Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci

Autor: Paul, Ds, Albers, Ca, Rendon, A, Voss, K, Stephens, J, Akkerman, Jan Willem N., Albers, Cornelis A., Ale, Algra, Abtehale Al Hussani, Hooman, Allayee, Franco, Anni, Asselbergs, Folkert W., Antony, Attwood, Beverley, Balkau, Stefania, Bandinelli, François, Bastardot, Saonli, Basu, Baumeister, Sebastian E., Jacques, Beckmann, Beben, Benyamin, Ginevra, Biino, Bis, Joshua C., Lorenzo, Bomba, Amélie, Bonnefond, Boomsma, Dorret I., Bradley, John R., François, Cambien, Chambers, John C., Marina, Ciullo, Cookson, William O., Francesco, Cucca, Ana, Cvejic, D'Adamo, ADAMO PIO, John, Danesh, Fabrice, Danjou, Debashish, Das, Gail, Davies, Paul IW de Bakker, de Boer, Rudolf A., Eco JC de Geus, Deary, Ian J., Dedoussis, George V., Panos, Deloukas, Maria, Dimitriou, Christian, Dina, Angela, Döring, Ulrich, Elling, David, Ellinghaus, Paul, Elliott, Gunnar, Engström, Jeanette, Erdmann, Tõnu, Esko, Evans, David M., Eyjolfsson, Gudmundur I., Mario, Falchi, Wei, Feng, Ferreira, Manuel A., Luigi, Ferrucci, Krista, Fischer, Folsom, Aaron R., Paolo, Fortina, Andre, Franke, Lude, Franke, Frazer, Ian H., Philippe, Froguel, Renzo, Galanello, Ganesh, Santhi K., Garner, Stephen F., Gasparini, Paolo, Bernd, Genser, Gibson, Quince D., Christian, Gieger, Girotto, Giorgia, Glazer, Nicole L., Martin, Gögele, Goodall, Alison H., Andreas, Greinacher, Gudbjartsson, Daniel F., Chris, Hammond, Harris, Sarah E., Jaana, Hartiala, Anna Liisa Hartikainen, Hazen, Stanley L., Heckbert, Susan R., Hedblad, Bo, Christian, Hengstenberg, Micha, Hersch, Hicks, Andrew A., Hilma, Holm, Jouke Jan Hottenga, Thomas, Illig, Marjo Riitta Jarvelin, Jennifer, Jolley, Steve, Jupe, Mika, Kähönen, Naoyuki, Kamatani, Stavroula, Kanoni, Kema, Ido P., Kemp, John P., Jyoti, Khadake, Kay Tee Khaw, Kleber, Marcus E., Kooner, Jaspal S., Peter, Kovacs, Brigitte, Kühnel, Marie Christine Kyrtsonis, Yann, Labrune, Vasiliki, Lagou, Claudia, Langenberg, Terho, Lehtimäki, Xinzhong, Li, Liming, Liang, Lifelines Cohort Study, Heather Lloyd Jones, Ruth JF Loos, Lopez, Lorna M., Thomas, Lumley, Leo Pekka Lyytikäinen, Winfried, Maerz, Reedik, Mägi, Massimo, Mangino, Martin, Nicholas G., Andrea, Maschio, Irene Mateo Leach, Barbara, Mcknight, Stuart, Meacham, Medland, Sarah E., Christa, Meisinger, Olle, Melander, Yasin, Memari, Andres, Metspalu, Kathy, Miller, Mitchell, Braxton D., Moffatt, Miriam F., Montgomery, Grant W., Carmel, Moore, Federico, Murgia, Yusuke, Nakamura, Matthias, Nauck, Gerjan, Navis, Nolte, Ilja M., Ute, Nöthlings, Teresa, Nutile, Yukinori, Okada, Isleifur, Olafsson, Onundarson, Pall T., O’Reilly, Paul F., Ouwehand, Willem H., Debora, Parracciani, Afshin, Parsa, Paul, Dirk S., Penninger, Josef M., Penninx, Brenda W., Mario, Pirastu, Pirastu, Nicola, Giorgio, Pistis, Eleonora, Porcu, Laura, Portas, David, Porteous, Anneli, Pouta, Pramstaller, Peter