A 7872 cDNA microarray and its use in bovine functional genomics

Everts, Robin E.; Band, Mark; Liu, Z. Lewis; Kumar, Charu G.; Liu, Lei; Loor, Juan J.; Oliveira, Rosane; Lewin, Harris A.

doi:10.1016/j.vetimm.2005.02.003

Cited by 52 publications

(38 citation statements)

References 41 publications

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“…It contains 7800 cDNA inserts from term placenta (Everts et al 2005) and 2400 cDNA inserts from extra-embryonic tissues of bovine embryos (D14-D24) as well as young foetuses (D36 and D64). The corresponding libraries are indexed in Unigene as Lib.…”

Section: Inra Bovine 10k Arraymentioning

confidence: 99%

A small set of extra-embryonic genes defines a new landmark for bovine embryo staging

Degrelle¹,

Cao²,

Heyman³

et al. 2011

Reproduction

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Axis specification in mouse is determined by a sequence of reciprocal interactions between embryonic and extra-embryonic tissues so that a few extra-embryonic genes appear as 'patterning' the embryo. Considering these interactions as essential, but lacking in most mammals the genetically driven approaches used in mouse and the corresponding patterning mutants, we examined whether a molecular signature originating from extra-embryonic tissues could relate to the developmental stage of the embryo proper and predict it. To this end, we have profiled bovine extra-embryonic tissues at peri-implantation stages, when gastrulation and early neurulation occur, and analysed the subsequent expression profiles through the use of predictive methods as previously reported for tumour classification. A set of six genes (CALM1, CPA3, CITED1, DLD, HNRNPDL, and TGFB3), half of which had not been previously associated with any extra-embryonic feature, appeared significantly discriminative and mainly dependent on embryonic tissues for its faithful expression. The predictive value of this set of genes for gastrulation and early neurulation stages, as assessed on naive samples, was remarkably high (93%). In silico connected to the bovine orthologues of the mouse patterning genes, this gene set is proposed as a new trait for embryo staging. As such, this will allow saving the bovine embryo proper for molecular or cellular studies. To us, it offers as well new perspectives for developmental phenotyping and modelling of embryonic/extra-embryonic co-differentiation.

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Section: Inra Bovine 10k Arraymentioning

confidence: 99%

A small set of extra-embryonic genes defines a new landmark for bovine embryo staging

Degrelle¹,

Cao²,

Heyman³

et al. 2011

Reproduction

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“…This new approach may be helpful not only in elucidating metabolic pathways in cells but also in understanding the complex mechanism of implantation. Several systems have been developed as custom-made and/or commercial arrays, such as cDNA or OligoArray systems for analyzing cattle gene profiles [17][18][19][20][21]. Primarily, genome-wide expression profiling systems are assembled, and the detailed gene functions and signal cascades are analyzed using bioinformatics.…”

Section: Developing a Bovine Cdna Microarraymentioning

confidence: 99%

“…Another group established bovine placental cDNA microarrays at almost the same time as this study. Their array consisted of 3,244 of 7,872 genes annotated from placental and splenic tissues [17,21]. The array for this study consisted of approximately 1,780 of 3,995 identified genes and contained 16 out of 21 PAGs that were bovine trophoblast cell specific [18,28,29]; however, the other array system involved only 10 of these placental-specific genes [17].…”

Section: Developing a Bovine Cdna Microarraymentioning

confidence: 99%

Analysis of Uteroplacental-specific Molecules and Their Functions During Implantation and Placentation in the Bovine

Hashizume

2007

Journal of Reproduction and Development

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Abstract. In cattle, the mechanisms underlying implantation and placental development are still unclear. Synepitheliochorial placentation in cattle is noninvasive, and thus generates limited interest in terms of degradation and remodeling of endometrial tissues. The overall purpose of this study was three-fold: (1) to examine the gene circuitry around the implantation window, (2) to understand development of the placenta during the peri-implantation period by using a uteroplacental cDNA microarray, and (3) to study the roles of molecules involved in endometrial remodeling. Bovine trophoblastic binucleate cell-specific molecules, such as pregnancy-associated glycoproteins (PAGs), placental lactogen (PL), and prolactin-related proteins (PRPs), were markedly expressed in binucleate cells (BNCs) around implantation. The expression of PRP-1 was specific to the caruncular (CAR) area of the gravid uterine horn. Gelatinases (MMP-2 and -9) in association with heparanase may be central to endometrial remodeling. In situ hybridization analyses of PAGs, PRPs, PL, and heparanase suggested that BNCs expressed these molecules simultaneously. Future studies will further investigate the specific roles of these molecules in placentogenesis. The uteroplacental cDNA microarray presented cascades of molecular signatures not only for the endometrium but also for the intricate dialogue at the level of the feto-maternal interface in cattle. Placentome morphogenesis potentially parallels the dynamic multigenic circuitry and regulates the cell cycle in the endometrium. The roles of BNCs and their secreted molecules remain an enigma, particularly with regard to the adhesion process and endometrial remodeling, which is the focus of this study.

