Deliverables Documents, reports (1) Detailed plan of dissemination and communication actions Websites, patent fillings, videos etc. (2) ENHPATHY's website V2. V3 of the ENHPATHY public website including ESRs profiles V1 of the public website and launch of the STED programme V2 of the ENHPATHYs public website with link to the password secured intranet Social media accounts set up First press release V1 a digital brochure to summarize all communication tools and actions Launch of STED programme Other (3) Supervisory Board of the network Supervisory Board operational All organisational boards operational All organisational boards are operational "Start of the #EnhancerInArt programme" Contact local cultural organizations and build a list of partnering artists Design develop and content editing of the ENHPATHYs blog A digital brochure of the EnhancerInArt is sent to cultural organizations Publications Peer reviewed articles (36) Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness Author(s): Pachano T, Sánchez-Gaya V, Ealo T, Mariner-Faulí M, Bleckwehl T, Asenjo HG, Respuela P, Cruz-Molina S, Muñoz-San Martín M, Haro E, van IJcken WFJ, Landeira D, Rada-Iglesias A Published in: Nature Genetics, 2021, Page(s) 53(7):1036-1049, ISSN 1061-4036 Publisher: Nature Publishing Group DOI: 10.1038/s41588-021-00888-x Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression Author(s): Vos ESM, Valdes-Quezada C, Huang Y, Allahyar A, Verstegen MJAM, Felder A-K, van der Vegt F, Uijttewaal ECH, Krijger PHL, and de Laat W Published in: Nature Genetics, 2020, Page(s) 52, 1227-1238, ISSN 1061-4036 Publisher: Nature Publishing Group DOI: 10.1016/j.molcel.2021.06.008 Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription Author(s): Russo M., Piccolo V., Polizzese D., Prosperini E., Borriero C., Polletti S., Bedin F., Marenda M., Michieletto D., Mandana G.M., Rodighiero S., Cuomo A., Natoli G Published in: Genes and Development, Issue Vol. 37 (21-24), 2023, Page(s) 1017-1040, ISSN 1549-5477 Publisher: Cold Spring Harbor Laboratory Press DOI: 10.1101/gad.351057.123 Chromatin modules and their implication in genomic organization and gene regulation Author(s): van Mierlo, G., Pushkarev, O., Kribelbauer, J. F., & Deplancke, B. Published in: Trends in Genetics, Issue Volume 39, Issue 2, 2023, Page(s) 140-153, ISSN 0168-9525 Publisher: Elsevier BV DOI: 10.1016/j.tig.2022.11.003 Epromoters are new players in the regulatory landscape with potential pleiotropic roles Author(s): Juliette Malfait, Jing Wan, Salvatore Spicuglia Published in: BioEssays : news and reviews in molecular, cellular and developmental biology, Issue Vol. 45 (10), 2023, Page(s) e2300012, ISSN 1521-1878 Publisher: Wiley DOI: 10.1002/bies.202300012 3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome Author(s): Michal Wlasnowolski, Michal Kadlof, Kaustav Sengupta, Dariusz Plewczynski Published in: Nucleic Acids Research, Issue Vol. 51 (W1), 2023, Page(s) W5-W10, ISSN 1362-4962 Publisher: Oxford University Press DOI: 10.1093/nar/gkad354 Chronic inflammation promotes cancer progression as a second hit Author(s): Monika Burocziova, Srdjan Grusanovic, Karolina Vanickova, Sladjana Kosanovic, Meritxell Alberich-Jorda Published in: Experimental Hematology, Issue 128, 2023, Page(s) 30–37, ISSN 1873-2399 Publisher: Elsevier Science DOI: 10.1016/j.exphem.2023.09.002 PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies Author(s): Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski Published in: BMC Bioinformatics, Issue 22(1), 2021, ISSN 1471-2105 Publisher: BioMed Central DOI: 10.1186/s12859-021-03984-1 Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows Author(s): Teresa Szczepińska, Ayatullah Faruk Mollah, Dariusz Plewczynski Published in: International Journal of Molecular Sciences, Issue Vol. 22 (21), 2022, ISSN 1422-0067 Publisher: Multidisciplinary Digital Publishing Institute (MDPI) DOI: 10.3390/ijms222111591 Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression Author(s): Artemy Zhigulev, Zandra Norberg, Julie Cordier, Rapolas Spalinskas, Hassan Bassereh, Niclas Björn, Sailendra Pradhananga, Henrik Gréen, Pelin Sahlén