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issn:1567-133
1.  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
2.  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
3.  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
4.  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
5.  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
6.  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
7.  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
8.  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
9.  Characterisation of the Drosophila procollagen lysyl hydroxylase, dPlod 
Gene Expression Patterns  2011;11(1-2):72-78.
The lysyl hydroxylase (LH) family of enzymes has important roles in the biosynthesis of collagen. In this paper we present the first description of Drosophila LH3 (dPlod), the only lysyl hydroxylase encoded in the fly genome. We have characterised in detail the developmental expression patterns of dPlod RNA and protein during embryogenesis. Consistent with its predicted function as a collagen-modifying enzyme, we find that dPlod is highly expressed in type-IV collagen-producing cells, particularly the haemocytes and fat body. Examination of dPlod subcellular localisation reveals that it is an endoplasmic reticulum resident protein, that partially overlaps with intracellular type-IV collagen. Furthermore, we show that dPlod is required for type-IV collagen secretion from haemocytes and fat body, and thus establish that LH3 enzyme function is conserved across widely separated animal phyla. Our findings, and the new tools we describe, establish the fly as an attractive model in which to study this important collagen biosynthesis enzyme.
doi:10.1016/j.gep.2010.09.006
PMCID: PMC3044864  PMID: 20888931
Drosophila; dPlod; Plod; Collagen; Lysyl hydroxylase; LH3
10.  3D representation of Wnt and Frizzled gene expression patterns in the mouse embryo at embryonic day 11.5 (Ts19) 
Gene Expression Patterns  2008;8(5):331-348.
Wnt signalling is one of the fundamental cell communication systems operating in the embryo and the collection of 19 Wnt and 10 Frizzled (Fzd) receptor genes (in mouse and human) represent just part of a complex system to be unravelled. Here we present a spatially comprehensive set of data on the 3D distribution of Wnt and Fzd gene expression patterns at a carefully selected single stage of mouse development. Overviews and selected features of the patterns are presented and the full 3D data set, generated by fully described probes, is available to the research community through the Edinburgh Mouse Atlas of Gene Expression. In addition to being comprehensive, the data set has been generated and recorded in a consistent manner to facilitate comparisons between gene expression patterns with the capacity to generate matching virtual sections from the 3D representations for specific studies. Expression patterns in the left forelimb were selected for more detailed comparative description. In addition to confirming the previously published expression of these genes, our whole embryo and limb bud analyses significantly extend the data in terms of details of the patterns and the addition of previously undetected sites of expression. Our focussed analysis of expression domains in the limb, defined by just two gene families, reveals a surprisingly high degree of spatial complexity and underlines the enormous potential for local cellular interactions that exist within an emerging structure. This work also highlights the use of OPT to generate detailed high-quality, spatially complex expression data that is readily comparable between specimens and can be reviewed and reanalysed as required for specific studies. It represents a core set of data that will be extended with additional stages of development and through addition of potentially interacting genes and ultimately other cross-regulatory communication pathways operating in the embryo.
doi:10.1016/j.gep.2008.01.007
PMCID: PMC2452985  PMID: 18364260
Wnt; Fzd; OPT; Mouse embryo; 3D expression patterns; Comparative analysis

Results 1-10 (10)