A chronological expression profile of gene activity during embryonic mouse brain development.
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ABSTRACT:
SUBMITTER: Goggolidou P
PROVIDER: S-EPMC3843766 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning we conducted detailed transcriptional profiling during embryonic development of the mouse brain. 2400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected, as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Analysis of left-right asymmetry of expression revealed 35 genes as putatively asymmetric from a combined data set. Our data constitutes a valuable new resource for neuroscience and neuro-development, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders.
2014-03-01 | GSE44932 | GEO
Project description:The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning we conducted detailed transcriptional profiling during embryonic development of the mouse brain. 2400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected, as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Analysis of left-right asymmetry of expression revealed 35 genes as putatively asymmetric from a combined data set. Our data constitutes a valuable new resource for neuroscience and neuro-development, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders. Whole genome transcriptional profiling carried out on 24 samples during 3 stages of embryonic development of the mouse brain was carried out with matching left-right asymmetry on four biological replicates at each stage.
2014-03-01 | E-GEOD-44932 | biostudies-arrayexpress
Project description:The transcriptome of the brain changes during development, reflecting processes that determine functional specialization of brain regions. We analyzed gene expression, measured using in situ hybridization across the full developing mouse brain, to quantify functional specialization of brain regions. Surprisingly, we found that during the time that the brain becomes anatomically regionalized in early development, transcription specialization actually decreases reaching a low, "neurotypic", point around birth. This decrease of specialization is brain-wide, and mainly due to biological processes involved in constructing brain circuitry. Regional specialization rises again during post-natal development. This effect is largely due to specialization of plasticity and neural activity processes. Post-natal specialization is particularly significant in the cerebellum, whose expression signature becomes increasingly different from other brain regions. When comparing mouse and human expression patterns, the cerebellar post-natal specialization is also observed in human, but the regionalization of expression in the human Thalamus and Cortex follows a strikingly different profile than in mouse.
| S-EPMC3777910 | biostudies-literature
Project description:Germ cells undergo many developmental transitions before ultimately becoming either eggs or sperm, and during embryonic development these transitions include epigenetic reprogramming, quiescence, and meiosis. To begin understanding the transcriptional regulation underlying these complex processes, we examined the spatial and temporal expression of TAF4b, a variant TFIID subunit required for fertility, during embryonic germ cell development. By analyzing published datasets and using our own experimental system to validate these expression studies, we determined that both Taf4b mRNA and protein are highly germ cell-enriched and that Taf4b mRNA levels dramatically increase from embryonic day 12.5-18.5. Surprisingly, additional mRNAs encoding other TFIID subunits are coordinately upregulated through this time course, including Taf7l and Taf9b. The expression of several of these germ cell-enriched TFIID genes is dependent upon Dazl and/or Stra8, known regulators of germ cell development and meiosis. Together, these data suggest that germ cells employ a highly specialized and dynamic form of TFIID to drive the transcriptional programs that underlie mammalian germ cell development.
| S-EPMC7010400 | biostudies-literature
Project description:The Caenorhabditis elegans heterochronic gene lin-28 regulates developmental timing in the nematode trunk. We report the dynamic expression patterns of Lin-28 homologues in mouse and chick embryos. Whole mount in situ hybridization revealed specific and intriguing expression patterns of Lin-28 in the developing mouse and chick limb bud. Mouse Lin-28 expression was detected in both the forelimb and hindlimb at E9.5, but disappeared from the forelimb at E10.5, and finally from the forelimb and hindlimb at E11.5. Chicken Lin-28, which was first detected in the limb primordium at stage 15/16, was also downregulated as the stage proceeded. The amino acid sequences of mouse and chicken Lin-28 genes are highly conserved and the similar expression patterns of Lin-28 during limb development in mouse and chicken suggest that this heterochronic gene is also conserved during vertebrate limb development.
| S-EPMC2262948 | biostudies-literature
Project description:This article contains data related to the research articles "Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences" (Feng et al., 2009) [1] and "Systems Biology of facial development: contributions of ectoderm and mesenchyme" (Hooper et al., 2017 In press) [2]. Embryonic mammalian craniofacial development is a complex process involving the growth, morphogenesis, and fusion of distinct facial prominences into a functional whole. Aberrant gene regulation during this process can lead to severe craniofacial birth defects, including orofacial clefting. As a means to understand the genes involved in facial development, we had previously dissected the embryonic mouse face into distinct prominences: the mandibular, maxillary or nasal between E10.5 and E12.5. The prominences were then processed intact, or separated into ectoderm and mesenchyme layers, prior analysis of RNA expression using microarrays (Feng et al., 2009, Hooper et al., 2017 in press) [1], [2]. Here, individual gene expression profiles have been built from these datasets that illustrate the timing of gene expression in whole prominences or in the separated tissue layers. The data profiles are presented as an indexed and clickable list of the genes each linked to a graphical image of that gene?s expression profile in the ectoderm, mesenchyme, or intact prominence. These data files will enable investigators to obtain a rapid assessment of the relative expression level of any gene on the array with respect to time, tissue, prominence, and expression trajectory.
