Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays

Adjaye, James; Herwig, Ralf; Herrmann, Doris; Wruck, Wasco; Benkahla, Alia; Brink, Thore C.; Nowak, Monika Anna; Carnwath, Joseph Wallace; Hultschig, Claus; Niemann, Heinrich; Lehrach, Hans

doi:10.1186/1471-2164-5-83

Cited by 74 publications

(39 citation statements)

References 27 publications

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“…The number of genes detected as expressed exclusively in the oocyte was rather low [166 (12%)]. This unexpectedly low number of oocyteexpressed genes detected might be due partly to the fact that the comparative sequence homology for the majority of the genes presented as probes on the array is low and thus undetected as expressed with the high stringency of the hybridization protocol previously described (3). In support of this finding is the fact that in our previous studies using the same array platform (4) we detected ϳ6,000 genes expressed in the human blastocyst, whereas only 1,324 were detected as expressed in the bovine blastocyst.…”

Section: Global Data Analysismentioning

confidence: 90%

“…This corresponds to four technical replicates for oocytes and blastocysts, respectively. Full details of labeling and hybridization reactions, slide washing (0.2ϫ SSC-0.1% SDS, 55°C), and scanning are described elsewhere (3,4).…”

Section: Methodsmentioning

confidence: 99%

“…We previously demonstrated the feasibility and high reproducibility of crossspecies analysis using a human cDNA microarray. Messenger RNAs derived from human and bovine fetal brains were compared, and the correlation coefficient of cross-hybridization between orthologous genes was 0.94 (3). We now report the first comparative transcriptome profile of bovine oocytes and blastocysts using a human 15,529 gene chip (the ENSEMBL chip) as an initial step to gain insight into gene expression and regulation during preimplantation development.…”

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confidence: 99%

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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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Section: Global Data Analysismentioning

confidence: 90%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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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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“…Analysis of gene expression patterns in early embryos using cDNA microarray provides insight into the function of gene regulatory networks leading to unravel the molecular mechanisms underlying developmental abnormalities (Adjaye et al 2004). Therefore, we focused on searching for genes that regulate the developmental competence of embryos to term.…”

Section: Discussionmentioning

confidence: 99%

Bovine blastocysts with developmental competence to term share similar expression of developmentally important genes although derived from different culture environments

Ghanem¹,

Salilew‐Wondim²,

Gad³

et al. 2011

Reproduction

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This study was conducted to investigate the gene expression profile of in vivo-derived bovine embryo biopsies based on pregnancy outcomes after transferring to recipients. For this, biopsies of 30-40% embryos were taken from grade I blastocysts (International Embryo Transfer Society Manual) and the remaining 60-70% of the intact embryos were transferred to recipients. Frozen biopsies were pooled into three distinct groups based on the pregnancy outcome after transferring the corresponding parts, namely those resulting in no pregnancy (NP), pregnancy loss (PL), and calf delivery (CD). Array analysis revealed a total of 41 and 43 genes to be differentially expressed between biopsies derived from blastocysts resulting in NP versus CD and PL versus CD respectively. Genes regulating placental development and embryo maternal interaction (PLAC8) were found to be upregulated in embryo biopsies that ended up with CD. Embryo biopsies that failed to induce pregnancy were enriched with mitochondrial transcripts (Fl405) and stress-related genes (HSPD1). Overall, gene expression profiles of blastocysts resulting in NP and CD shared similar expression profiles with respect to genes playing significant roles in preimplantation development of embryo. Finally, comparing the transcript signatures of in vivo-and in vitro-derived embryos with developmental competence to term revealed a similarity in the relative abundance of 18 genes. Therefore, we were able to present a genetic signature associated with term developmental competence independent of the environmental origin of the transferred blastocysts.

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“…These results confirmed that a large number of genes were differentially expressed, thereby validating the use of cross-species hybridizations for nonhuman primate studies. Adjaye et al [30] used human and bovine fetal brain target samples on a human cDNA microarray.…”

Section: Discussionmentioning

confidence: 99%

Microarray analysis of a pyrethroid resistant African malaria vector, Anopheles funestus, from southern Africa

Christian

Strode

Ranson

et al. 2011

Pesticide Biochemistry and Physiology

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Anopheles funestus is one of the major malaria vectors in southern Africa and several populations in this region are resistant to pyrethroids. The current study uses a microarray based approach to identify genes up-regulated in the pyrethroid resistant population, FUMOZ, from Mozambique. As the full set of detoxification genes in An. funestus are unknown, this study investigated the utility of the An. gambiae 'detox chip' to screen for differentially expressed detoxification genes in An. funestus. Differential expression of detoxification genes in three day old adult females and males from the FUMOZ resistant strain and the FANG susceptible strain was identified using the An. gambiae 'detox chip'.After optimization of the hybridization conditions, over 90% of the probes showed a positive signal. Only three genes were significantly (p<0.001) differentially expressed in the females, CYP6P9 (5.4-fold), COI (2.7-fold) and CYP6M7 (1.8-fold). The same genes were also significantly differentially expressed in the adult males, CYP6P9 (6.0-fold), COI (2.9-fold) and CYP6M3 (3.6-fold) together with an additional 21 transcripts.Quantitative PCR (qPCR) analysis was conducted to validate the microarray results. This study demonstrated that heterologous hybridization is a helpful tool in identifying detoxification genes differentially expressed in An. funestus strains. Keywords:Microarrays, An. funestus, 'detox chip', pyrethroid resistance, cytochrome P450. 3 IntroductionIn 2008 In this study we investigated the use of the An. gambiae 'detox chip' in determining potential genes associated with insecticide resistance in a southern African An. funestus resistant strain (FUMOZ-R) and a susceptible strain (FANG). Selected significantly overexpressed genes from the microarray results were validated using qPCR. 5 Materials and methods Mosquito strainsTwo An. funestus strains were used in this study. The FUMOZ-R strain originated from Mozambique and has been maintained under selection pressure with permethrin. FANG ori ginates f rom Angol a and is susceptible to all known insecti cides. Details on the insecticide resistance status of these colonies can be found in the study by Hunt et al.[20]. Both strains are maintained in standard insectary conditions of 25°C with 80% relative humidity and 12 h day/night, 45 min dusk/dawn lighting cycle. Sample preparation and microarray hybridizationsFemale and male An. funestus adults were separated on day of emergence and fed on 10%sugar solution until they were three days old (without prior exposure to pyrethroids). The transcription levels in the three day old resistant FUMOZ-R adult females were compared to the susceptible females of the same age. The same was done for the males. Each comparison in all experiments consisted of three independent biological replicates and two technical repeats which included dye swaps to control for dye bias. There were four within-array replicate spots per microarray slide. Total RNA was extracted from three batches of fifteen three day old adult fema...

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Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays

Cited by 74 publications

References 27 publications

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

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

Bovine blastocysts with developmental competence to term share similar expression of developmentally important genes although derived from different culture environments

Microarray analysis of a pyrethroid resistant African malaria vector, Anopheles funestus, from southern Africa

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