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Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Thursday, 2015 January 15
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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PubMed Results

Items 1 - 4 of 4

1.	Nature. 2014 Nov 20;515(7527):371-5. doi: 10.1038/nature13985. Principles of regulatory information conservation between mouse and human. Cheng Y1, Ma Z1, Kim BH2, Wu W3, Cayting P1, Boyle AP1, Sundaram V4, Xing X4, Dogan N5, Li J1, Euskirchen G1, Lin S6, Lin Y7, Visel A8, Kawli T1, Yang X1, Patacsil D1, Keller CA5, Giardine B5; Mouse ENCODE Consortium1, Kundaje A1, Wang T4, Pennacchio LA9, Weng Z2, Hardison RC5, Snyder MP1. Collaborators: Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman B, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender M, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, de Sousa BL, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent W, Santos MR, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen R, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Kellis M, Mortazavi A, Weissman SM, Stamatoyannopoulos J, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B. Abstract To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human-mouse erythroid progenitor, lymphoblast and embryonic stem-cell lines. By combining the genome-wide transcription factor occupancy repertoires, associated epigenetic signals, and co-association patterns, here we deduce several evolutionary principles of gene regulatory features operating since the mouse and human lineages diverged. The genomic distribution profiles, primary binding motifs, chromatin states, and DNA methylation preferences are well conserved for TF-occupied sequences. However, the extent to which orthologous DNA segments are bound by orthologous TFs varies both among TFs and with genomic location: binding at promoters is more highly conserved than binding at distal elements. Notably, occupancy-conserved TF-occupied sequences tend to be pleiotropic; they function in several tissues and also co-associate with many TFs. Single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences.
	PMID: 25409826 [PubMed - indexed for MEDLINE]
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2.	Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. A comparative encyclopedia of DNA elements in the mouse genome. Yue F1, Cheng Y2, Breschi A3, Vierstra J4, Wu W5, Ryba T6, Sandstrom R4, Ma Z2, Davis C7, Pope BD6, Shen Y8, Pervouchine DD3, Djebali S3, Thurman RE4, Kaul R4, Rynes E4, Kirilusha A9, Marinov GK9, Williams BA9, Trout D9, Amrhein H9, Fisher-Aylor K9, Antoshechkin I9, DeSalvo G9, See LH7, Fastuca M7, Drenkow J7, Zaleski C7, Dobin A7, Prieto P3, Lagarde J3, Bussotti G3, Tanzer A10, Denas O11, Li K11, Bender MA12, Zhang M13, Byron R13, Groudine MT14, McCleary D8, Pham L8, Ye Z8, Kuan S8, Edsall L8, Wu YC15, Rasmussen MD15, Bansal MS15, Kellis M16, Keller CA5, Morrissey CS5, Mishra T5, Jain D5, Dogan N5, Harris RS5, Cayting P2, Kawli T2, Boyle AP2, Euskirchen G2, Kundaje A2, Lin S2, Lin Y2, Jansen C17, Malladi VS2, Cline MS18, Erickson DT2, Kirkup VM18, Learned K18, Sloan CA2, Rosenbloom KR18, Lacerda de Sousa B19, Beal K20, Pignatelli M20, Flicek P20, Lian J21, Kahveci T22, Lee D23, Kent WJ18, Ramalho Santos M19, Herrero J24, Notredame C3, Johnson A4, Vong S4, Lee K4, Bates D4, Neri F4, Diegel M4, Canfield T4, Sabo PJ4, Wilken MS25, Reh TA25, Giste E4, Shafer A4, Kutyavin T4, Haugen E4, Dunn D4, Reynolds AP4, Neph S4, Humbert R4, Hansen RS4, De Bruijn M26, Selleri L27, Rudensky A28, Josefowicz S28, Samstein R28, Eichler EE4, Orkin SH29, Levasseur D30, Papayannopoulou T31, Chang KH30, Skoultchi A32, Gosh S32, Disteche C33, Treuting P34, Wang Y35, Weiss MJ36, Blobel GA37, Cao X38, Zhong S38, Wang T39, Good PJ40, Lowdon RF40, Adams LB40, Zhou XQ40, Pazin MJ40, Feingold EA40, Wold B9, Taylor J11, Mortazavi A17, Weissman SM21, Stamatoyannopoulos JA4, Snyder MP2, Guigo R3, Gingeras TR7, Gilbert DM6, Hardison RC5, Beer MA23, Ren B8; Mouse ENCODE Consortium. Abstract The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases. PMCID: PMC4266106 [Available on 2015/5/20]
	PMID: 25409824 [PubMed - indexed for MEDLINE]
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3.	Nature. 2014 Nov 20;515(7527):346-7. doi: 10.1038/515346a. Genomics: mice in the ENCODE spotlight. Carninci P1.
	PMID: 25409821 [PubMed - indexed for MEDLINE]
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4.	Nature. 2014 Nov 20;515(7527):323. doi: 10.1038/515323a. 'Platinum' genome takes on disease. Callaway E.
	PMID: 25409806 [PubMed - indexed for MEDLINE]
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