Experts and Doctors on chromatin immunoprecipitation in Vancouver, British Columbia, Canada

Summary

Locale: Vancouver, British Columbia, Canada
Topic: chromatin immunoprecipitation

Top Publications

  1. Cohen C, Crome S, Macdonald K, Dai E, Mager D, Levings M. Human Th1 and Th17 cells exhibit epigenetic stability at signature cytokine and transcription factor loci. J Immunol. 2011;187:5615-26 pubmed publisher
    ..These data also question the broad applicability of the new model of Th cell lineage plasticity to in vivo-polarized human Th cell subsets. ..
  2. Long M, Rossi F. Targeted cell fusion facilitates stable heterokaryon generation in vitro and in vivo. PLoS ONE. 2011;6:e26381 pubmed publisher
    ..Finally, H?7 was also capable of increasing the contribution of transplanted fibroblasts to skeletal muscle repair in vivo, suggesting that this strategy could be used for therapeutic gene delivery. ..
  3. Rebollo R, Karimi M, Bilenky M, Gagnier L, Miceli Royer K, Zhang Y, et al. Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genet. 2011;7:e1002301 pubmed publisher
    ..However, the B3galtl gene is subject to transcriptional silencing via IAP-induced heterochromatin. Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness. ..
  4. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007;4:651-7 pubmed
    ..ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%. ..
  5. Fejes A, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones S. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics. 2008;24:1729-30 pubmed publisher
    ..1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks Source files for FindPeaks 3.1 are available for academic use. ..
  6. Wederell E, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, et al. Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res. 2008;36:4549-64 pubmed publisher
    ..Our comprehensive results for in vivo Foxa2-binding sites in the mouse liver will contribute to resolving transcriptional regulatory networks that are important for adult liver function. ..
  7. Robertson A, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, et al. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res. 2008;18:1906-17 pubmed publisher
  8. Xu Q, Guo H, Zhang X, Tang B, Cai F, Zhou W, et al. Hypoxia regulation of ATP13A2 (PARK9) gene transcription. J Neurochem. 2012;122:251-9 pubmed publisher
  9. Finkbeiner M, Astanehe A, To K, Fotovati A, Davies A, Zhao Y, et al. Profiling YB-1 target genes uncovers a new mechanism for MET receptor regulation in normal and malignant human mammary cells. Oncogene. 2009;28:1421-31 pubmed publisher
    ..Finally, silencing YB-1 or MET attenuated anchorage-independent growth of BLBC cell lines. Together, these findings implicate MET as a target of YB-1 that work in concert to promote BLBC growth. ..

