Biological interpretations of transcriptomic profiles in mammalian oocytes and embryos

Rodriguez-Zas, Sandra L.; Schellander, K.; Lewin, Harris A.

doi:10.1530/rep-07-0426

Cited by 22 publications

(13 citation statements)

References 73 publications

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“…The gene expression across critical developmental transitions is highly dynamic and has been shown to have long-term impacts on the normal development in mammalian and fish species [25–29]. In particular, the embryo-to-larval stage is a crucial period in the life of marine fish [30].…”

Section: Discussionmentioning

confidence: 99%

Developmental transcriptomic analyses for mechanistic insights into critical pathways involved in embryogenesis of pelagic mahi-mahi (Coryphaena hippurus)

Mager

Grosell

et al. 2017

PLoS ONE

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Mahi-mahi (Coryphaena hippurus) is a commercially and ecologically important species of fish occurring in tropical and temperate waters worldwide. Understanding early life events is crucial for predicting effects of environmental stress, which is largely restricted by a lack of genetic resources regarding expression of early developmental genes and regulation of pathways. The need for anchoring developmental stages to transcriptional activities is highlighted by increasing evidence on the impacts of recurrent worldwide oil spills in this sensitive species during early development. By means of high throughput sequencing, we characterized the developmental transcriptome of mahi-mahi at three critical developmental stages, from pharyngula embryonic stage (24 hpf) to 48 hpf yolk-sac larva (transition 1), and to 96 hpf free-swimming larva (transition 2). With comparative analysis by multiple bioinformatic tools, a larger number of significantly altered genes and more diverse gene ontology terms were observed during transition 2 than transition 1. Cellular and tissue development terms were more significantly enriched in transition 1, while metabolism related terms were more enriched in transition 2, indicating a switch progressing from general embryonic development to metabolism during the two transitions. Special focus was given on the most significant common canonical pathways (e.g. calcium signaling, glutamate receptor signaling, cAMP response element-binding protein signaling, cardiac β-adrenergic signaling, etc.) and expression of developmental genes (e.g. collagens, myosin, notch, glutamate metabotropic receptor etc.), which were associated with morphological changes of nervous, muscular, and cardiovascular system. These data will provide an important basis for understanding embryonic development and identifying molecular mechanisms of abnormal development in fish species.

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Section: Discussionmentioning

confidence: 99%

Developmental transcriptomic analyses for mechanistic insights into critical pathways involved in embryogenesis of pelagic mahi-mahi (Coryphaena hippurus)

Mager

Grosell

et al. 2017

PLoS ONE

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“…However, IVC with FCS specifically affects important growth factors and cytokines (Pdgfa,Tdgf1,Ghr,Eps8,Mitf,Dusp6,Col4a1,Socs3,Cish), that have been shown to promote blastocyst formation and increases the rate of development in mouse, cow and rat (Hardy & Spanos 2002). Interestingly, three of these genes have been differentially expressed in somatic cell nuclear transfer (Rodriguez-Zas et al 2008). Moreover, it has been reported that some growth factors may be epigenetic regulators of embryo development (Warburton et al 1992).…”

Section: Discussionmentioning

confidence: 99%

Analysis of gene transcription alterations at the blastocyst stage related to the long-term consequences of in vitro culture in mice

Fernández‐González¹,

Hourcade²,

López‐Vidriero³

et al. 2009

Reproduction

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We have reported that in vitro culture (IVC) of preimplantation mouse embryos in the presence of FCS produces long-term effects (LTE) on development, growth and behaviour of the offspring at adult age. To analyse the mechanisms underlying this phenomenon, we have examined development and global alterations in gene expression in the mouse blastocysts produced in the presence of FCS, conditions known to be suboptimal and that generate LTE. Embryos cultured in vitro in KSOM and in KSOMCFCS had a reduced number of cells in the inner cell mass at the blastocyst stage compared with in vivo derived embryos; however, only culture in KSOMCFCS leads to a reduction in the number of trophoblast cells. Gene expression levels were measured by comparison among three groups of blastocysts (in vivo, IVC in KSOM and IVC in KSOMCFCS). Different patterns of gene expression and development were found between embryos cultured in vitro or in vivo. Moreover, when we compared the embryos produced in KSOM versus KSOMCFCS, we observed that the presence of FCS affected the expression of 198 genes. Metabolism, proliferation, apoptosis and morphogenetic pathways were the most common processes affected by IVC. However, the presence of FCS during IVC preferentially affected genes associated with certain molecular and biological functions related to epigenetic mechanisms. These results suggest that culture-induced alterations in transcription at the blastocyst stage related to epigenetic mechanisms provide a foundation for understanding the molecular origin at the time of preimplantation development of the long-term consequences of IVC in mammals.

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“…By adopting a transcript counting methodology (Anders and Huber, 2010) developed for efficient and cost-effective high-throughput analysis, we will be able to detect differential expression of known protein-coding genes, non-coding RNAs (ncRNAs) and newly identified transcripts compared with sibling controls (Airik et al, 2005; Rodriguez-Zas et al, 2008; Tsutsumi et al, 2008). Bioinformatic analysis could then be used to identify candidate pathways and downstream targets that might be affected (Lu et al, 2009).…”

Section: The Value Of Systematic Transcriptomicsmentioning

confidence: 99%

Deciphering the Mechanisms of Developmental Disorders (DMDD): a new programme for phenotyping embryonic lethal mice

Mohun¹,

Adams

Baldock

et al. 2013

Disease Models &Amp; Mechanisms

102

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SummaryInternational efforts to test gene function in the mouse by the systematic knockout of each gene are creating many lines in which embryonic development is compromised. These homozygous lethal mutants represent a potential treasure trove for the biomedical community. Developmental biologists could exploit them in their studies of tissue differentiation and organogenesis; for clinical researchers they offer a powerful resource for investigating the origins of developmental diseases that affect newborns. Here, we outline a new programme of research in the UK aiming to kick-start research with embryonic lethal mouse lines. The ‘Deciphering the Mechanisms of Developmental Disorders’ (DMDD) programme has the ambitious goal of identifying all embryonic lethal knockout lines made in the UK over the next 5 years, and will use a combination of comprehensive imaging and transcriptomics to identify abnormalities in embryo structure and development. All data will be made freely available, enabling individual researchers to identify lines relevant to their research. The DMDD programme will coordinate its work with similar international efforts through the umbrella of the International Mouse Phenotyping Consortium [see accompanying Special Article (Adams et al., 2013)] and, together, these programmes will provide a novel database for embryonic development, linking gene identity with molecular profiles and morphology phenotypes.

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Biological interpretations of transcriptomic profiles in mammalian oocytes and embryos

Cited by 22 publications

References 73 publications

Developmental transcriptomic analyses for mechanistic insights into critical pathways involved in embryogenesis of pelagic mahi-mahi (Coryphaena hippurus)

Developmental transcriptomic analyses for mechanistic insights into critical pathways involved in embryogenesis of pelagic mahi-mahi (Coryphaena hippurus)

Analysis of gene transcription alterations at the blastocyst stage related to the long-term consequences of in vitro culture in mice

Deciphering the Mechanisms of Developmental Disorders (DMDD): a new programme for phenotyping embryonic lethal mice

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