissues, and epithelial tissues exhibited spots of IFITM3 without cell surface staining. Co-localization of the intracellular IFITM3 spot with the endoplasmic reticulum, Golgi apparatus or endolysosomes was not observed. That relatively high levels of IFITM3 were found throughout the posterior primitive streak and its derivatives is consistent with evidence that IFITM3, like STELLA, is part of a larger stem/progenitor cell pool at the posterior end of the primitive streak that forms the base of the allantois and builds the fetal-umbilical connection, thus further obfuscating practical phenotypic distinctions between so-called PGCs and surrounding soma.
doi:10.1016/j.gep.2013.04.003
PMCID: PMC3704145  PMID: 23639725
Allantoic Core Domain; allantois; branchial arches; IFITM2; IFITM3; endothelium; Flk1; foregut; FRAGILIS; hematopoietic cells; hindgut; MIL-1; mouse; primitive streak; primordial germ cells; PGCs; Runx1; ventral ectodermal ridge
10.  Temporal and tissue specific gene expression patterns of the zebrafish kinesin-1 heavy chain family, kif5s, during development 
Gene expression patterns : GEP  2013;13(7):271-279.
Homo- and heterodimers of Kif5 proteins form the motor domain of Kinesin-1, a major plus-end directed microtubule motor. Kif5s have been implicated in the intracellular transport of organelles, vesicles, proteins, and RNAs in many cell types. There are three mammalian KIF5s. KIF5A and KIF5C proteins are strictly neural in mouse whereas, KIF5B is ubiquitously expressed. Mouse knockouts indicate crucial roles for KIF5 in development and human mutations in KIF5A lead to the neurodegenerative disease Hereditary Spastic Paraplegia. However, the developmental functions and the extent to which individual kif5 functions overlap have not been elucidated. Zebrafish possess five kif5 genes: kif5Aa, kif5Ab, kif5Ba, kif5Bb, and kif5C. Here we report their tissue specific expression patterns in embryonic and larval stages. Specifically, we find that kif5As are strictly zygotic and exhibit neural-specific expression. In contrast, kif5Bs exhibit strong maternal contribution and are ubiquitously expressed. Lastly, kif5C exhibits weak maternal expression followed by enrichment in neural populations. In addition, kif5s show distinct expression domains in the larval retina.
doi:10.1016/j.gep.2013.05.002
PMCID: PMC3754906  PMID: 23684767
Microtubules; Intracellular transport; Trigeminal ganglia; Posterior lateral line ganglia; Retina; Neurons; Hindbrain; Spinal cord; Digestive tract
11.  Glial enriched gene expression profiling identifies novel factors regulating the proliferation of specific glial subtypes in the Drosophila brain 
Gene Expression Patterns  2014;16(1):61-68.
Highlights
•Global gene expression analysis identifies glial specific transcriptomes.•Different glial subtypes have distinct but overlapping transcriptomes.•foxO and tramtrack69 are novel regulators of glial subtype specific proliferation.
Glial cells constitute a large proportion of the central nervous system (CNS) and are critical for the correct development and function of the adult CNS. Recent studies have shown that specific subtypes of glia are generated through the proliferation of differentiated glial cells in both the developing invertebrate and vertebrate nervous systems. However, the factors that regulate glial proliferation in specific glial subtypes are poorly understood. To address this we have performed global gene expression analysis of Drosophila post-embryonic CNS tissue enriched in glial cells, through glial specific overexpression of either the FGF or insulin receptor. Analysis of the differentially regulated genes in these tissues shows that the expression of known glial genes is significantly increased in both cases. Conversely, the expression of neuronal genes is significantly decreased. FGF and insulin signalling drive the expression of overlapping sets of genes in glial cells that then activate proliferation. We then used these data to identify novel transcription factors that are expressed in glia in the brain. We show that two of the transcription factors identified in the glial enriched gene expression profiles, foxO and tramtrack69, have novel roles in regulating the proliferation of cortex and perineurial glia. These studies provide new insight into the genes and molecular pathways that regulate the proliferation of specific glial subtypes in the Drosophila post-embryonic brain.
doi:10.1016/j.gep.2014.09.001
PMCID: PMC4222725  PMID: 25217886
Glia; Drosophila; Cortex; Perineurial; foxO; Tramtrack
12.  Expression of Isl1 during mouse development 
Gene expression patterns : GEP  2013;13(8):407-412.