| S-EPMC5561971 | biostudies-literature
Project description:BACKGROUND: Reelin is an extracellular glycoprotein of crucial importance in the developmental organisation of neurons in the mammalian cerebral cortex and other laminated brain regions. The pig possesses a gyrencephalic brain that bears resemblance to the human brain. In order to establish an animal model for neuronal migration disorders in the pig, we have studied the expression pattern and structure of Reelin during pig brain development. RESULTS: We determined the sequence of pig Reelin mRNA and protein and identified a high degree of homology to human Reelin. A peak in Reelin mRNA and protein expression is present during the period of major neurogenesis and neuronal migration. This resembles observations for human brain development. Immunohistochemical analysis showed the highest expression of Reelin in the Cajal-Reztius cells of the marginal zone, in resemblance with observations for the developing brain in humans and other mammalian species. CONCLUSIONS: We conclude that the pig might serve as an alternative animal model to study Reelin functions and that manipulation of the pig Reelin could allow the establishment of an animal model for human neuronal migration disorders.
| S-EPMC2895594 | biostudies-literature
Project description:Dab2ip (DOC-2/DAB2 interacting protein) is a RasGAP protein which shows a growth-inhibitory effect in human prostate cancer cell lines. Recent studies have shown that Dab2ip also plays an important role in regulating dendrite development and neuronal migration during brain development. In this study, we provide a more complete description of the mouse Dab2ip (mDab2ip) gene locus and examined DNA methylation and expression of Dab2ip during cerebellar development. Analysis of cDNA sequences in public databases revealed a total of 20 possible exons for mDab2ip gene, spanning over 172kb. Using Cap Analysis of Gene Expression (CAGE) data available through FANTOM5 project, we deduced five different transcription start sites for mDab2ip. Here, we characterized three different mDab2ip transcript variants beginning with exon 1. These transcripts varied by the presence or absence of exons 3 and 5, which encode a putative nuclear localization signal and the N-terminal region of a PH-domain, respectively. The 5' region of the mDab2ip gene contains three putative CpG islands (CpG131, CpG54, and CpG85). Interestingly, CpG54 and CpG85 are localized on exons 3 and 5. Bisulfate DNA sequencing showed that methylation level of CpG54 remained constant whereas methylation of CpG85 increased during cerebellar development. Real-time PCR analysis showed that the proportion of PH-domain containing mDab2ip transcripts increased during cerebellar development, in correlation with the increase in CpG85 methylation. These data suggest that site-specific methylation of mDab2ip gene during cerebellar development may play a role in inclusion of exon 5, resulting in a Dab2ip transcript variant that encodes a full pleckstrin homology (PH) domain.
| S-EPMC4473857 | biostudies-literature
Project description:Recently, sequence analyses have identified a large number of opposite strand transcripts in the vertebrate genome. Although the transcripts appear to be spliced and polyadenylated, many of them are predicted to represent noncoding RNAs. High levels of noncoding transcripts of the Six3 Opposite Strand (Six3OS) were recently identified in the embryonic and postnatal retina of the mouse. In this study, we expanded those initial expression analyses, elucidated in detail the developmental expression profile of mouse Six3OS in the brain and visual system, and compared it with that of Six3. Our results show that Six3OS expression overlaps extensively with that of Six3 and is not altered in Six3-null embryos.
| S-EPMC1986792 | biostudies-literature
Project description:BackgroundThe base excision repair pathway is responsible for repairing small DNA base lesions caused by endogenous and exogenous damaging agents. Repair is initiated by DNA glycosylases that recognize and remove the lesions. NEIL3 is one of 11 mammalian DNA glycosylases identified to date and it was discovered on the basis of sequence homology to the E. coli Fpg and Nei glycosylases. Difficulties in purifying the protein have limited its biochemical characterization and in contrast to the other glycosylases, its function remains unclear.ResultsIn this study we describe the expression pattern of Neil3 during mouse embryonic development with special focus on brain development. We have also looked at the expression of NEIL3 in several normal and tumor tissues. Quantitative real-time PCR and in situ hybridization revealed that Neil3 was highly expressed at embryonic days 12-13, when neurogenesis starts. The expression decreased during development and in the adult brain,Neil3 could not be detected in any of the brain areas examined by quantitative real-time PCR. During embryogenesis and in newborn mice specific expression was observed in areas known to harbour neural stem and progenitor cells such as the subventricular zone and the dentate gyrus. Finally, NEIL3 expression was higher in tumors compared to normal tissues, except for testis and pancreas.ConclusionOur findings indicate that mammalian NEIL3 is specifically expressed in brain areas where neurogenesis takes place during development and that its expression is tightly regulated both temporally and spatially. In addition, NEIL3 seems to be upregulated in tumor tissues compared to normal tissues. Altogether, mammalian NEIL3 seems to be highly expressed in cells with high proliferative potential.
| S-EPMC2686684 | biostudies-literature