Published in: Life science alliance, Issue Vol. 7 (3), 2024, ISSN 2575-1077 Publisher: Life science alliance DOI: 10.26508/lsa.202302244 Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression. Author(s): E.S. Vos; Christian Valdes-Quezada; Yike Huang; Amin Allahyar; Marjon J.A.M. Verstegen; Anna-Karina Felder; Floor van der Vegt; Esther C.H. Uijttewaal; Peter H.L. Krijger; Wouter de Laat Published in: Molecular Cell, Issue 81, 15, 2021, Page(s) 3082-3095, ISSN 1097-2765 Publisher: Cell Press DOI: 10.1016/j.molcel.2021.06.008 Prediction of chromatin looping using deep hybrid learning (DHL) Author(s): Mateusz Chiliński, Anup Kumar Halder, Dariusz Plewczynski Published in: Quantitative Biology, Issue 11(2), 2023, Page(s) 155-162, ISSN 2095-4689 Publisher: Higher Education Press DOI: 10.15302/j-qb-022-0315 GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks Author(s): Kamal, A.; Arnold, C.; Claringbould, A.; Moussa, R.; Servaas, N.H.; Kholmatov, M.; Daga, N.; Nogina, D.; Mueller-Dott, S.; Reyes-Palomares, A.; Palla, G.; Sigalova, O.; Bunina, D.; Pabst, C.; Zaugg, J.B. Published in: Molecular Systems Biology, Issue 19: e11627, 2023, ISSN 1744-4292 Publisher: Nature Publishing Group DOI: 10.15252/msb.202311627 Hematopoietic stem cells undergo a lymphoid to myeloid switch in early stages of emergency granulopoiesis Author(s): Vanickova K, Milosevic M, Ribeiro Bas I, Burocziova M, Yokota A, Danek P, Grusanovic S, Chiliński M, Plewczynski D, Rohlena J, Hirai H, Rohlenova K, Alberich-Jorda M Published in: EMBO Journal, Issue 42, 2023, Page(s) e113527, ISSN 1460-2075 Publisher: Wiley Blackwell DOI: 10.15252/embj.2023113527 Current challenges in understanding the role of enhancers in disease Author(s): Judith Barbara Zaugg; Pelin Sahlén; Robin Andersson; Meritxell Alberich-Jorda; Wouter de Laat; Bart Deplancke; Jorge Ferrer; Susanne Mandrup; Gioacchino Natoli; Dariusz Plewczynski; Alvaro Rada-Iglesias; Salvatore Spicuglia Published in: Nature Structural & Molecular Biology, Issue 29, 2022, Page(s) 1148–1158 (2022), ISSN 1545-9985 Publisher: Springer Nature DOI: 10.1038/s41594-022-00896-3 Protocol to study sufficiency of cis-regulatory elements in mouse embryonic stem cells using a CRISPR-mediated knockin approach Author(s): Tomas Pachano; Alvaro Rada-Iglesias Published in: STAR Protocols, 2022, Page(s) 3(3): 101492, ISSN 2666-1667 Publisher: Elsevier DOI: 10.1016/j.xpro.2022.101492 From DNA human sequence to the chromatin higher order organisation and its biological meaning: Using biomolecular interaction networks to understand the influence of structural variation on spatial genome organisation and its functional effect. Author(s): Mateusz Chiliński, Kaustav Sengupta, Dariusz Plewczynski Published in: Seminars in cell & developmental biology, Issue Vol. 121, 2022, Page(s) 171-185, ISSN 1096-3634 Publisher: Academic Press DOI: 10.1016/j.semcdb.2021.08.007 The interaction between enhancer variants and environmental factors as an overlooked aetiological paradigm in human complex disease Author(s): Sarah Robert, Alvaro Rada-Iglesias Published in: BioEssays : news and reviews in molecular, cellular and developmental biology, Issue Vol. 45 (10), 2023, Page(s) e2300038, ISSN 1521-1878 Publisher: Wiley DOI: 10.1002/bies.202300038 Multi-scale phase separation by explosive percolation with single-chromatin loop resolution Author(s): Kaustav Sengupta, Michał Denkiewicz, Mateusz Chiliński, Teresa Szczepińska, Ayatullah Faruk Mollah, Sevastianos Korsak, Raissa D'Souza, Yijun Ruan, Dariusz Plewczynski Published in: Computational and structural biotechnology journal, Issue 20, 2022, Page(s) 3591-3603, ISSN 2001-0370 Publisher: Elsevier DOI: 10.1016/j.csbj.2022.06.063 Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes Author(s): Niels J. Rinzema, Konstantinos Sofiadis, Sjoerd J. D. Tjalsma, Marjon J. A. M. Verstegen, Yuva Oz, Christian Valdes-Quezada, Anna-Karina Felder, Teodora Filipovska, Stefan van der Elst, Zaria de Andrade dos Ramos, Ruiqi Han, Peter H. L. Krijger & Wouter de Laat Published in: Nature Structural Molecular Biology, Issue 29, 2022, Page(s) 563–574, ISSN 1545-9993 Publisher: Nature