P., Inga, Prokopenko, Psaty, Bruce M., Janne, Pullat, Aparna, Radhakrishnan, Olli, Raitakari, Ramiro Ramirez Solis, Augusto, Rendon, Ried, Janina S., Ring, Susan M., Robino, Antonietta, Rotter, Jerome I., Daniela, Ruggiero, Aimo, Ruokonen, Cinzia, Sala, Andres, Saluments, Samani, Nilesh J., Jennifer, Sambrook, Serena, Sanna, David, Schlessinger, Schmidt, Carsten O., Stefan, Schreiber, Heribert, Schunkert, James, Scott, Joban, Sehmi, Jovana Serbanovic Canic, So Youn Shin, Shuldiner, Alan R., Rob, Sladek, Smit, Johannes H., George Davey Smith, Gustav Smith, J., Smith, Nicholas L., Harold, Snieder, Nicole, Soranzo, Rossella, Sorice, Spector, Timothy D., Starr, John M., Kari, Stefansson, Derek, Stemple, Jonathan, Stephens, Michael, Stumvoll, Patrick, Sulem, Atsushi, Takahashi, Sian Tsung Tan, Toshiko, Tanaka, Clara, Tang, Weihong, Tang, WH Wilson Tang, Kent, Taylor, Albert, Tenesa, Alexander, Teumer, Swee Lay Thein, Unnur, Thorsteinsdottir, Daniela, Toniolo, Anke, Tönjes, Traglia, Michela, Manuela, Uda, Sheila, Ulivi, Pim van der Harst, Ellen van der Schoot, C., van Gilst, Wiek H., Joost van Pelt, L., van Veldhuisen, Dirk J., Niek, Verweij, Visscher, Peter M., Uwe, Völker, Peter, Vollenweider, Katrin, Voss, Wareham, Nicholas J., Lorenz, Wernisch, Harm Jan Westra, Whitfield, John B., Herich, Wichmann, Wiggins, Kerri L., Gonneke, Willemsen, Winkelmann, Bernhard R., Gerald, Wirnsberger, Bruce HR Wolffenbuttel, Jian, Yang, Tsun Po Yang, Weihua, Zhang, Jing Hua Zhao, Paavo, Zitting, Jaap Jan Zwaginga, van der Harst, P, Chambers, Jc, Soranzo, N, Ouwehand, Wh, Deloukas, P.
Přispěvatelé: Paul, D, Albers, Ca, Rendon, A, Voss, K, Stephens, J, Jan Willem N., Akkerman, Cornelis A., Alber, Ale, Algra, Abtehale Al, Hussani, Hooman, Allayee, Franco, Anni, Folkert W., Asselberg, Antony, Attwood, Beverley, Balkau, Stefania, Bandinelli, François, Bastardot, Saonli, Basu, Sebastian E., Baumeister, Jacques, Beckmann, Beben, Benyamin, Ginevra, Biino, Joshua C., Bi, Lorenzo, Bomba, Amélie, Bonnefond, Dorret I., Boomsma, John R., Bradley, François, Cambien, John C., Chamber, Marina, Ciullo, William O., Cookson, Francesco, Cucca, Ana, Cvejic, D'Adamo, ADAMO PIO, John, Danesh, Fabrice, Danjou, Debashish, Da, Gail, Davie, Paul IW de, Bakker, Rudolf A., de Boer, Eco JC de, Geu, Ian J., Deary, George V., Dedoussi, Panos, Delouka, Maria, Dimitriou, Christian, Dina, Angela, Döring, Ulrich, Elling, David, Ellinghau, Paul, Elliott, Gunnar, Engström, Jeanette, Erdmann, Tõnu, Esko, David M., Evan, Gudmundur I., Eyjolfsson, Mario, Falchi, Wei, Feng, Manuel A., Ferreira, Luigi, Ferrucci, Krista, Fischer, Aaron R., Folsom, Paolo, Fortina, Andre, Franke, Lude, Franke, Ian H., Frazer, Philippe, Froguel, Renzo, Galanello, Santhi K., Ganesh, Stephen F., Garner, Gasparini, Paolo, Bernd, Genser, Quince D., Gibson, Christian, Gieger, Girotto, Giorgia, Nicole