The LIM-homeodomain transcription factor Isl1 plays essential roles in cell proliferation, differentiation and survival during embryogenesis. To better visualize Isl1 expression and provide insight into the role of Isl1 during development, we generated an Isl1 nuclear LacZ (nLacZ) knockin mouse line and analyzed Isl1nlacZ expression during development by Xgal staining and compared expression of Isl1nlacZ with endogenous Isl1 by coimmunostaining with antibodies to Isl1 and β-galactosidase. Results demonstrated that during development Isl1 nuclear LacZ is expressed in a pattern that recapitulates its endogenous protein expression. Consistent with previous in situ and immunohistochemistry data, we observed Isl1nlacZ expression in multiple tissues and cell types, including the central and peripheral nervous system, neural retina, inner ear, pharyngeal mesoderm and endoderm and their derivatives (craniofacial structures, thymus, thyroid gland and trachea), cardiovascular system (cardiac outflow tract, carotid arteries, umbilical vessels, sinoatrial node and atrial septum), gastrointestinal system (oral epithelium, stomach, pancreas, mesentery) and hindlimb. In some cases, Isl1nlacZ appears to be more readily detectable than Isl1 protein when expression level is low, and in others, Isl1nlacZ appears to act as a lineage tracer, likely owing to perdurance of the nuclear localized beta-galactosidase.
doi:10.1016/j.gep.2013.07.001
PMCID: PMC4134129  PMID: 23906961
Isl1; LIM-homeodomain; transgenic; gene expression; development
13.  Expression patterns of cadherin genes in Drosophila oogenesis 
In Drosophila oogenesis, the follicular epithelium that envelops the oocyte is patterned by a small set of inductive signals and gives rise to an elaborate three-dimensional eggshell. Several eggshell structures provide sensitive readouts of the patterning signals, but the formation of these structures is still poorly understood. In other systems, epithelial morphogenesis is guided by the spatial patterning of cell adhesion and cytoskeleton genes. As a step towards developing a comprehensive description of patterning events leading to eggshell morphogenesis, we report the expression of Drosophila cadherins, calcium dependent adhesion molecules that are repeatedly used throughout development. We found that 9/17 of Drosophila cadherins are expressed in the follicular epithelium in dynamic patterns during oogenesis. In late oogenesis, the expression patterns of cadherin genes in the main body follicle cells is summarized using a compact set of simple geometric shapes, reflecting the integration of the EGFR and DPP inductive signals. The multi-layered composite patterning of the cadherins is hypothesized to play a key role in the formation of the eggshell. Of particular note is the complex patterning of the region of the follicular epithelium that gives rise to the dorsal appendages, which are tubular structures that serve as respiratory organs for the developing embryo.
doi:10.1016/j.gep.2008.09.001
PMCID: PMC4096819  PMID: 18817893
Drosophila; cadherin; oogenesis; gene expression; morphogenesis; adhesion; pattern formation; follicle cell; epithelium
14.  Developmental expression of mouse Follistatin-like 1 (Fstl1): dynamic regulation during organogenesis of the kidney and lung 
Gene expression patterns : GEP  2006;7(4):491-500.
Follistatin-like 1 (Fstl1) is a distantly related homolog of the Activin and Bone Morphogenetic Protein antagonist Follistatin. Interestingly, this molecule also has homology with the extracellular matrix modifying protein BM-40/SPARC/osteonectin. Previous studies in chick have identified Fstl1 as a regulator of early mesoderm patterning, somitogenesis, myogenesis and neural development. In this study, we determine the developmental expression pattern of Fstl1 during mouse development. We find that Fstl1 is ubiquitously expressed in the early embryo, and that expression becomes regionalized later during development. In the majority of tissues, Fstl1 is strongly expressed in the mesenchymal component and excluded from the epithelium. Notable exceptions include the central nervous system, in which Fstl1 expression is entirely absent with the exception of the choroid plexi and floor plate, the lung, in which Fstl1 expression can be seen in airway epithelia and the kidney, in which collecting ducts and nascent nephron epithelia express the highest levels of Fstl1.
doi:10.1016/j.modgep.2006.10.009
PMCID: PMC4043338  PMID: 17129766
Follistatin; activin antagonist; BMP antagonist; bone development; gonad development; gut development; heart development; kidney development; limb development; lung development; neural development; skin development; tooth development
15.  Expression of cyclin D1, cyclin D2, and N-myc in embryos of the direct developing frog Eleutherodactylus coqui, with a focus on limbs 
Gene expression patterns : GEP  2013;13(0):142-149.