More Information

Publications34

  1. An B, Poon S, So W, Hammond G, Leung P. Rapid effect of GNRH1 on follicle-stimulating hormone beta gene expression in LbetaT2 mouse pituitary cells requires the progesterone receptor. Biol Reprod. 2009;81:243-9 pubmed publisher
    ..We conclude that the rapid effect of GNRH1 on Fshb expression in LbetaT2 cells is mediated by PGR phosphorylation and loading at the PRE within the Fshb promoter together with NCOA3. ..
  2. Kim S, Nian C, McIntosh C. Adipocyte expression of the glucose-dependent insulinotropic polypeptide receptor involves gene regulation by PPARĪ³ and histone acetylation. J Lipid Res. 2011;52:759-70 pubmed publisher
  3. Rossetto D, Cramet M, Wang A, Steunou A, Lacoste N, Schulze J, et al. Eaf5/7/3 form a functionally independent NuA4 submodule linked to RNA polymerase II-coupled nucleosome recycling. EMBO J. 2014;33:1397-415 pubmed publisher
    ..Taken together, these results lead to a model where Eaf5/7/3 associates with elongating polymerase to promote the disruption of nucleosomes in its path, but also their refolding in its wake. ..
  4. Kwon A, Arenillas D, Worsley Hunt R, Wasserman W. oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets. G3 (Bethesda). 2012;2:987-1002 pubmed publisher
    ..oPOSSUM-3 is available at http://opossum.cisreg.ca. ..
  5. Astanehe A, Finkbeiner M, Krzywinski M, Fotovati A, Dhillon J, Berquin I, et al. MKNK1 is a YB-1 target gene responsible for imparting trastuzumab resistance and can be blocked by RSK inhibition. Oncogene. 2012;31:4434-46 pubmed publisher
    ..In conclusion, this unbiased integrated approach identified MNK1 as a player in mediating trastuzumab resistance as a consequence of YB-1 activation, and demonstrated RSK inhibition as a means to overcome recalcitrance to trastuzumab. ..
  6. Cullum R, Alder O, Hoodless P. The next generation: using new sequencing technologies to analyse gene regulation. Respirology. 2011;16:210-22 pubmed publisher
    ..The advances made by pairing NGS with strategic experimental protocols will continue to impact the research community. ..
  7. Lubieniecka J, de Bruijn D, Su L, van Dijk A, Subramanian S, van de Rijn M, et al. Histone deacetylase inhibitors reverse SS18-SSX-mediated polycomb silencing of the tumor suppressor early growth response 1 in synovial sarcoma. Cancer Res. 2008;68:4303-10 pubmed publisher
    ..Furthermore, our work highlights a possible mechanism behind the efficacy of a clinically applicable HDAC inhibitor in synovial sarcoma treatment. ..
  8. Sulistyoningrum D, Singh R, Devlin A. Epigenetic regulation of glucocorticoid receptor expression in aorta from mice with hyperhomocysteinemia. Epigenetics. 2012;7:514-21 pubmed publisher
    ..These findings show methylation and silencing of vascular Nr3c1 expression and suggest a role for epigenetic regulation of gene expression in HHcy. ..
  9. Leung D, Dong K, Maksakova I, Goyal P, Appanah R, Lee S, et al. Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing. Proc Natl Acad Sci U S A. 2011;108:5718-23 pubmed publisher
    ..Taken together, these observations reveal that in mESCs, the H3K9 KMTase G9a is required for the establishment, but not for the maintenance, of silencing of newly integrated proviruses...
  10. Portales Casamar E, Thongjuea S, Kwon A, Arenillas D, Zhao X, Valen E, et al. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 2010;38:D105-10 pubmed publisher
    ..Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches. ..
  11. Tennant B, Islam R, Kramer M, Merkulova Y, Kiang R, Whiting C, et al. The transcription factor Myt3 acts as a pro-survival factor in ?-cells. PLoS ONE. 2012;7:e51501 pubmed publisher
    ..These data are an important step in clarifying the regulatory networks responsible for ?-cell survival, and point to Myt3 as a potential therapeutic target for improving functional ?-cell mass. ..
  12. Astanehe A, Finkbeiner M, Hojabrpour P, To K, Fotovati A, Shadeo A, et al. The transcriptional induction of PIK3CA in tumor cells is dependent on the oncoprotein Y-box binding protein-1. Oncogene. 2009;28:2406-18 pubmed publisher
    ..In conclusion, YB-1 is the first reported oncogene to induce the expression of PIK3CA through transcriptional control of its promoter. ..
