Orphan CpG islands boost the regulatory activity of poised enhancers and dictate the responsiveness of their target genes.

Pachano T, Sánchez-Gaya V, Mariner-Faulí M, Ealo T, Asenjo H.G., Respuela P, Cruz-Molina S, van Ijcken W.F.J , Landeira D, Rada-Iglesias A#. bioRxiv 2020.08.05.237768; doi: https://doi.org/10.1101/2020.08.05.237768

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Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies.

Sánchez-Gaya V, Mariner-Faulí M, Rada-Iglesias A#. Front Genet. 2020 Jul 20;11:688. doi: 10.3389/fgene.2020.00688. eCollection 2020. Review. PMID: 32765580

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GARLIC: A Bioinformatic Toolkit for Etiologically Connecting Diseases and Cell Type-Specific Regulatory Maps.

Nikoli? M, Papantonis A, Rada-Iglesias A#. Hum Mol Genet. 2017 Feb 15;26(4):742-752. PMID:28007912.

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Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation.

Cieslak, A., G. Charbonnier, M. Tesio, E. L. Mathieu, M. Belhocine, A. Touzart, C. Smith, G. Hypolite, G. P. Andrieu, J. H. A. Martens, E. Janssen-Megens, M. Gut, I. Gut, N. Boissel, A. Petit, D. Puthier, E. Macintyre, H. G. Stunnenberg, S. Spicuglia* and V. Asnafi*. J Exp Med (2020). 217(9): (9): e20192360

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Widespread Enhancer Activity from Core Promoters.

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Genome-wide characterization of mammalian promoters with distal enhancer functions.

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CapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals.

Vanhille L., A. Griffon, M.A. Maqbool, J. Zacarias, L.T.M. Dao, N. Fernandez, B. Ballester, J.C. Andrau, S. Spicuglia. Nat. Comm. 6:6905 (2015)

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3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.

Wlasnowolski M, Sadowski M, Czarnota T, Jodkowska K, Szalaj P, Tang Z, Ruan Y, Plewczynski D. Nucleic Acids Res. 2020 May 22:gkaa388. doi: 10.1093/nar/gkaa388. PMID: 32442297

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Chromatin topology reorganization and transcription repression by PML-RAR? in acute promyeloid leukemia.

Wang P, Tang Z, Lee B, Zhu JJ, Cai L, Szalaj P, Tian SZ, Zheng M, Plewczynski D, Ruan X, Liu ET, Wei CL, Ruan Y. Genome Biol. 2020 May 11;21(1):110. doi: 10.1186/s13059-020-02030-2. PMID: 32393309

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Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.

Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, ?liwi?ska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczy?ski D, Ruan Y, Wilczy?ski GM. Nat Commun. 2020 May 1;11(1):2120. doi: 10.1038/s41467-020-15987-2. PMID: 32358536

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H3K4 tri-methylation provides an epigenetic signature of active enhancers.

Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau J.C, Ferrier P and Spicuglia S EMBO J., 30, 4198–10. (2011).

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High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related Pathways.

Åkerborg Ö, Spalinskas R, Pradhananga S, Anil A, Höjer P, Poujade FA, Folkersen L, Eriksson PP, Sahlén P. Circ Genom Precis Med. 2019 Mar;12(3):e002353. doi: 10.1161/CIRCGEN.118.002353.

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Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells.

Al Bkhetan Z, Kadlof M, Kraft A, Plewczynski D. Methods. 2019 Aug 15;166:83-90. doi: 10.1016/j.ymeth.2019.03.002.

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Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S. Nat Genet. 2019 Apr;51(4):716-727. doi: 10.1038/s41588-019-0359-1.

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Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip.

Bio?anin M, Bues J, Dainese R, Amstad E, Deplancke B. Lab Chip. 2019 Apr 23;19(9):1610-1620. doi:10.1039/c9lc00014c.

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Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs.

Laugsch M, Bartusel M, Rehimi R, Alirzayeva H, Karaolidou A, Crispatzu G, Zentis P, Nikolic M, Bleckwehl T, Kolovos P, van Ijcken WFJ, Šari? T, Koehler K, Frommolt P, Lachlan K, Baptista J, Rada-Iglesias A. Cell Stem Cell. 2019 May 2;24(5):736-752.e12. doi:10.1016/j.stem.2019.03.004.

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ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer.

Chen W, Schwalie PC, Pankevich EV, Gubelmann C, Raghav SK, Dainese R, Cassano M, Imbeault M, Jang SM, Russeil J, Delessa T, Duc J, Trono D, Wolfrum C, Deplancke B. Nat Commun. 2019 Apr 18;10(1):1809. doi: 10.1038/s41467-019-09803-9.

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PRC2 facilitates the regulatory topology required for poised enhancer function during pluripotent stem cell differentiation.

Cruz-Molina S, Respuela P, Tebartz C, Kolovos P, Nikolic M, Fueyo R, van Ijcken W.F.J, Grosveld F, Frommolt P, Bazzi H, Rada-Iglesias A#.  Cell Stem Cell. 2017 May 4;20(5):689-705. PMID:28285903.

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High-throughput identification of human SNPs affecting regulatory element activity.

van Arensbergen J, Pagie L, FitzPatrick VD, de Haas M, Baltissen MP, Comoglio F, van der Weide RH, Teunissen H, Võsa U, Franke L, de Wit E, Vermeulen M, Bussemaker HJ, van Steensel B. Nat Genet. 2019 Jul;51(7):1160-1169. doi:10.1038/s41588-019-0455-2.

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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. Nat Genet. 2019 Jul;51(7):1137-1148. doi:10.1038/s41588-019-0457-0.

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4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis

Krijger PHL, Geeven G, Bianchi V, Hilvering CRE, de Laat W. Methods. 2020 Jan 1;170:17-32. doi: 10.1016/j.ymeth.2019.07.014.

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Spatial chromatin architecture alteration by structural variations in human genomes at the population scale.

Sadowski M, Kraft A, Szalaj P, Wlasnowolski M, Tang Z, Ruan Y, Plewczynski D. Genome Biol. 2019 Jul 30;20(1):148. doi:10.1186/s13059-019-1728-x.

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Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells.

Comoglio F, Simonatto M, Polletti S, Liu X, Smale ST, Barozzi I, Natoli G. Genes Dev. 2019 Sep 1;33(17-18):1159-1174. doi: 10.1101/gad.326348.119.

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Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions.

Ibarra IL, Hollmann NM, Klaus B, Augsten S, Velten B, Hennig J, Zaugg JB. Nat Commun. 2020 Jan 8;11(1):124. doi:10.1038/s41467-019-13888-7.

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Determinants of enhancer and promoter activities of regulatory elements.

Andersson R, Sandelin A. Nat Rev Genet. 2019 Oct 11. doi: 10.1038/s41576-019-0173-8.

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