3D Chromatin organization

ICO - Germans Trias i Pujol

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



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

Our group combines cutting-edge experimental and bioinformatics approaches to understand the specific 3D chromatin organization of haematopoietic 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.

We are currently seeking enthusiastic new members, so if you are interested in studying chromatin organization, please contact us.


Every cell in our body has about 2 metres of linear DNA containing the genes that shape our being. This DNA, which is the same in every cell, is not-randomly packed into the nucleus of a few microns diameter, and the manner in which it is wrapped plays a fundamental role in regulating genome function.  In some cases it does this by putting regulatory elements, such as enhancer, and target gene promoters into physical contact.  In fact, this can partially explain how cells encoding the same genetic information are phenotypically and functionally different.It has been estimated that the genome harbours around one million regulatory elements, some of these are cell-type specific, but the vast majority of interactions between these elements and the corresponding regulated gene are uncharted, constituting a major missing link in understanding genome control.

Chromatin interactions are crucial for cellular health due to their main role in genome expression regulation and errors in these interactions give rise to the development of a broad range of diseases including blood cancer. The investigation of these altered 3D structures can help us to improve our knowledge of the tumour process, providing new opportunities for the development of novel treatment approaches and diagnostic strategies.

Additionally, genetic studies have identified thousands of single nucleotide polymorphisms and mutations associated with blood cancer, but most of them expand non-coding regions, which makes them difficult to interpret. Interestingly these non-coding genetic variants cluster on DNA hypersensitivity sites, which are the hallmark of a regulatory element, pointing to a potential role for these genetic variants in the deregulation of target genes. By studying the physical interactions between gene promoter and regulatory elements we are able to connect blood cancer genetic alterations to putative target genes, prioritizing new disease-candidate genes and pathways, and revealing insights into genomic regulatory mechanisms underlying cancer. The interpretation of non-coding variation will also help us to improve the prediction of patient outcome as well as allowing us to design better and more personalized treatments.

The main research goals of our lab are:

  • Defining the cell type-specific 3D chromatin organization in human haematopoietic cells
  • Identifying the altered DNA topology in blood cancer
  • Prioritizing new candidate genes and pathways related to blood cancer


Biola Javierre
Logo green and blue no words
Group Leader

Selected publications

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, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P

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

Cell 17 Nov 2016, 167 (5) 1369-1384.e19.
Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are uncharted, constituting a major missing link in understanding genome control. Here, we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types. We show that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers. Promoter interactomes reflect lineage relationships of the hematopoietic tree, consistent with dynamic remodeling of nuclear architecture during differentiation. Interacting regions are enriched in genetic variants linked with altered expression of genes they contact, highlighting their functional role. We exploit this rich resource to connect non-coding disease variants to putative target promoters, prioritizing thousands of disease-candidate genes and implicating disease pathways. Our results demonstrate the power of primary cell promoter interactomes to reveal insights into genomic regulatory mechanisms underlying common diseases.
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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

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

Nat. Genet. Oct 2015, 47 (10) 1179-1186. Epub 31 Ago 2015
The Polycomb repressive complexes PRC1 and PRC2 maintain embryonic stem cell (ESC) pluripotency by silencing lineage-specifying developmental regulator genes. Emerging evidence suggests that Polycomb complexes act through controlling spatial genome organization. We show that PRC1 functions as a master regulator of mouse ESC genome architecture by organizing genes in three-dimensional interaction networks. The strongest spatial network is composed of the four Hox gene clusters and early developmental transcription factor genes, the majority of which contact poised enhancers. Removal of Polycomb repression leads to disruption of promoter-promoter contacts in the Hox gene network. In contrast, promoter-enhancer contacts are maintained in the absence of Polycomb repression, with accompanying widespread acquisition of active chromatin signatures at network enhancers and pronounced transcriptional upregulation of network genes. Thus, PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network. We propose that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.
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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

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

Nat Commun 13 Jul 2017, 8 16058. Epub 13 Jul 2017
Linking non-coding genetic variants associated with the risk of diseases or disease-relevant traits to target genes is a crucial step to realize GWAS potential in the introduction of precision medicine. Here we set out to determine the mechanisms underpinning variant association with platelet quantitative traits using cell type-matched epigenomic data and promoter long-range interactions. We identify potential regulatory functions for 423 of 565 (75%) non-coding variants associated with platelet traits and we demonstrate, through ex vivo and proof of principle genome editing validation, that variants in super enhancers play an important role in controlling archetypical platelet functions.
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Siersbæk R, Madsen JGS, Javierre BM, Nielsen R, Bagge EK, Cairns J, Wingett SW, Traynor S, Spivakov M, Fraser P, Mandrup S

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation.

Mol. Cell 4 May 2017, 66 (3) 420-435.e5.
Interactions between transcriptional promoters and their distal regulatory elements play an important role in transcriptional regulation; however, the extent to which these interactions are subject to rapid modulations in response to signals is unknown. Here, we use promoter capture Hi-C to demonstrate a rapid reorganization of promoter-anchored chromatin loops within 4 hr after inducing differentiation of 3T3-L1 preadipocytes. The establishment of new promoter-enhancer loops is tightly coupled to activation of poised (histone H3 lysine 4 mono- and dimethylated) enhancers, as evidenced by the acquisition of histone H3 lysine 27 acetylation and the binding of MED1, SMC1, and P300 proteins to these regions, as well as to activation of target genes. Intriguingly, formation of loops connecting activated enhancers and promoters is also associated with extensive recruitment of corepressors such as NCoR and HDACs, indicating that this class of coregulators may play a previously unrecognized role during enhancer activation.
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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

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

Genome Biol. 4 Sep 2017, 18 (1) 165. Epub 4 Sep 2017
Autoimmune disease-associated variants are preferentially found in regulatory regions in immune cells, particularly CD4
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