Publishing Group DOI: 10.1038/s41594-022-00787-7 Chronic inflammation decreases HSC fitness by activating the druggable Jak/Stat3 signaling pathway Author(s): Grusanovic S, Danek P, Kuzmina M, Adamcova MK, Burocziova M, Mikyskova R, Vanickova K, Kosanovic S, Pokorna J, Reinis M, Brdicka T, Alberich-Jorda M Published in: EMBO reports, Issue 24 (1), 2022, Page(s) e54729, ISSN 1469-3178 Publisher: Wiley Blackwell DOI: 10.15252/embr.202254729 The dynamic role of cohesin in maintaining human genome architecture Author(s): Agarwal A; Korsak S; Choudhury A; Plewczynski D; Published in: BioEssays : news and reviews in molecular, cellular and developmental biology, Issue Vol. 45 (10), 2023, Page(s) e2200240, ISSN 1521-1878 Publisher: Wiley DOI: 10.1002/bies.202200240 Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells Author(s): Helena G. Asenjo; María Alcazar-Fabra; Mencía Espinosa-Martínez; Lourdes Lopez-Onieva; Amador Gallardo; Emilia Dimitrova; Angelika Feldmann; Tomas Pachano; Jordi Martorell-Marugán; Pedro Carmona-Sáez; Antonio Sanchez-Pozo; Álvaro Rada-Iglesias; Robert J. Klose; David Landeira Published in: Nature Communications, Issue 4, 2023, Page(s) 180, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-023-35859-9 The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo Author(s): Crispatzu G, Rehimi R, Pachano T, Bleckwehl T, Cruz-Molina S, Xiao C, Mahabir-Brenner E, Bazzi H, Rada-Iglesias A Published in: Nature Communications, 2021, Page(s) 12(1):4344, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-021-24641-4 Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells Author(s): Helena G. Asenjo; María Alcazar-Fabra; Mencía Espinosa-Martínez; Lourdes Lopez-Onieva; Amador Gallardo; Emilia Dimitrova; Angelika Feldmann; Tomas Pachano; Jordi Martorell-Marugán; Pedro Carmona-Sáez; Antonio Sanchez-Pozo; Álvaro Rada-Iglesias; Robert J. Klose; David Landeira Published in: Nature Communications, Issue 14, 2023, Page(s) 180 (2023), ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-023-35859-9 Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions Author(s): Mateusz Chiliński, Jakub Lipiński, Abhishek Agarwal, Yijun Ruan & Dariusz Plewczynski Published in: Scientific Reports, Issue 13(1), 2023, ISSN 2045-2322 Publisher: Nature Publishing Group DOI: 10.1038/s41598-023-38865-5 Enhancer-gene specificity in development and disease Author(s): Tomás Pachano; Endika Haro; Alvaro Rada-Iglesias Published in: Development, Issue 149 (11), 2022, ISSN 1477-9129 Publisher: The Company of Biologists DOI: 10.1242/dev.186536 cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling. Author(s): Michal Wlasnowolski, Pawel Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski Published in: Bioinformatics, Issue Volume 39, Issue 10, 2023, ISSN 1367-4811 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btad588 ConsensuSV—from the whole-genome sequencing data to the complete variant list Author(s): Mateusz Chiliński, Dariusz Plewczynski Published in: Bioinformatics, Issue Volume 38, Issue 24, 2022, Page(s) 5440-5442, ISSN 1367-4811 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btac709 Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy Author(s): Zofia Parteka-Tojek, Jacqueline Jufen Zhu, Byoungkoo Lee, Karolina Jodkowska, Ping Wang, Jesse Aaron, Teng-Leong Chew, Krzysztof Banecki, Dariusz Plewczynski, Yijun Ruan Published in: Scientific Reports, Issue 12(1), 2022, ISSN 2045-2322 Publisher: Nature Publishing Group DOI: 10.1038/s41598-022-12568-9 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Author(s): Bleckwehl T, Crispatzu G, Schaaf K, Respuela P, Bartusel M, Benson L, Clark SJ, Dorighi KM, Barral A, Laugsch M, van IJcken WFJ, Manzanares M, Wysocka J, Reik W, Rada-Iglesias A Published in: Nature Communications, 2021, Page(s) 12(1):5771., ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-021-26065-6 POSTRE: a tool to predict the pathological effects of human structural variants Author(s): Víctor Sánchez-Gaya; Álvaro Rada-Iglesias Published in: Nucleic Acids Research, Issue 51(9): e54, 2023, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkad225 Transcription factors: Bridge between cell signaling and gene regulation Author(s): Paula Weidemüller, Maksim Kholmatov, Evangelia Petsalaki, Judith B Zaugg Published in: PROTEOMICS, 2021, Page(s) 2021 Dec;21(23-24):e2000034, ISSN 1615-9853 Publisher: John Wiley & Sons Ltd. DOI: 10.1002/pmic.202000034 Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells Author(s): Jesper G. S. Madsen, Maria S. Madsen, Alexander Rauch, Sofie Traynor, Elvira L. Van Hauwaert, Anders K. Haakonsson, Biola M. Javierre, Mette Hyldahl, Peter Fraser & Susanne Mandrup Published in: Nature Genetics, 2020, Page(s) 52, 1227-1238, ISSN 1061-4036 Publisher: Nature Publishing Group DOI: 10.1038/s41588-020-0709-z Epromoters function as a hub to recruit key transcription factors required for the inflammatory response Author(s): Santiago-Algarra D, Souaid C, Singh H, Dao LTM, Hussain S, Medina-Rivera A, Ramirez-Navarro L, Castro-Mondragon JA, Sadouni N, Charbonnier G, Spicuglia S Published in: Nature Communications, 2021, Page(s) 18;12(1):6660, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-021-26861-0 Interplay between regulatory elements and chromatin topology in cellular lineage determination Author(s): V. Shukla, A. Cetnarowska, M. Hyldahl, S. Mandrup Published in: Trends in genetics, Issue 38 (10), 2022, Page(s) 1048-1061, ISSN 0168-9525 Publisher: Elsevier BV DOI: 10.1016/j.tig.2022.05.011 Book chapters (1) Targeted Chromosome Conformation Capture (HiCap) Author(s): Artemy Zhigulev & Pelin Sahlén Published in: Methods in molecular biology, Issue 2532, 2022, Page(s) 75-94, ISSN 1940-6029 Publisher: Humana Press DOI: 10.1007/978-1-0716-2497-5_5 Other (2) Context transcription factors establish cooperative environments and mediate enhancer communication Author(s): Kribelbauer, J. F., Pushkarev, O., Gardeux, V., Russeil, J., van Mierlo, G., & Deplancke, B. Published in: bioRxiv, 2023, ISSN 1552-2466 Publisher: Cold Spring Harbor Laboratory DOI: 10.1101/2023.05.05.539543 Non-coding variants impact cis-regulatory coordination in a cell type-specific manner Author(s): Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. Published in: bioRxiv, 2023, ISSN 1552-2466 Publisher: Cold Spring Harbor Laboratory DOI: 10.1101/2023.10.11.561870 Conference proceedings (4) ccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model Author(s): Anup Kumar Halder, Abhishek Agarwal, Sevastianos Korsak, Karolina Jodkowska & Dariusz Plewczynski Published in: Pattern Recognition and Machine Intelligence, Issue LNCS,volume 14301, 2023, ISBN 978-3-031-45169-0 Publisher: Springer Nature DOI: 10.1007/978-3-031-45170-6_91 The role of rare enhancer variants in bicuspid aortic valve pathology Author(s): A. Zhigulev, K. Lång, S. Pradhananga, R. Spalinskas, A. Franco-Cereceda, H. Björck, P. Eriksson, P. Sahlén Published in: Atherosclerosis, Issue 355, 2022, ISSN 0021-9150 Publisher: Elsevier BV DOI: 10.1016/j.atherosclerosis.2022.06.194 Development Of A Versatile And Low-Cost Droplet Microfluidic Platform For Single-Nuclei Atac-Sequencing Author(s): Robert Baber, Mahsan Banijamali, Pontus Höjer, Afshin Ahmadian, and Aurélie Vigne Published in: Proceedings of the 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021, 2021, Page(s) 1767-1768 Publisher: Chemical and Biological Microsystems Society Consensus-Based Identification and Comparative Analysis of Structural Variants and Their Influence on 3D Genome Structure Using Long- and Short-Read Sequencing Technologies in Polish Families Author(s): Mateusz Chiliński, Sachin Gadakh, Kaustav Sengupta, Karolina Jodkowska, Natalia Zawrotna, Jan Gawor, Michal Pietal & Dariusz Plewczynski Published in: Issue 404, 2022, Page(s) 41–49 Publisher: Springer DOI: 10.1007/978-981-19-0105-8_5 Non-peer reviewed articles (1) Understanding enhancer function to understand human disease. Author(s): Salvatore Spicuglia, Alvaro Rada-Iglesias Published in: BioEssays : news and reviews in molecular, cellular and developmental biology, Issue Vol. 45 (10), 2023, Page(s) e2300149, ISSN 1521-1878 Publisher: Wiley DOI: 10.1002/bies.202300149 Searching for OpenAIRE data... There was an error trying to search data from OpenAIRE No results available