L., Glazer, Martin, Gögele, Alison H., Goodall, Andreas, Greinacher, Daniel F., Gudbjartsson, Chris, Hammond, Sarah E., Harri, Jaana, Hartiala, Anna Liisa, Hartikainen, Stanley L., Hazen, Susan R., Heckbert, Bo, Hedblad, Christian, Hengstenberg, Micha, Hersch, Andrew A., Hick, Hilma, Holm, Jouke Jan, Hottenga, Thomas, Illig, Marjo Riitta, Jarvelin, Jennifer, Jolley, Steve, Jupe, Mika, Kähönen, Naoyuki, Kamatani, Stavroula, Kanoni, Ido P., Kema, John P., Kemp, Jyoti, Khadake, Kay Tee, Khaw, Marcus E., Kleber, Jaspal S., Kooner, Peter, Kovac, Brigitte, Kühnel, Marie Christine, Kyrtsoni, Yann, Labrune, Vasiliki, Lagou, Claudia, Langenberg, Terho, Lehtimäki, Xinzhong, Li, Liming, Liang, Lifelines Cohort, Study, Heather Lloyd, Jone, Ruth JF, Loo, Lorna M., Lopez, Thomas, Lumley, Leo Pekka, Lyytikäinen, Winfried, Maerz, Reedik, Mägi, Massimo, Mangino, Nicholas G., Martin, Andrea, Maschio, Irene Mateo, Leach, Barbara, Mcknight, Stuart, Meacham, Sarah E., Medland, Christa, Meisinger, Olle, Melander, Yasin, Memari, Andres, Metspalu, Kathy, Miller, Braxton D., Mitchell, Miriam F., Moffatt, Grant W., Montgomery, Carmel, Moore, Federico, Murgia, Yusuke, Nakamura, Matthias, Nauck, Gerjan, Navi, Ilja M., Nolte, Ute, Nöthling, Teresa, Nutile, Yukinori, Okada, Isleifur, Olafsson, Pall T., Onundarson, Paul F., O’Reilly, Willem H., Ouwehand, Debora, Parracciani, Afshin, Parsa, Dirk S., Paul, Josef M., Penninger, Brenda W., Penninx, Mario, Pirastu, Pirastu, Nicola, Giorgio, Pisti, Eleonora, Porcu, Laura, Porta, David, Porteou, Anneli, Pouta, Peter P., Pramstaller, Inga, Prokopenko, Bruce M., Psaty, Janne, Pullat, Aparna, Radhakrishnan, Olli, Raitakari, Ramiro Ramirez, Soli, Augusto, Rendon, Janina S., Ried, Susan M., Ring, Robino, Antonietta, Jerome I., Rotter, Daniela, Ruggiero, Aimo, Ruokonen, Cinzia, Sala, Andres, Salument, Nilesh J., Samani, Jennifer, Sambrook, Serena, Sanna, David, Schlessinger, Carsten O., Schmidt, Stefan, Schreiber, Heribert, Schunkert, James, Scott, Joban, Sehmi, Jovana Serbanovic, Canic, So Youn, Shin, Alan R., Shuldiner, Rob, Sladek, Johannes H., Smit, George Davey, Smith, J., Gustav Smith, Nicholas L., Smith, Harold, Snieder, Nicole, Soranzo, Rossella, Sorice, Timothy D., Spector, John M., Starr, Kari, Stefansson, Derek, Stemple, Jonathan, Stephen, Michael, Stumvoll, Patrick, Sulem, Atsushi, Takahashi, Sian Tsung, Tan, Toshiko, Tanaka, Clara, Tang, Weihong, Tang, WH Wilson, Tang, Kent, Taylor, Albert, Tenesa, Alexander, Teumer, Swee Lay, Thein, Unnur, Thorsteinsdottir, Daniela, Toniolo, Anke, Tönje, Traglia, Michela, Manuela, Uda, Sheila, Ulivi, Pim van der, Harst, C., Ellen van der Schoot, Wiek H., van Gilst, L., Joost van Pelt, Dirk J., van Veldhuisen, Niek, Verweij, Peter M., Visscher, Uwe, Völker, Peter, Vollenweider, Katrin, Vo, Nicholas J., Wareham, Lorenz, Wernisch, Harm Jan, Westra, John