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Javierre Lab

 

 

Welcome to the Javierre laboratory!

We are a group of passionate scientists with an insatiable thirst for learning about spatio-temporal organization of the genome.

Our group, at the Josep Carreras Leukaemia Research Institute (IJC), combines cutting-edge experimental and computational approaches to understand the specific 3D chromatin organization of hematopoietic cells and its alteration in blood cancers. Our long-term goal is to keep taking steps forwards in the fight against cancer.  We will be unstoppable until we cure it. To do so, we have established a close collaboration with the Barcelona Supercomputing Center and we have the privilege of using the MareNostrum supercomputer.

 

Research

Almost every cell in our body has about 2 metres of linear DNA containing all the genes that shape our being. This DNA, which is the same in almost every cell, is not randomly packed into the nucleus that measures a few microns in diameter, and the manner in which it is wrapped plays a fundamental role in regulating genome expression.  In fact, this can partially explain how cells encoding the same genetic information are phenotypically and functionally different.

The main research goals of our lab are:

1. Defining the cell type-specific 3D chromatin organization in blood cells.

2. Identifying the altered DNA topology in blood cancer.

3. Describing new candidate genes and pathways related to malignant transformation.

 

1. Hematopoiesis

All blood cells originate from hematopoietic stem cells, which are the apex of a differentiation cascade of progenitor cell types that give rise to billions of newly differentiated cells every day. Hematopoiesis is essential for the immune response, and its alteration can give rise to the development of cancer, immunodeficiency, allergy and autoimmunity. Despite its clinical relevance,  hematopoiesis is not completely understood. We aim to apply integrative omics approach to better understand this physiological process.

  

Team

 

Biola M. Javierre

Group Leader

Born in 1983 in Huesca (Spain), Biola studied Biology and Biochemistry at the University of Navarra (2006) and received her PhD in Molecular Biology (Epigenetics) from the Autonomous University of Madrid in 2011, where she worked under the supervision of Dr.  Manel Esteller and Dr. Esteban Ballestar at the CNIO.  She performed her postdoctoral training in Chromatin Dynamics (Peter Fraser Laboratory) in Cambridge (UK) from 2012 to 2017. Since March 2018, Biola is Junior PI at the Josep Carreras Reseach Center (IJC), first as Ramon y Cajal Fellow, and then as Junior PI La Caixa. In addition, Biola is part of the Bioinfo4Women Program at the Barcelona Supercomputing Center. In 2019, UNESCO and L’Oréal Women in Science Foundation recognised Biola as one out of the fifteen most promising young women scientists worldwide.

 

Biola loves running although she has not time because of her little trouble makers.

  

Publications

Last 5 years. For the complete list click HERE.

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Under review
bioRxiv 620260; doi: https://doi.org/10.1101/620260

Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility.

Watt S, Vasquez L, Walter K, Mann AL, Kundu K, Chen L, Yan Y, Ecker S, Burden F, Farrow S, Farr B, Iotchkova V, Elding H, Mead D, Tardaguila M, Ponstingl H, Richardson D, Datta A, Flicek P, Clarke L, Downes K, Pastinen T, Fraser, P, Frontini M, Javierre BM #, Spivakov M#, Soranzo N#.
#Corresponding author.

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Trends Immunol. 2019.

From Loops to Looks: Transcription Factors and Chromatin Organization Shaping Terminal B Cell Differentiation

Azagra A, Marina-Zarate E, Ramiro AR, Javierre BM# and Parra M#.
# Corresponding Author

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Leukemia. 2019

B-cell leukemia transdifferentiation to macrophage involves reconfiguration of DNA methylation for long-range regulation

Bueno-Costa A, Piñeyro D, Soler M, Javierre BM Raurel-Vila H, Subirana_Granés M, Pasquali L, Martinez-Climent JA, Esteller M

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Nat Genet. 2019

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes.

Miguel-Escalada I, Bonàs-Guarch S, Cebola I, Ponsa-Cobas J, Mendieta-Esteban J, Atla G, Javierre BM, Rolando DMY, Farabella I, Morgan CC, García-Hurtado J, Beucher A, Morán I, Pasquali L, Ramos-Rodríguez M, Appel EVR, Linneberg A, Gjesing AP, Witte DR, Pedersen O, Grarup N, Ravassard P, Torrents D, Mercader JM, Piemonti L, Berney T, de Koning EJP, Kerr-Conte J, Pattou F, Fedko IO, Groop L, Prokopenko I, Hansen T, Marti-Renom MA, Fraser P, Ferrer J.

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J. Vis. Exp. 2018.

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions.

Schoenfelder S*#, Javierre BM*#, Furlan-Magaril M, Wingett SW & Fraser P#. * Equally contributed.
#Corresponding author

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Nat Commun. 2018.

Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.

 Choy M, Javierre BM, Williams SG, Baross SL, Liu Y, Wingett SW, Akbarov A, Wallace C, Freire-Pritchett P, Rugg-Gunn PJ, Spivakov M, Fraser P & Keavney BD.

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Nat Med. 2018.

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.

Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M. Kulis M, Serra F, Javierre BM, Wintgett SW, Clot G, Queirós AC, Castellano G, Ullrich S, Palumbo E, Enjuanes A, Martín-García D, Beà S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, López-Guillermos A, Frase P, Yaspo ML, Guigó R, Siebert R, Martí-Renom MA, Puente XS, López-Otín C, Gut I, Stunnenberg HG, Campo E & Martin-Subero JI.

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Cell Rep. 2018.

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition.

Novo CL, Javierre BM, Cairns J, Segonds-Pichon A, Wingett SW, Freire-Pritchett P, Furlan-Magaril M, Schoenfelder S, Fraser P, Rugg-Gunn PJ.

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Genome Biol. 2017.

Chromosome contacts in activated T cells identify autoimmune disease-candidate genes.

Burren OS# , Rubio-García A#, Javierre BM# , Rainbow DB#, Cairns J, Cooper NJ, Lambourne JJ, Schofield E, Castro-Dopico X, Ferreira RC, Coulson R, Burden F, Rowlston SP, Downes K, Wingett SW, Frontini M, Ouwehand WH, Fraser P, Spivakov M, Todd JA, Wicker LS, Cutler AJ, Wallace C. 
# Equally contributed

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Nat Commun. 2017.

Platelet function is modified by common sequence variation in megakaryocyte super enhancers

Petersen R#, Lambourne JJ#, Javierre BM#, Grassi L#, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M. 
# Equally contributed

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Mol Cell 2017.

Dynamic rewiring of promoter-anchored chromatin loops during adipocyte differentiation

Siersbæk R#, Madsen JGS#, Javierre BM#, Nielsen R, Bagge EK, Cairns J, Wingett SW, Traynor S, Spivakov M, FraseR P, Mandrup S. 
# Equally contributed

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Nat Struct Mol Biol. 2017.

Genome wide mapping of long range contacts unveils DNA Double Strand Breaks clustering at damaged active genes.

Aymard F, Aguirrebengoa M, Guillou E, Javierre BM, Bugler B, Arnould C, Rocher V, Iacovoni J, Biernacka A, Ginalski K, Rowicka-Kudlicka M, Pasero P, Fraser P, and Legube G.

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Cell. 2016.

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F; BLUEPRINT Consortium., Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P.

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Cell. 2016.

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.

Stunnenberg HG; International Human Epigenome Consortium, Hirst M.

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Genome Biol. 2016.

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity.

Pancaldi V, Carrillo-de-Santa-Pau E, Javierre BM, Juan D, Fraser P, Spivakov M, Valencia A, Rico D.

  

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Genome Biol. 2016.

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.

Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M.

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Genome Biol. 2016.

IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation.

Vento-Tormo R, Company C, Rodríguez-Ubreva J, de la Rica L, Urquiza JM, Javierre BM, Sabarinathan R, Luque A, Esteller M, Aran JM, Álvarez-Errico D, Ballestar E.

  

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25 de enero de 2025

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome.

Schoenfelder S#, Sugar R#, Dimond A#, Javierre BM#, Armstrong H#, Mifsud B, Dimitrova E, Matheson L, Tavares-Cadete F, Furlan-Magaril M, Segonds-Pichon A, Jurkowski W, Wingett SW, Tabbada K, Andrews S, Herman B, LeProust E, Osborne CS, Koseki H, Fraser P, Luscombe NM, Elderkin S. 
# Equally contributed

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Genome Biol. 2015.

Comparison of Hi-C results using in-solution versus in-nucleus ligation.

Nagano T, Várnai C, Schoenfelder S, Javierre BM, Wingett SW, Fraser P.

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Genome Res. 2015.

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.

Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P.

  

 

Funding

 

News

Hello World!

12th March 2020 

 

Today we launch the group's  website. You can also follow as on Twitter @JavierreLab or @BiolaMJavierre

 
 

Contact Us | Join us

We are currently seeking enthusiastic new members, so if you are interested in studying chromatin organization, please contact us. We offer a friendly, collaborative atmosphere and direct one-to-one supervision.

Our lab is located at the Josep Carreras Leukaemia Research Institute (IJC) in Badalona, Barcelona, Spain.

IJC Building, Campus ICO-Germans Trias i Pujol
Ctra de Can Ruti, Camí de les Escoles s/n
08916 Badalona, Barcelona

 

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