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“…First-strand aa-cDNA was purified and fluorescently labeled as previously described (68). The aa-cDNA synthesis and labeling procedures were also carried out on a standard reference RNA sample developed in our laboratory for microarray studies (13). Labeled cDNA samples were purified and hybridized to a microarray consisting of 7,653 cattle spleen-and placenta-derived cDNAs as described previously (13,68).…”

Section: Radiation Hybrid Mappingmentioning

confidence: 99%

“…The aa-cDNA synthesis and labeling procedures were also carried out on a standard reference RNA sample developed in our laboratory for microarray studies (13). Labeled cDNA samples were purified and hybridized to a microarray consisting of 7,653 cattle spleen-and placenta-derived cDNAs as described previously (13,68). Slides were scanned using an Axon 4000B scanner, images were analyzed with GenePix 4.0 (Molecular Devices, Union City, CA), and data were normalized with GeneSpring 5.0 (Silicon Genetics, Redwood City, CA) using the approach of Band et al (5).…”

Section: Radiation Hybrid Mappingmentioning

confidence: 99%

Discovery of eight novel divergent homologs expressed in cattle placenta

Larson

Kumar

Everts

et al. 2006

Physiological Genomics

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Ten divergent homologs were identified using a subtractive bioinformatic analysis of 12,614 cattle placenta expressed sequence tags followed by comparative, evolutionary, and gene expression studies. Among the 10 divergent homologs, 8 have not been identified previously. These were named as follows: cattle cerebrum and skeletal muscle-specific transcript 1 (CSSMST1), cattle intestine-specific transcript 1 (CIST1), hepatitis A virus cellular receptor 1 amino-terminal domain-containing protein (HAVCRNDP), prolactin-related proteins 8, 9, and 11 (PRP8, PRP9, and PRP11, respectively) and secreted and transmembrane protein 1A and 1B (SECTM1A and SECTM1B, respectively). In addition, two previously known divergent genes were identified, trophoblast Kunitz domain protein 1 (TKDP1) and a new splice variant of TKDP4. Nucleotide substitution analysis provided evidence for positive selection in members of the PRP gene family, SECTM1A and SECTM1B. Gene expression profiles, motif predictions, and annotations of homologous sequences indicate immunological and reproductive functions of the divergent homologs. The genes identified in this study are thus of evolutionary and physiological importance and may have a role in placental adaptations. molecular evolution; bovine genome; comparative genomics THE PLACENTA DEMONSTRATES remarkable variation among eutherian mammals, and it is believed that the vast diversity of placental architectures seen in different mammalian lineages is the result of adaptive evolution (8, 47). Two major selective forces likely driving adaptation of the placenta are fetalmaternal conflict over nutrient resource allocation and maintenance of immunologic tolerance of the fetal semi-allograft (45,66). Cattle possess a synepitheliochorial placenta arranged as placentomes consisting of a fetal cotyledon interdigitating with a maternal caruncle. The cattle embryonal trophoblast contains granulated binucleate cells at the microvillar junction with cytoplasmic projections that penetrate the maternal uterine endometrium (70, 72). Ruminant-specific genes with expression localized to the trophoblast have been identified, including the interferon-genes (54) The expression of these genes at sites of direct contact between fetal and maternal cells suggests that they represent molecular adaptations mediating maternal-fetal interaction during pregnancy (8,55).Comparisons between the whole genome sequences of human, mouse, and rat revealed extensive lineage-specific expansions in gene families associated with reproduction, immunity, chemosensation, detoxification, and proteolysis (48, 52). The identification of orthologous relationships for ϳ80% of genes in the human and mouse genomes indicates that lineagespecific gene family expansion likely represents a major route of mammalian evolution. These lineage-specific paralogs are believed to represent adaptive innovations on the basis of evidence that positive selection has operated on a subset of proteins functioning in reproduction and immunity (48). It is likely that the ...

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A 7872 cDNA microarray and its use in bovine functional genomics

Cited by 52 publications

References 41 publications

A small set of extra-embryonic genes defines a new landmark for bovine embryo staging

A small set of extra-embryonic genes defines a new landmark for bovine embryo staging

Analysis of Uteroplacental-specific Molecules and Their Functions During Implantation and Placentation in the Bovine

Discovery of eight novel divergent homologs expressed in cattle placenta

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