B., Whitfield, Herich, Wichmann, Kerri L., Wiggin, Gonneke, Willemsen, Bernhard R., Winkelmann, Gerald, Wirnsberger, Bruce HR, Wolffenbuttel, Jian, Yang, Tsun Po, Yang, Weihua, Zhang, Jing Hua, Zhao, Paavo, Zitting, Jaap Jan, Zwaginga, van der Harst, P, Chambers, Jc, Soranzo, N, Ouwehand, Wh, Deloukas, P., Biological Psychology, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, EMGO+ - Mental Health, Neuroscience Campus Amsterdam - Brain Imaging Technology, Neuroscience Campus Amsterdam - Brain Mechanisms in Health & Disease, Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England, UCL, UCL Canc Inst, London WC1E 6BT, England, Univ Cambridge, Dept Haematol, Cambridge CB2 0PT, England, Natl Hlth Serv NHS Blood & Transplant, Cambridge CB2 0PT, England, Radboud Univ Nijmegen, Med Ctr, Dept Human Genet, NL-6500 HB Nijmegen, Netherlands, Inst Publ Hlth, MRC Biostat Unit, Cambridge CB2 0SR, England, NIHR Biomed Res Ctr, Cambridge CB2 0PT, England, Univ Groningen, Univ Med Ctr Groningen, Dept Cardiol, NL-9713 GZ Groningen, Netherlands, Univ Groningen, Univ Med Ctr Groningen, Dept Genet, NL-9713 GZ Groningen, Netherlands, Univ London Imperial Coll Sci Technol & Med, Dept Epidemiol & Biostat, London W2 1NY, England, Hammersmith Hosp, Imperial Coll Healthcare NHS Trust, London W12 0HS, England, Royal Brompton & Harefield Hosp NHS Trust, London SW3 6NP, England, Ealing Hosp NHS Trust, Southall UB1 3HW, Middx, England, Psychiatry, Epidemiology and Data Science, NCA - Brain mechanisms in health and disease, NCA - Neurobiology of mental health, EMGO - Mental health, NCA - Brain imaging technology, Cardiovascular Centre (CVC)
Jazyk: angličtina
Rok vydání: 2013
Předmět:
Netherlands Twin Register (NTR)
Erythrocytes
Genome-wide association study
UNCERTAINTY
Regulatory Sequences
Nucleic Acid
VARIANTS
ANNOTATION
COLORECTAL-CANCER
Histones
0302 clinical medicine
BINDING
Cluster Analysis
Myeloid Cells
Genetics (clinical)
Genetics
hematological trait
0303 health sciences
Chromosome Mapping
MRP4 ABCC4
Chromatin
Nucleosomes
Phenotype
Organ Specificity
030220 oncology & carcinogenesis
Blood Platelets
Quantitative Trait Loci
Biology
Quantitative trait locus
Polymorphism
Single Nucleotide
DYNAMIN 3
03 medical and health sciences
Quantitative Trait
Heritable
MEGAKARYOCYTES
Humans
Cell Lineage
ddc:610
GENOME-WIDE ASSOCIATION
Enhancer
Transcription factor
Gene
ChIA-PET
030304 developmental biology
Research
Genetic Variation
DNA
Chromatin Assembly and Disassembly
Genetic architecture
Gene Expression Regulation
Genome-Wide Association Study
Zdroj: Genome research (Online) 23 (2013): 1130–1141. doi:10.1101/gr.155127.113
info:cnr-pdr/source/autori:Paul DS, Albers CA, Rendon A, Voss K, Stephens J; HaemGen Consortium, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH, Deloukas P/titolo:Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci/doi:10.1101%2Fgr.155127.113/rivista:Genome research (Online)/anno:2013/pagina_da:1130/pagina_a:1141/intervallo_pagine:1130–1141/volume:23