Species of frogs that develop directly have removed the tadpole from their ontogeny and form adult structures precociously. To see whether cell cycle regulators could be involved in this altered embryogenesis, we examined the expression of ccnd1, ccnd2, and mycn in embryos of the direct developing frog, Eleutherodactylus coqui. Notable differences compared to embryos of Xenopus laevis, a species with a tadpole, included prominent expression of ccnd2 in the midbrain and ccnd1 in the mandibular neural crest. The former may contribute to the precocious appearance of the adult-type visual system and the latter to the adult-type jaw. Large domains of ccnd2 and mycn presage the early appearance of limb buds, and ccnd1 and mycn are implicated in digit development.
doi:10.1016/j.gep.2013.02.005
PMCID: PMC3657300  PMID: 23473789
16.  Characterization of transgenic zebrafish lines that express GFP in the retina, pineal gland, olfactory bulb, hatching gland, and optic tectum 
Gene expression patterns : GEP  2013;13(0):150-159.
Transgenic animals are powerful tools to study gene function in vivo. Here we characterize several transgenic zebrafish lines that express green fluorescent protein (GFP) under the control of the LCRRH2-RH2-1 or LCRRH2-RH2-2 green opsin regulatory elements. Using confocal immunomicroscopy, stereo-fluorescence microscopy, and Western blotting, we show that the Tg(LCRRH2-RH2-1:GFP)pt112 and Tg(LCRRH2-RH2-2:GFP)pt115 transgenic zebrafish lines express GFP in the pineal gland and certain types of photoreceptors. In addition, some of these lines also express GFP in the hatching gland, optic tectum, or olfactory bulb. Some of the expression patterns differ significantly from previously published similar transgenic fish lines, making them useful tools for studying the development of the corresponding tissues and organs. In addition, the variations of GFP expression among different lines corroborate the notion that transgenic expression is often subjected to position effect, thus emphasizing the need for careful verification of expression patterns when transgenic animal models are utilized for research.
doi:10.1016/j.gep.2013.02.006
PMCID: PMC3675662  PMID: 23499733
Crumbs2b; olfactory system; transgenic zebrafish; green opsin promoter; photoreceptor; retina
17.  Gene expression patterns in primary neuronal clusters of the Drosophila embryonic brain 
Gene expression patterns : GEP  2007;7(5):584-595.
The brain of Drosophila is formed by approximately 100 lineages, each lineage being derived from a stem cell-like neuroblast that segregates from the procephalic neurectoderm of the early embryo. A neuroblast map has been established in great detail for the early embryo, and a suite of molecular markers has been defined for all neuroblasts included in this map (Urbach and Technau, 2003a). However, the expression of these markers was not followed into later embryonic or larval stages, mainly due to the fact that anatomical landmarks to which expression patterns could be related had not been defined. Such markers, in the form of stereotyped clusters of neurons whose axons project along cohesive bundles (“primary axon bundles” or “PABs”) are now available (Younossi-Hartenstein et al., 2006). In the present study we have mapped the expression of molecular markers in relationship to primary neuronal clusters and their PABs. The markers we analyzed include many of the genes involved in patterning of the brain along the anteroposterior axis (cephalic gap genes, segment polarity genes) and dorso-ventral axis (columnar patterning genes), as well as genes expressed in the dorsal protocerebrum and visual system (early eye genes). Our analysis represents an important step along the way to identify neuronal lineages of the mature brain with genes expressed in the early embryo in discrete neuroblasts. Furthermore, the analysis helped us to reconstruct the morphogenetic movements that transform the two-dimensional neuroblast layer of the early embryo into the three-dimensional larval brain and provides the basis for deeper understanding of how the embryonic brain develops.
doi:10.1016/j.modgep.2007.01.004
PMCID: PMC3928073  PMID: 17300994
Drosophila; embryonic brain; brain development; Hox genes; pair rule genes; segment polarity genes; head gap genes; retinal patterning genes; columnar patterning genes
18.  Immunohistochemical analysis of sphingosine phosphate lyase expression during murine development 
Gene expression patterns : GEP  2012;13(1-2):21-29.
