We have been developing tools and resources that make it possible to analyze a large number of genes in various experimental conditions. In our earlier work, we 1) constructed cDNA libraries from early mouse embryos and stem cells and generated a large number of expressed sequence tags (ESTs), 2) developed a glass-slide microarray platform containing in situ-synthesized 60-mer oligonucleotide probes representing approximately 44,000 unique mouse transcripts, 3) produced web-based ANOVA-FDR software to provide user-friendly microarray data analysis, and 4) developed an algorithm and a fully-automated computational pipeline for transcript assembly from expressed sequences aligned to the mouse genome. In addition, we recently developed a comprehensive database and web browser of the binding sites of transcription factors (TFs) and cis-regulatory modules (CRMs) on the mouse genome. These resources and tools are now applied to the systematic analysis of gene regulatory networks in mouse embryonic stem cells. In our pilot project, we have demonstrated that it is possible to analyze and identify downstream target genes by monitoring the global gene expression patterns of mouse ES cell lines, when a gene encoding a specific TF (Pou5f1 or Oct4 in this case) is manipulated so that the gene can be overexpressed or repressed. We have extended this strategy to other key transcription factors (Sox2 and Nanog) in mouse ES cells. To further facilitate the analysis of gene regulatory networks, we have recently carried out the systematic repression of 105 TFs by shRNAs in mouse ES cells, followed by the microarray-based gene expression profiling. We are currently analyzing the data using various bioinformatics tools.

Agency
National Institute of Health (NIH)
Institute
National Institute on Aging (NIA)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIAAG000656-12
Application #
8148280
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
12
Fiscal Year
2010
Total Cost
$519,395
Indirect Cost
Name
National Institute on Aging
Department
Type
DUNS #
City
State
Country
Zip Code
Sharov, Alexei A (2016) Coenzyme world model of the origin of life. Biosystems 144:8-17
Li, Hoi Ming; Hiroi, Toyoko; Zhang, Yongqing et al. (2016) TCR? repertoire of CD4+ and CD8+ T cells is distinct in richness, distribution, and CDR3 amino acid composition. J Leukoc Biol 99:505-13
Sharov, Alexei A (2016) Evolution of natural agents: preservation, advance, and emergence of functional information. Biosemiotics 9:103-129
Sharova, Lioudmila V; Sharov, Alexei A; Piao, Yulan et al. (2016) Emergence of undifferentiated colonies from mouse embryonic stem cells undergoing differentiation by retinoic acid treatment. In Vitro Cell Dev Biol Anim 52:616-24
Yamamizu, Kohei; Sharov, Alexei A; Piao, Yulan et al. (2016) Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines. Sci Rep 6:25667
Teratani-Ota, Yusuke; Yamamizu, Kohei; Piao, Yulan et al. (2016) Induction of specific neuron types by overexpression of single transcription factors. In Vitro Cell Dev Biol Anim 52:961-973
Akiyama, Tomohiko; Xin, Li; Oda, Mayumi et al. (2015) Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells. DNA Res 22:307-18
Yamamizu, Kohei; Schlessinger, David; Ko, Minoru S H (2014) SOX9 accelerates ESC differentiation to three germ layer lineages by repressing SOX2 expression through P21 (WAF1/CIP1). Development 141:4254-66
Sherman-Baust, Cheryl A; Kuhn, Elisabetta; Valle, Blanca L et al. (2014) A genetically engineered ovarian cancer mouse model based on fallopian tube transformation mimics human high-grade serous carcinoma development. J Pathol 233:228-37
Piao, Yulan; Hung, Sandy Shen-Chi; Lim, Shiang Y et al. (2014) Efficient generation of integration-free human induced pluripotent stem cells from keratinocytes by simple transfection of episomal vectors. Stem Cells Transl Med 3:787-91

Showing the most recent 10 out of 22 publications