Genome Res. 23, 1130-1141 (2013)
Genome Research, 23(7), 1130-1141. Cold Spring Harbor Laboratory Press
Paul, D S, Albers, C A, Rendon, A, Voss, K, Stephens, J, Akkerman, J W, Algra, A, Al-Hussani, A, Allayee, H, Anni, F, Asselbergs, F W, Attwood, A, Balkau, B, Bandinelli, S, Bastardot, F, Basu, S, Baumeister, S E, Beckmann, J, Benyamin, B, Biino, G, Bis, J C, Bomba, L, Bonnefond, A, Boomsma, D I, Bradley, J R, Cambien, F, Ciullo, M, Cookson, W O, Cucca, F, Cvejic, A, d'Adamo, A P, Danesh, J, Danjou, F, Das, D, Davies, G, de Bakker, P I, de Boer, R A, de Geus, E J C, Deary, I J, Dedoussis, G V, Dimitriou, M, Dina, C, Döring, A, Elling, U, Ellinghaus, D, Elliott, P, Engström, G, Erdmann, J, Esko, T, Evans, D M, Eyjolfsson, G I, Falchi, M, Feng, W W, Ferreira, M A, Ferrucci, L, Fischer, K, Folsom, A R, Fortina, P, Franke, A, Franke, L, Frazer, I H, Froguel, P, Galanello, R, Ganesh, S, Garner, S F, Gasparini, P, Genser, B, Gibson, Q D, Gieger, C, Girotto, G, Glazer, N L, Gögele, M, Goodall, A H, Greinacher, A, Gudbjartsson, D F, Hammond, C J, Harris, S E, Hartiala, J, Hartikainen, A L, Hazen, S L, Heckbert, S R, Hedblad, B, Hengstenberg, C, Hersch, M, Hicks, A A, Holm, H, Hottenga, J J, Illig, T, Järvelin, M R, Jolley, J, Jupe, S, Kähönen, M, Kamatani, N, Kanoni, S, Kema, I P, Kemp, J P, Khadake, J, Khaw, K T, Kleber, M E, Kooner, J S, Kovacs, P, Kühnel, B, Kyrtsonis, M C, Labrune, Y, Lagou, V, Langenberg, C, Lehtimäki, T, Li, X, Liang, L, Lloyd-Jones, H, Loos, R J, Lopez, L M, Lumley, T, Lyytikäinen, L P, Maerz, W, Mägi, R, Mangino, M, Martin, N G, Maschio, A, Mateo Leach, I, McKnight, B, Meacham, S, Medland, S E, Meisinger, C, Melander, O, Memari, Y, Metspalu, A, Miller, K, Mitchell, B D, Moffatt, M F, Montgomery, G W, Moore, C, Murgia, F, Nakamura, Y, Nauck, M, Navis, G, Nolte, I M, Nöthlings, U, Nutile, T, Okada, Y, Olafsson, I, Onundarson, P T, O'Reilly, P F, Parracciani, D, Parsa, A, Penninger, J M, Penninx, B W J H, Pirastu, M, Pirastu, N, Pistis, G, Porcu, E, Portas, L, Porteous, D J, Pouta, A, Pramstaller, P P, Prokopenko, I, Psaty, B M, Pullat, J, Radhakrishnan, A, Raitakari, O, Ramirez-Solis, R, Ried, J S, Ring, S M, Robino, A, Rotter, J I, Ruggiero, D, Ruokonen, A, Sala, C, Saluments, A, Samani, N J, Sambrook, J, Sanna, S, Schlessinger, D, Schmidt, C O, Schreiber, S, Schunkert, H, Scott, J, Sehmi, J, Serbanovic-Canic, J, Shin, S Y, Shuldiner, A R, Sladek, R, Smit, J H, Smith, G D, Smith, J G, Smith, N L, Snieder, H, Sorice, R, Spector, T D, Starr, J M, Stefansson, K, Stemple, D, Stumvoll, M, Sulem, P, Takahashi, A, Tan, S T, Tanaka, T, Tang, C, Tang, W, Tang, W H, Taylor, K, Tenesa, A, Teumer, A, Thein, S, Thorsteinsdottir, U, Toniolo, D, Tönjes, A, Traglia, M, Uda, M, Ulivi, S, van der Schoot, E, van Gilst, W