Sphingosine-1-phosphate lyase (SPL) catalyzes the degradation of sphingosine-1-phosphate (S1P), a bioactive lipid that controls cell proliferation, migration and survival. Mice lacking SPL expression exhibit developmental abnormalities, runting and death during the perinatal period, suggesting that SPL plays a role in mammalian development and adaptation to extrauterine life. We investigated the pattern of SPL expression in the mouse embryo and placenta from day 8 to day 18. Our findings reveal that SPL is expressed in the developing brain and neural tube, Rathke’s pouch, first brachial arch, third brachial arch, optic stalk, midgut loops, and lung buds. Diffuse signal was high at E12, whereas a recognizable adult SPL pattern was evident by E15 and more intensely at E18, with strong expression in skin, nasal epithelium, intestinal epithelium, cartilage, thymus and pituitary gland. These findings suggest SPL may be involved in development of the mammalian central nervous system (CNS), anterior pituitary, trigeminal nerve, palate and facial bones, thymus and other organs. Our findings are consistent with the SPL expression pattern of the adult mouse and with congenital abnormalities observed in SPL mutant mice.
doi:10.1016/j.gep.2012.09.001
PMCID: PMC3562366  PMID: 23041657
sphingosine-1-phosphate; sphingosine phosphate lyase; S1P lyase; Sgpl1; embryogenesis; sphingolipid
19.  Expression of the Foxi2 and Foxi3 transcription factors during development of chicken sensory placodes and pharyngeal arches 
Gene expression patterns : GEP  2012;13(1-2):38-42.
Foxi2 and Foxi3 are members of the Foxi class of Forkhead transcription factors. The Foxi transcription factor family has been shown to play roles in the development of the inner ear and pharyngeal arch derivatives in zebrafish. We describe the expression of Foxi2 and Foxi3 in chicken embryos during the first three days of embryonic development. Foxi3 is initially expressed broadly in the pre-placodal ectoderm surrounding the neural plate, which will give rise to all craniofacial sensory organs. It then becomes restricted to a region immediately anterior to the first pair of somites that will give rise to the otic and epibranchial placodes, before becoming down-regulated from this region and restricted to the ectoderm and endoderm of the pharyngeal arches. In contrast, Foxi2 is initially expressed broadly in cranial ectoderm with the striking exception of the otic placode, and ultimately becomes restricted to pharyngeal arch ectoderm. These expression patterns provide an insight into the roles of these transcriptional regulators during the development of the inner ear and pharyngeal arch derivatives.
doi:10.1016/j.gep.2012.10.001
PMCID: PMC3562376  PMID: 23124078
Otic placode; Pharyngeal arch; Craniofacial development; Pre-placodal domain
20.  Comparative gene expression analysis of the fmnl family of formins during zebrafish development and implications for tissue specific functions 
Gene expression patterns : GEP  2012;13(1-2):30-37.
Fmlns belong to the Formin family, catalysts of linear Actin polymerization with mostly unknown roles in vivo. In cell culture Fmnls are involved in cell migration and adhesion and the formation of different types of protrusions including filopodia and blebs, suggesting important roles during development. Moreover, Fmnls can act downstream of Rac and Cdc42, mediators of cytoskeletal changes as targets of important pathways required for shaping tissues. The zebrafish genome encodes five Fmnls. Here we report their tissue specific expression patterns during early development and pharyngula stages. The fmnls show overlapping and distinct expression patterns, which suggest that they could regulate similar processes during development, but may also have independent functions. In particular, we find a strong maternal contribution of all fmnls, but distinct expression patterns in the developing brain eye, ear, heart and vascular system.
doi:10.1016/j.gep.2012.09.002
PMCID: PMC3562391  PMID: 23072729
Actin; vascular system; visual system; otic vesicles; brain
21.  Identification and developmental expression analysis of a novel homeobox gene closely linked to the mouse Twirler mutation 
Gene expression patterns : GEP  2006;6(6):10.1016/j.modgep.2005.11.012.
