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dc.contributor.authorXie, Dan
dc.contributor.authorChen, Chieh-Chun
dc.contributor.authorPtaszek, Leon M.
dc.contributor.authorXiao, Shu
dc.contributor.authorCao, Xiaoyi
dc.contributor.authorFang, Fang
dc.contributor.authorNg, Huck H.
dc.contributor.authorLewin, Harry A.
dc.contributor.authorCowan, Chad A.
dc.contributor.authorZhong, Sheng
dc.date.accessioned2015-03-02T21:50:21Z
dc.date.issued2010
dc.identifier.citationXie, D., C.-C. Chen, L. M. Ptaszek, S. Xiao, X. Cao, F. Fang, H. H. Ng, H. A. Lewin, C. Cowan, and S. Zhong. 2010. “Rewirable Gene Regulatory Networks in the Preimplantation Embryonic Development of Three Mammalian Species.” Genome Research 20 (6) (March 10): 804–815. doi:10.1101/gr.100594.109.en_US
dc.identifier.issn1088-9051en_US
dc.identifier.issn1549-5469en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:14068405
dc.description.abstractMammalian preimplantation embryonic development (PED) is thought to be governed by highly conserved processes. While it had been suggested that some plasticity of conserved signaling networks exists among different mammalian species, it was not known to what extent modulation of the genomes and the regulatory proteins could “rewire” the gene regulatory networks (GRN) that control PED. We therefore generated global transcriptional profiles from three mammalian species (human, mouse, and bovine) at representative stages of PED, including: zygote, two-cell, four-cell, eight-cell, 16-cell, morula and blastocyst. Coexpression network analysis suggested that 40.2% orthologous gene triplets exhibited different expression patterns among these species. Combining the expression data with genomic sequences and the ChIP-seq data of 16 transcription regulators, we observed two classes of genomic changes that contributed to interspecies expression difference, including single nucleotide mutations leading to turnover of transcription factor binding sites, and insertion of cis-regulatory modules (CRMs) by transposons. About 10% of transposons are estimated to carry CRMs, which may drive species-specific gene expression. The two classes of genomic changes act in concert to drive mouse-specific expression of MTF2, which links POU5F1/NANOG to NOTCH signaling. We reconstructed the transition of the GRN structures as a function of time during PED. A comparison of the GRN transition processes among the three species suggested that in the bovine system, POU5F1's interacting partner SOX2 may be replaced by HMGB1 (a TF sharing the same DNA binding domain with SOX2), resulting in rewiring of GRN by a trans change.en_US
dc.description.sponsorshipStem Cell and Regenerative Biologyen_US
dc.language.isoen_USen_US
dc.publisherCold Spring Harbor Laboratory Pressen_US
dc.relation.isversionofdoi:10.1101/gr.100594.109en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pubmed/20219939en_US
dash.licenseLAA
dc.titleRewirable gene regulatory networks in the preimplantation embryonic development of three mammalian speciesen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalGenome Researchen_US
dash.depositing.authorCowan, Chad A.
dc.date.available2015-03-02T21:50:21Z
dc.identifier.doi10.1101/gr.100594.109*
workflow.legacycommentsFLAG3. 6 months after publication all Genome Research articles fall under a CC-BY-NC license (http://genome.cshlp.org/site/misc/GR_LicenseToPublish_2014_v4.pdf; see also http://genome.cshlp.org/site/misc/terms.xhtml)en_US
dash.contributor.affiliatedPtaszek, Leon
dash.contributor.affiliatedCowan, Chad


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