Whole-genome approaches for large-scale gene identification and expression analysis in mammalian preimplantation embryos

Adjaye, James

doi:10.1071/rd04075

Cited by 24 publications

(16 citation statements)

References 70 publications

(81 reference statements)

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“…The Wnt/b-catenin signaling pathway was active in the group of up-regulated genes upon differentiation of hESCs. It has been previously shown that activation of the canonical WNT pathway is operative during mouse and human preimplantation development [55][56][57]. The ERK/MAPK signaling pathway is also active in the group of genes upregulated, and a previous study showed that this activation improves the proliferative and invasive potential of human trophoblast cells [58].…”

Section: Signaling Pathways With Candidate Roles In Trophoblast Diffementioning

confidence: 96%

Transcriptomic Signature of Trophoblast Differentiation in a Human Embryonic Stem Cell Model1

Marchand

Horcajadas

Esteban

et al. 2011

Biology of Reproduction

100

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Identification of genes involved in trophoblast differentiation is of great interest in understanding cellular and molecular mechanisms involved in placental development and is relevant clinically to fetal development, fertility, and maternal health. Herein, we investigated differentiation of human embryonic stem cells (hESCs) down the trophoblast lineage by culture with bone morphogenetic protein 4 (BMP4) over a 10-day period. Within 2 days, the stemness markers POU5F1 and NANOG were markedly down-regulated, followed temporally by up-regulation of the CDX2, KRT7, HLA-G, ID2, CGA, and CGB trophoblast markers. To understand, on a global scale, changes in the transcriptome during the differentiation of hESCs down the trophoblast lineage, a large-scale microarray analysis was performed. Through whole-genome analysis, more than 3800 genes displayed statistically significant and 2-fold or greater changes in expression during the time course. Of those genes that showed the largest increases, many were involved in processes associated with trophoblast biology; however, novel genes were also identified. Some of them are hypothesized to be associated mainly with extracellular matrix remodeling (e.g., NID2) and cell migration and invasion (e.g., RAB25). Using Ingenuity pathways analysis software to identify signaling pathways involved in trophoblast differentiation or function, we discovered that many genes are involved in WNT/beta-catenin, ERK/MAPK, NFKB, and calcium signaling pathways, suggesting potential roles for these families in trophoblast development. This work provides an in vitro functional genomic model with which to identify genes involved in trophoblast development.

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Section: Signaling Pathways With Candidate Roles In Trophoblast Diffementioning

confidence: 96%

Transcriptomic Signature of Trophoblast Differentiation in a Human Embryonic Stem Cell Model1

Marchand

Horcajadas

Esteban

et al. 2011

Biology of Reproduction

100

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“…The following reagents were added to each 0.5 ml of RNase-free tube: 5 l total RNA (i.e., 3 ng for the reference and Ϸ3 ng for the oocyte samples) and 300 ng of an anchored T7-Oligo(dT) 24 V promoter primer (Ambion). The reaction tubes were incubated in a preheated PCR machine at 70°C for 2 min and transferred to ice.…”

Section: Methodsmentioning

confidence: 99%

The transcriptome of human oocytes

Kocabas¹,

Crosby

Ross³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

176

128

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The identification of genes and deduced pathways from the mature human oocyte can help us better understand oogenesis, folliculogenesis, fertilization, and embryonic development. Human metaphase II oocytes were used within minutes after removal from the ovary, and its transcriptome was compared with a reference sample consisting of a mixture of total RNA from 10 different normal human tissues not including the ovary. RNA amplification was performed by using a unique protocol. Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays were used for hybridizations. Compared with reference samples, there were 5,331 transcripts significantly up-regulated and 7,074 transcripts significantly down-regulated in the oocyte. Of the oocyte up-regulated probe sets, 1,430 have unknown function. A core group of 66 transcripts was identified by intersecting significantly up-regulated genes of the human oocyte with those from the mouse oocyte and from human and mouse embryonic stem cells. GeneChip array results were validated using RT-PCR in a selected set of oocyte-specific genes. Within the up-regulated probe sets, the top overrepresented categories were related to RNA and protein metabolism, followed by DNA metabolism and chromatin modification. This report provides a comprehensive expression baseline of genes expressed in in vivo matured human oocytes. Further understanding of the biological role of these genes may expand our knowledge on meiotic cell cycle, fertilization, chromatin remodeling, lineage commitment, pluripotency, tissue regeneration, and morphogenesis.genechip ͉ microarray ͉ RT-PCR ͉ pluripotency ͉ RNA amplification

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“…Therefore, it is necessary to pool large amounts of biological material and/or amplify the RNA without significantly altering the relative levels of individual mRNAs. Protocols for effective and nonbiased amplification of RNA from single oocytes and embryos have been developed (1,2,4,11), and transcript profiling of murine, porcine, and bovine oocytes and embryos has been reported (21,27,30,52,58,64,70). We previously demonstrated the feasibility and high reproducibility of crossspecies analysis using a human cDNA microarray.…”

mentioning

confidence: 98%

“…Advances in cDNA array technology have made possible large-scale analysis of the transcriptome of the mammalian genome in a quantitative manner. However, integration of suitable genomic methods and bioinformatic tools is a prerequisite for this kind of analysis (1,33).…”

mentioning

confidence: 99%

Conserved molecular portraits of bovine and human blastocysts as a consequence of the transition from maternal to embryonic control of gene expression

Adjaye

Herwig

Brink

et al. 2007

Physiological Genomics

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The present study investigated mRNA expression profiles of bovine oocytes and blastocysts by using a cross-species hybridization approach employing an array consisting of 15,529 human cDNAs as probe, thus enabling the identification of conserved genes during human and bovine preimplantation development. Our analysis revealed 419 genes that were expressed in both oocytes and blastocysts. The expression of 1,324 genes was detected exclusively in the blastocyst, in contrast to 164 in the oocyte including a significant number of novel genes. Genes indicative for transcriptional and translational control (ELAVL4, TACC3) were overexpressed in the oocyte, whereas cellular trafficking (SLC2A14, SLC1A3), proteasome (PSMA1, PSMB3), cell cycle (BUB3, CCNE1, GSPT1), and protein modification and turnover (TNK1, UBE3A) genes were found to be overexpressed in blastocysts. Transcripts implicated in chromatin remodeling were found in both oocytes (NASP, SMARCA2) and blastocysts (H2AFY, HDAC7A). The trophectodermal markers PSG2 and KRT18 were enriched 5- and 50-fold in the blastocyst. Pathway analysis revealed differential expression of genes involved in 107 distinct signaling and metabolic pathways. For example, phosphatidylinositol signaling and gluconeogenesis were prominent pathways identified in the blastocyst. Expression patterns in bovine and human blastocysts were to a large extent identical. This analysis compared the transcriptomes of bovine oocytes and blastocysts and provides a solid foundation for future studies on the first major differentiation events in blastocysts and identification of a set of markers indicative for regular mammalian development.

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Whole-genome approaches for large-scale gene identification and expression analysis in mammalian preimplantation embryos

Cited by 24 publications

References 70 publications

Transcriptomic Signature of Trophoblast Differentiation in a Human Embryonic Stem Cell Model1

Transcriptomic Signature of Trophoblast Differentiation in a Human Embryonic Stem Cell Model1

The transcriptome of human oocytes

Conserved molecular portraits of bovine and human blastocysts as a consequence of the transition from maternal to embryonic control of gene expression

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