Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

Autor: Ecker, Simone, Chen, Lu, Pancaldi, Vera, Bagger, Frederik O., Fernández, José María, Carrillo de Santa Pau, Enrique, Juan, David, Mann, Alice L., Watt, Stephen, Casale, Francesco Paolo, Sidiropoulos, Nikos, Rapin, Nicolas Philippe Jean-Pierre, Merkel, Angelika, Stunnenberg, Hendrik G, Stegle, Oliver, Frontini, Mattia, Downes, Kate, Pastinen, Tomi, Kuijpers, Taco W, Rico, Daniel, Valencia, Alfonso, Beck, Stephan, Soranzo, Nicole, Paul, Dirk S., Albers, Cornelis A., Amstislavskiy, Vyacheslav, Ashford, Sofie, Bomba, Lorenzo, Bujold, David, Burden, Frances, Busche, Stephan, Caron, Maxime, Chen, Shu-Huang, Cheung, Warren A., Clarke, Laura, Colgiu, Irina, Datta, Avik, Delaneau, Oliver, Elding, Heather, Farrow, Samantha, Garrido-Martín, Diego, Ge, Bing, Guigo, Roderic, Iotchkova, Valentina, Kundu, Kousik, Kwan, Tony, Lambourne, John J., Lowy, Ernesto, Mead, Daniel, Pourfarzad, Farzin, Redensek, Adriana, Rehnstrom, Karola, Rendon, Augusto, Richardson, David M., Risch, Thomas, Rowlston, Sophia, Shao, Xiaojian, Simon, Marie Michelle, Sultan, Marc, Walter, Klaudia, Wilder, Steven P., Yan, Ying, Antonarakis, Stylianos E., Bourque, Guillaume, Dermitzakis, Emmanouil T., Flicek, Paul, Lehrach, Hans, Martens, Joost H A, Yaspo, Marie-Laure, Ouwehand, Willem H.
Jazyk: angličtina
Rok vydání: 2017
Předmět:
Zdroj: Ecker, S, Chen, L, Pancaldi, V, Bagger, F O, Fernández, J M, Carrillo de Santa Pau, E, Juan, D, Mann, A L, Watt, S, Casale, F P, Sidiropoulos, N, Rapin, N P J-P, Merkel, A, Stunnenberg, H G, Stegle, O, Frontini, M, Downes, K, Pastinen, T, Kuijpers, T W, Rico, D, Valencia, A, Beck, S, Soranzo, N, Paul, D S, Albers, C A, Amstislavskiy, V, Ashford, S, Bomba, L, Bujold, D, Burden, F, Busche, S, Caron, M, Chen, S-H, Cheung, W A, Clarke, L, Colgiu, I, Datta, A, Delaneau, O, Elding, H, Farrow, S, Garrido-Martín, D, Ge, B, Guigo, R, Iotchkova, V, Kundu, K, Kwan, T, Lambourne, J J, Lowy, E, Mead, D, Pourfarzad, F, Redensek, A, Rehnstrom, K, Rendon, A, Richardson, D M, Risch, T, Rowlston, S, Shao, X, Simon, M M, Sultan, M, Walter, K, Wilder, S P, Yan, Y, Antonarakis, S E, Bourque, G, Dermitzakis, E T, Flicek, P, Lehrach, H, Martens, J H A, Yaspo, M-L & Ouwehand, W H 2017, ' Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types ', Genome Biology, vol. 18, no. 1, 18 . https://doi.org/10.1186/s13059-017-1156-8
DOI: 10.1186/s13059-017-1156-8
Popis: Background: A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. Results: We apply a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14+CD16-monocytes, CD66b+CD16+neutrophils, and CD4+CD45RA+naïve T cells from the same 125 healthy individuals. We discover substantially increased variability in neutrophils compared to monocytes and T cells. In neutrophils, genes with hypervariable expression are found to be implicated in key immune pathways and are associated with cellular properties and environmental exposure. We also observe increased sex-specific gene expression differences in neutrophils. Neutrophil-specific DNA methylation hypervariable sites are enriched at dynamic chromatin regions and active enhancers. Conclusions: Our data highlight the importance of transcriptional and epigenetic variability for the key role of neutrophils as the first responders to inflammatory stimuli. We provide a resource to enable further functional studies into the plasticity of immune cells, which can be accessed from: http://blueprint-dev.bioinfo.cnio.es/WP10/hypervariability.
Databáze: OpenAIRE
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