The Twirler mutation arose spontaneously and causes inner ear defects in heterozygous and cleft lip and/or cleft palate in homozygous mutant mice, providing a unique animal model for investigating the molecular mechanisms of inner ear and craniofacial development. Here we report the identification of a novel homeobox gene, Iroquois-related homeobox like-1 (Irxl1), from the Twirler locus. Irxl1 encodes a TALE-family homeodomain protein with its homeodomain exhibiting the highest amino acid sequence identity (54%) to those of invertebrate Iroquois and vertebrate Irx subfamily members. The putative Irxl1 protein lacks the Iro-box, a conserved motif in all known members of the Irx subfamily. Searching the databases showed that Irxl1 orthologs exist in Xenopus, chick, and mammals. In situ hybridization analyses of mouse embryos at various developmental stages showed that Irxl1 mRNA is highly expressed in the frontonasal process and palatal mesenchyme during primary and secondary palate development. In addition, Irxl1 mRNA is strongly expressed in mesenchyme surrounding the developing inner ear, in discrete regions of the developing mandible, in the dermamyotome during somite differentiation, and in a subset of muscular structures in late embryonic stages. The developmental expression pattern indicates that Irxl1 is a good candidate gene for the Twirler gene.
doi:10.1016/j.modgep.2005.11.012
PMCID: PMC3869088  PMID: 16426902
cleft lip; cleft palate; craniofacial development; dermamyotome; homeobox; homeodomain; Hox; intervertebral disc; Iroquois; Irx; Irxl1; mandible; palate development; secondary palate; skeletal muscle; somite; TALE; Twirler mutation
22.  Dynamic expression of neurexophilin1 during zebrafish embryonic development☆ 
Gene Expression Patterns  2013;13(8):395-401.
Highlights
•Spatial and temporal expression of nxph1 during zebrafish embryonic development.•High conservation of neurexophilins among vertebrates.•High homology of nxph1 between zebrafish and other vertebrates.•Expression of nxph1 in various clusters of post-mitotic neurons and in glia.•Zebrafish is a good model to understand the in vivo function of neurexophilin in vertebrates.
Neurexophilin 1 (Nxph1) is a specific endoligand of α-neurexins that is essential for trans-synaptic activation. Here, we report its dynamic expression during development in zebrafish. Our study revealed an early onset of expression of nxph1. RT-PCR on a series of embryonic stages showed that it is maternally deposited, although only readily detectable by whole mount in situ hybridization by 22 hpf. During embryogenesis and larval stages, the zygotic transcript is expressed dynamically in various clusters of post-mitotic neurons and in glia in the central nervous system.
doi:10.1016/j.gep.2013.07.006
PMCID: PMC3838620  PMID: 23880144
Neurexophilins; Synapses; Neurexins; Epiphysis; Zebrafish; Interneurons; Neurons
23.  Expression of skeletogenic genes during arm regeneration in the brittle star Amphiura filiformis☆ 
Gene Expression Patterns  2013;13(8):464-472.
Highlights
•Analysis of brittle star regenerating arms using differentiation markers.•Identification of the early segregation of skeletal and muscle progenitor cells.•Expression of skeletal and non-skeletal genes at different stages of regeneration.•Combinatorial role of TF genes in early specification of skeletal cells.•Same TF genes identify different skeletal structures later in regeneration.
