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  • 1
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    Mapping and analysis of chromatin state dynamics in nine human cell types (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-03-29
    Description: Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088773/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088773/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ernst, Jason -- Kheradpour, Pouya -- Mikkelsen, Tarjei S -- Shoresh, Noam -- Ward, Lucas D -- Epstein, Charles B -- Zhang, Xiaolan -- Wang, Li -- Issner, Robbyn -- Coyne, Michael -- Ku, Manching -- Durham, Timothy -- Kellis, Manolis -- Bernstein, Bradley E -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01HG004037/HG/NHGRI NIH HHS/ -- RC1HG005334/HG/NHGRI NIH HHS/ -- U54 HG004570/HG/NHGRI NIH HHS/ -- U54 HG004570-01/HG/NHGRI NIH HHS/ -- U54 HG004570-02/HG/NHGRI NIH HHS/ -- U54 HG004570-02S1/HG/NHGRI NIH HHS/ -- U54 HG004570-03/HG/NHGRI NIH HHS/ -- U54 HG004570-03S1/HG/NHGRI NIH HHS/ -- U54 HG004570-04/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 May 5;473(7345):43-9. doi: 10.1038/nature09906. Epub 2011 Mar 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21441907" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Line ; Cell Line, Tumor ; *Cell Physiological Phenomena ; Cells, Cultured ; Chromatin/*genetics/*metabolism ; *Chromosome Mapping ; Gene Expression Regulation ; Genome, Human/genetics ; Hep G2 Cells ; Humans ; Promoter Regions, Genetic/genetics ; Reproducibility of Results ; Transcription Factors/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Live attenuated malaria vaccine designed to protect through hepatic CD8(+) T cell immunity (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-10
    Description: Our goal is to develop a vaccine that sustainably prevents Plasmodium falciparum (Pf) malaria in 〉/=80% of recipients. Pf sporozoites (PfSPZ) administered by mosquito bites are the only immunogens shown to induce such protection in humans. Such protection is thought to be mediated by CD8(+) T cells in the liver that secrete interferon-gamma (IFN-gamma). We report that purified irradiated PfSPZ administered to 80 volunteers by needle inoculation in the skin was safe, but suboptimally immunogenic and protective. Animal studies demonstrated that intravenous immunization was critical for inducing a high frequency of PfSPZ-specific CD8(+), IFN-gamma-producing T cells in the liver (nonhuman primates, mice) and conferring protection (mice). Our results suggest that intravenous administration of this vaccine will lead to the prevention of infection with Pf malaria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Epstein, J E -- Tewari, K -- Lyke, K E -- Sim, B K L -- Billingsley, P F -- Laurens, M B -- Gunasekera, A -- Chakravarty, S -- James, E R -- Sedegah, M -- Richman, A -- Velmurugan, S -- Reyes, S -- Li, M -- Tucker, K -- Ahumada, A -- Ruben, A J -- Li, T -- Stafford, R -- Eappen, A G -- Tamminga, C -- Bennett, J W -- Ockenhouse, C F -- Murphy, J R -- Komisar, J -- Thomas, N -- Loyevsky, M -- Birkett, A -- Plowe, C V -- Loucq, C -- Edelman, R -- Richie, T L -- Seder, R A -- Hoffman, S L -- 5R44AI055229-07/AI/NIAID NIH HHS/ -- 5R44AI058375-05/AI/NIAID NIH HHS/ -- 5R44AI058499-05/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):475-80. doi: 10.1126/science.1211548. Epub 2011 Sep 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Military Malaria Vaccine Program, Naval Medical Research Center, Silver Spring, MD 20910, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21903775" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Animals ; Antibodies, Protozoan/blood/immunology ; Antigens, Protozoan/immunology ; CD8-Positive T-Lymphocytes/*immunology ; Humans ; Injections, Intravenous ; Injections, Subcutaneous ; Interferon-gamma/biosynthesis/immunology ; Liver/*immunology ; Macaca mulatta ; Malaria Vaccines/administration & dosage/adverse effects/*immunology ; Malaria, Falciparum/*prevention & control ; Mice ; Middle Aged ; Plasmodium falciparum/*immunology ; Rabbits ; Sporozoites/*immunology ; Vaccines, Attenuated/administration & dosage/adverse effects/immunology ; Young Adult
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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