1. Characteristics and mechanism of phase change material W0.03Sb2Te etched by Cl2/BCl3 inductively coupled plasmas

    Thin Solid Films 593:67 (2015)

    Inductively coupled plasma (ICP) etching of phase change material W0.03Sb2Te (WST) films is studied using Cl2/BCl3 gas mixture. The effects of gas-mixing ratio, bias power, gas pressure, applying ICP power on the variations of etch rate, etch profiles, and surface roughness are investi...
  2. Regulation of AURKC expression by CpG island methylation in human cancer cells.

    Tumor Biology 36(10):8147 (2015) PMID 25990457

    AURKC, a member of the Aurora kinase gene family, is highly expressed in testis but is either moderately expressed or repressed in most somatic cells. Varying expression of AURKC has been observed in human cancers, but the underlying mechanisms of differential expression have been investigated o...
  3. Cell-autonomous activation of Hedgehog signaling inhibits brown adipose tissue development.

    PNAS 112(16):5069 (2015) PMID 25848030 PMCID PMC4413261

    Although recent studies have shown that brown adipose tissue (BAT) arises from progenitor cells that also give rise to skeletal muscle, the developmental signals that control the formation of BAT remain largely unknown. Here, we show that brown preadipocytes possess primary cilia and can respond...
  4. Phase-change properties of GeSbTe thin films deposited by plasma-enchanced atomic layer depositon.

    Nanoscale Research Letters 10:89 (2015) PMID 25852385 PMCID PMC4385138

    Phase-change access memory (PCM) appears to be the strongest candidate for next-generation high-density nonvolatile memory. The fabrication of ultrahigh-density PCM depends heavily on the thin-film growth technique for the phase-changing chalcogenide material. In this study, Ge2Sb2Te5 (GST) and ...
  5. On the meaning of the word 'epimutation': a comment.

    Trends in Genetics 31(1):1 (2015) PMID 25480537

  6. Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome.

    Genome Biology 16(1):211 (2015) PMID 26420038 PMCID PMC4589031

    DNA methylation is an epigenetic mechanism central to development and maintenance of complex mammalian tissues, but our understanding of its role in intestinal development is limited. We use whole genome bisulfite sequencing, and find that differentiation of mouse colonic intestinal stem cells t...
  7. CDC42 inhibition suppresses progression of incipient intestinal tumors.

    Cancer Research 74(19):5480 (2014) PMID 25113996 PMCID PMC4184946

    Mutations in the APC or β-catenin genes are well-established initiators of colorectal cancer, yet modifiers that facilitate the survival and progression of nascent tumor cells are not well defined. Using genetic and pharmacologic approaches in mouse colorectal cancer and human colorectal cancer ...
  8. Targeted p16(Ink4a) epimutation causes tumorigenesis and reduces survival in mice.

    Journal of Clinical Investigation 124(9):3708 (2014) PMID 25061879 PMCID PMC4151219

    Cancer has long been viewed as a genetic disease; however, epigenetic silencing as the result of aberrant promoter DNA methylation is frequently associated with cancer development, suggesting an epigenetic component to the disease. Nonetheless, it has remained unclear whether an epimutation (an ...
  9. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing.

    Nucleic Acids Research 42(6):e43 (2014) PMID 24391148 PMCID PMC3973287

    Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quant...
  10. Major epigenetic development distinguishing neuronal and non-neuronal cells occurs postnatally in the murine hypothalamus.

    Human Molecular Genetics 23(6):1579 (2014) PMID 24186871 PMCID PMC3929094

    Prenatal and early postnatal environment can persistently alter one's risk of obesity. Environmental effects on hypothalamic developmental epigenetics constitute a likely mechanism underlying such 'developmental programming' of energy balance regulation. To advance our understanding of these pro...
  11. Developmentally programmed 3' CpG island methylation confers tissue- and cell-type-specific transcriptional activation.