The brittle star Amphiura filiformis, which regenerates its arms post autotomy, is emerging as a useful model for studying the molecular underpinnings of regeneration, aided by the recent availability of some molecular resources. During regeneration a blastema initially is formed distally to the amputation site, and then a rapid rebuild is obtained by adding metameric units, which will eventually differentiate and become fully functional. In this work we first characterize the developmental process of the regenerating arms using two differentiation markers for muscle and skeletal structures – Afi-trop-1 and Afi-αcoll. Both genes are not expressed in the blastema and newly added undifferentiated metameric units. Their expression at different regenerating stages shows an early segregation of muscle and skeletal cells during the regenerating process, long before the metameric units become functional. We then studied the expression of a set of genes orthologous of the sea urchin transcription factors involved in the development of skeletal and non-skeletal mesoderm: Afi-ets1/2, Afi-alx1, Afi-tbr, Afi-foxB and Afi-gataC. We found that Afi-ets1/2, Afi-alx1, Afi-foxB and Afi-gataC are all expressed at the blastemal stage. As regeneration progresses those genes are expressed in a similar small undifferentiated domain beneath the distal growth cap, while in more advanced metameric units they become restricted to different skeletal domains. Afi-foxB becomes expressed in non-skeletal structures. This suggests that they might play a combinatorial role only in the early cell specification process and that subsequently they function independently in the differentiation of different structures. Afi-tbr is not present in the adult arm tissue at any stage of regeneration. In situ hybridization results have been confirmed with a new strategy for quantitative PCR (QPCR), using a subdivision of the three stages of regeneration into proximal (differentiated) and distal (undifferentiated) arm segments.
doi:10.1016/j.gep.2013.09.002
PMCID: PMC3838619  PMID: 24051028
Regeneration; Brittle star; Transcription factors; Skeleton; ets1/2; tbr; gataC; foxB; alx1
24.  Cloning and expression analysis of Fgf5, 6 and 7 during early chick development 
Gene expression patterns : GEP  2012;12(7-8):245-253.
FGFs1 with similar sequences can play different roles depending on the model organisms examined. Determining these roles requires knowledge of spatio-temporal Fgf gene expression patterns. In this study, we report the cloning of chick Fgf5, 6 and 7, and examine their gene expression patterns by whole mount in situ hybridization. We show that Fgf5's spatio-temporally restricted expression pattern indicates a potentially novel role during inner ear development. Fgf6 and Fgf7, although belonging to different subfamilies with diverged sequences, are expressed in similar patterns within the mesoderm. Alignment of protein sequences and phylogenetic analysis demonstrate that FGF5 and FGF6 are highly conserved between chick, human, mouse and zebrafish. FGF7 is similarly conserved except for the zebrafish, which has considerably diverged.
doi:10.1016/j.gep.2012.05.002
PMCID: PMC3434314  PMID: 22634565
Development; Fibroblast growth factor; otic placode; pharyngeal arch; pharyngeal endoderm
25.  EXPRESSION OF SCLEROSTIN IN THE DEVELOPING ZEBRAFISH (DANIO) BRAIN AND SKELETON 
Gene expression patterns : GEP  2012;12(7-8):228-235.
Sclerostin is a highly conserved, secreted, cystine-knot protein which regulates osteoblast function. Humans with mutations in the sclerostin gene (SOST), manifest increased axial and appendicular skeletal bone density with attendant complications. In adult bone, sclerostin is expressed in osteocytes and osteoblasts. Danio rerio sclerostin-like protein is closely related to sea bass sclerostin, and is related to chicken and mammalian sclerostins. Little is known about the expression of sclerostin in early developing skeletal or extra-skeletal tissues. We assessed sclerostin (sost) gene expression in developing zebrafish (Danio rerio) embryos with whole mount is situ hybridization methods. The earliest expression of sost RNA was noted during 12 hours post-fertilization (hpf). At 15 hpf, sost RNA was detected in the developing nervous system and in Kupffer’s vesicle. At 18, 20 and 22 hpf, expression in rhombic lip precursors was seen. By 24 hpf, expression in the upper and lower rhombic lip and developing spinal cord was noted. Expression in the rhombic lip and spinal cord persisted through 28 hpf and then diminished in intensity through 44 hpf. At 28 hpf, sost expression was noted in developing pharyngeal cartilage; expression in pharyngeal cartilage increased with time. By 48 hpf, sost RNA was clearly detected in the developing pharyngeal arch cartilage. Sost RNA was abundantly expressed in the pharyngeal arch cartilage, and in developing pectoral fins, 72, 96 and 120 hpf. Our study is the first detailed analysis of sost gene expression in early metazoan development.
doi:10.1016/j.gep.2012.04.003
PMCID: PMC3435489  PMID: 22575304
Sclerostin; sost; skeleton; cartilage; brain

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