  13. Stratford A, Fry C, Desilets C, Davies A, Cho Y, Li Y, et al. Y-box binding protein-1 serine 102 is a downstream target of p90 ribosomal S6 kinase in basal-like breast cancer cells. Breast Cancer Res. 2008;10:R99 pubmed publisher
    ..This provides a newly described mechanism whereby YB-1 is activated in breast cancer. This implicates the EGFR/RSK/YB-1 pathway as an important component of BLBC, providing an important opportunity for therapeutic intervention. ..
  14. Viringipurampeer I, Ferreira T, DeMaria S, Yoon J, Shan X, Moosajee M, et al. Pax2 regulates a fadd-dependent molecular switch that drives tissue fusion during eye development. Hum Mol Genet. 2012;21:2357-69 pubmed publisher
    ..Furthermore, our data suggest that future therapeutic strategies may be based on small molecule drugs that can bypass the gene defects causing common congenital tissue fusion defects. ..
  15. Zhang X, Robertson G, Woo S, Hoffman B, Gottardo R. Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data. PLoS ONE. 2012;7:e32095 pubmed publisher
  16. Chow J, Hall L, Baldry S, Thorogood N, Lawrence J, Brown C. Inducible XIST-dependent X-chromosome inactivation in human somatic cells is reversible. Proc Natl Acad Sci U S A. 2007;104:10104-9 pubmed
  17. Argiropoulos B, Yung E, Xiang P, Lo C, Kuchenbauer F, Palmqvist L, et al. Linkage of the potent leukemogenic activity of Meis1 to cell-cycle entry and transcriptional regulation of cyclin D3. Blood. 2010;115:4071-82 pubmed publisher
    ..This study provides strong evidence linking the growth-promoting activities of Meis1 to the cyclin D-pRb cell-cycle control pathway...
  18. Mathelier A, Wasserman W. The next generation of transcription factor binding site prediction. PLoS Comput Biol. 2013;9:e1003214 pubmed publisher
    ..These results demonstrate the capacity of TFFMs to accurately model DNA-protein interactions, while providing a single unified framework suitable for the next generation of TFBS prediction. ..
  19. Shiota M, Zardan A, Takeuchi A, Kumano M, Beraldi E, Naito S, et al. Clusterin mediates TGF-?-induced epithelial-mesenchymal transition and metastasis via Twist1 in prostate cancer cells. Cancer Res. 2012;72:5261-72 pubmed publisher
    ..Taken together, our findings indicate that CLU is an important mediator of TGF-?-induced EMT, and suggest that CLU suppression may represent a promising therapeutic option for suppressing prostate cancer metastatic progression. ..
  20. Doheny J, Mottus R, Grigliatti T. Telomeric position effect--a third silencing mechanism in eukaryotes. PLoS ONE. 2008;3:e3864 pubmed publisher
  21. Hentrich T, Schulze J, Emberly E, Kobor M. CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures. Bioinformatics. 2012;28:717-8 pubmed publisher
    ..It integrates into typical analysis workflows and enables rapid graphical assessment and comparison of genome-wide data at a glance. https://github.com/cmmt/chromatra. ..
  22. Fu Y, Chang A, Chang L, Niessen K, Eapen S, Setiadi A, et al. Differential regulation of transforming growth factor beta signaling pathways by Notch in human endothelial cells. J Biol Chem. 2009;284:19452-62 pubmed publisher
    ..This is the first evidence that Notch activation affects R-Smad expression and that cooperative induction of histone acetylation at specific promoters underlies the selective synergy between Notch and TGFbeta signaling pathways. ..
  23. Selva D, Hogeveen K, Hammond G. Repression of the human sex hormone-binding globulin gene in Sertoli cells by upstream stimulatory transcription factors. J Biol Chem. 2005;280:4462-8 pubmed
  24. Aristizabal M, Negri G, Benschop J, Holstege F, Krogan N, Kobor M. High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8. PLoS Genet. 2013;9:e1003758 pubmed publisher
    ..Here, loss of CDK8 suppressed the reduced mRNA expression and RNAPII occupancy levels of CTD truncation mutants. ..
  25. Chiu H, Yong T, Wang J, Wang Y, Vessella R, Ueda T, et al. Induction of neuronal apoptosis inhibitory protein expression in response to androgen deprivation in prostate cancer. Cancer Lett. 2010;292:176-85 pubmed publisher
    ..04) in clinical samples of prostate cancer from patients receiving ADT. Expression of NAIP may be associated with enhanced survival of prostate cancer in response to castration. ..