    Molecular and Cellular Biology 33(9):1845 (2013) PMID 23459939 PMCID PMC3624169

    During development, a small but significant number of CpG islands (CGIs) become methylated. The timing of developmentally programmed CGI methylation and associated mechanisms of transcriptional regulation during cellular differentiation, however, remain poorly characterized. Here, we used genome...
  12. Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island.

    Nucleic Acids Research 40(15):7257 (2012) PMID 22600741 PMCID PMC3424568

    Repression of many tumor suppressor genes in cancer is concurrent with aberrantly increased DNA methylation levels at promoter CpG islands (CGIs). About one-fourth of empirically defined human promoters are surrounded by or contain clustered repetitive elements. It was previously observed that a...
  13. Effects of TET2 mutations on DNA methylation in chronic myelomonocytic leukemia.

    Epigenetics 7(2):201 (2012) PMID 22395470 PMCID PMC3335912

    TET2 enzymatically converts 5-methyl-cytosine to 5-hydroxymethyl-cytosine, possibly leading to loss of DNA methylation. TET2 mutations are common in myeloid leukemia and were proposed to contribute to leukemogenesis through DNA methylation. To expand on this concept, we studied chronic myelomono...
  14. Ni-doped GST materials for high speed phase change memory applications

    Materials Research Bulletin (2011)

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  15. Frequent alteration of MLL3 frameshift mutations in microsatellite deficient colorectal cancer.

    PLoS ONE 6(8):e23320 (2011) PMID 21853109 PMCID PMC3154922

    MLL3 is a histone 3-lysine 4 methyltransferase with tumor-suppressor properties that belongs to a family of chromatin regulator genes potentially altered in neoplasia. Mutations in MLL3 were found in a whole genome analysis of colorectal cancer but have not been confirmed by a separate study. We...
  16. DNA methylation profiles of primary colorectal carcinoma and matched liver metastasis.

    PLoS ONE 6(11):e27889 (2011) PMID 22132162 PMCID PMC3221680

    The contribution of DNA methylation to the metastatic process in colorectal cancers (CRCs) is unclear. We evaluated the methylation status of 13 genes (MINT1, MINT2, MINT31, MLH1, p16, p14, TIMP3, CDH1, CDH13, THBS1, MGMT, HPP1 and ERα) by bisulfite-pyrosequencing in 79 CRCs comprising 36 CRCs w...
  17. Association between folate levels and CpG Island hypermethylation in normal colorectal mucosa.

    Cancer Prevention Research 3(12):1552 (2010) PMID 21149331 PMCID PMC3058541

    Gene-specific promoter methylation of several genes occurs in aging normal tissues and may predispose to tumorigenesis. In the present study, we investigate the association of blood folate levels and dietary and lifestyle factors with CpG island (CGI) methylation in normal colorectal mucosa. Sub...
  18. Characteristic methylation profile in CpG island methylator phenotype-negative distal colorectal cancers.

    International Journal of Cancer 127(9):2095 (2010) PMID 20131317

    Aberrant DNA methylation is involved in colon carcinogenesis. Although the CpG island methylator phenotype (CIMP) is defined as a subset of colorectal cancers (CRCs) with remarkably high levels of DNA methylation, it is not known whether epigenetic processes are also involved in CIMP-negative tu...
  19. Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer.

    Genome Research 20(10):1369 (2010) PMID 20716667 PMCID PMC2945186

    Epigenetic silencing plays an important role in cancer development. An attractive hypothesis is that local DNA features may participate in differential predisposition to gene hypermethylation. We found that, compared with methylation-resistant genes, methylation-prone genes have a lower frequenc...
  20. Characterization of microRNAs involved in embryonic stem cell states.

    Stem Cells and Development 19(7):935 (2010) PMID 20128659 PMCID PMC3128320

    Studies of embryonic stem cells (ESCs) reveal that these cell lines can be derived from differing stages of embryonic development. We analyzed common changes in the expression of microRNAs (miRNAs) and mRNAs in 9 different human ESC (hESC) lines during early commitment and further examined the e...