H, van Pelt, L J, van Veldhuisen, D J, Verweij, N, Visscher, P M, Völker, U, Vollenweider, P, Wareham, N J, Wernisch, L, Westra, H J, Whitfield, J B, Wichmann, H E, Wiggins, K L, Willemsen, G, Winkelmann, B R, Wirnsberger, G, Wolffenbuttel, B H, Yang, J, Yang, T P, Zhang, J H, Zhao, J H, Zitting, P, Zwaginga, JJ, van der Harst, P, Chambers, J C, Soranzo, N, Ouwehand, W H & Deloukas, P 2013, ' Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci ', Genome Research, vol. 23, no. 7, pp. 1130-1141 . https://doi.org/10.1101/gr.155127.113
Genome Research; Vol 23
Genome Research, 23(7), 1130-1141. COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
ISSN: 1549-5469
1088-9051
0310-1002
Popis: To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access. Nearly three-quarters of the 143 genetic signals associated with platelet and erythrocyte phenotypes identified by meta-analyses of genome-wide association (GWA) studies are located at non-protein-coding regions. Here, we assessed the role of candidate regulatory variants associated with cell type-restricted, closely related hematological quantitative traits in biologically relevant hematopoietic cell types. We used formaldehyde-assisted isolation of regulatory elements followed by next-generation sequencing (FAIRE-seq) to map regions of open chromatin in three primary human blood cells of the myeloid lineage. In the precursors of platelets and erythrocytes, as well as in monocytes, we found that open chromatin signatures reflect the corresponding hematopoietic lineages of the studied cell types and associate with the cell type-specific gene expression patterns. Dependent on their signal strength, open chromatin regions showed correlation with promoter and enhancer histone marks, distance to the transcription start site, and ontology classes of nearby genes. Cell type-restricted regions of open chromatin were enriched in sequence variants associated with hematological indices. The majority (63.6%) of such candidate functional variants at platelet quantitative trait loci (QTLs) coincided with binding sites of five transcription factors key in regulating megakaryopoiesis. We experimentally tested 13 candidate regulatory variants at 10 platelet QTLs and found that 10 (76.9%) affected protein binding, suggesting that this is a frequent mechanism by which regulatory variants influence quantitative trait levels. Our findings demonstrate that combining large-scale GWA data with open chromatin profiles of relevant cell types can be a powerful means of dissecting the genetic architecture of closely related quantitative traits. Marie-Curie Initial Training Network NETSIM British Heart Foundation RG/09/12/28096 National Institutes for Health RP-PG-0310-1002 Wellcome Trust 098051 info:eu-repo/grantAgreement/EC/FP7/282510
Databáze: OpenAIRE
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