Molecular basis of human enhanceropathies

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Detailed plan of dissemination and communication actions

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

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

Targeted Chromosome Conformation Capture (HiCap)

Auteurs: Artemy Zhigulev & Pelin Sahlén
Publié dans: Methods in molecular biology, Numéro 2532, 2022, Page(s) 75-94, ISSN 1940-6029
Éditeur: Humana Press
DOI: 10.1007/978-1-0716-2497-5_5

Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription

Auteurs: 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
Publié dans: Genes and Development, Numéro Vol. 37 (21-24), 2023, Page(s) 1017-1040, ISSN 1549-5477
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.351057.123

Chromatin modules and their implication in genomic organization and gene regulation

Auteurs: van Mierlo, G., Pushkarev, O., Kribelbauer, J. F., & Deplancke, B.
Publié dans: Trends in Genetics, Numéro Volume 39, Numéro 2, 2023, Page(s) 140-153, ISSN 0168-9525
Éditeur: Elsevier BV
DOI: 10.1016/j.tig.2022.11.003

Epromoters are new players in the regulatory landscape with potential pleiotropic roles

Auteurs: Juliette Malfait, Jing Wan, Salvatore Spicuglia
Publié dans: BioEssays : news and reviews in molecular, cellular and developmental biology, Numéro Vol. 45 (10), 2023, Page(s) e2300012, ISSN 1521-1878
Éditeur: 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

Auteurs: Michal Wlasnowolski, Michal Kadlof, Kaustav Sengupta, Dariusz Plewczynski
Publié dans: Nucleic Acids Research, Numéro Vol. 51 (W1), 2023, Page(s) W5-W10, ISSN 1362-4962
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad354

Chronic inflammation promotes cancer progression as a second hit

Auteurs: Monika Burocziova, Srdjan Grusanovic, Karolina Vanickova, Sladjana Kosanovic, Meritxell Alberich-Jorda
Publié dans: Experimental Hematology, Numéro 128, 2023, Page(s) 30–37, ISSN 1873-2399
Éditeur: Elsevier Science
DOI: 10.1016/j.exphem.2023.09.002

PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies

Auteurs: Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski
Publié dans: BMC Bioinformatics, Numéro 22(1), 2021, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-021-03984-1

Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows

Auteurs: Teresa Szczepińska, Ayatullah Faruk Mollah, Dariusz Plewczynski
Publié dans: International Journal of Molecular Sciences, Numéro Vol. 22 (21), 2022, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222111591

Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression

Auteurs: Artemy Zhigulev, Zandra Norberg, Julie Cordier, Rapolas Spalinskas, Hassan Bassereh, Niclas Björn, Sailendra Pradhananga, Henrik Gréen, Pelin Sahlén
Publié dans: Life science alliance, Numéro Vol. 7 (3), 2024, ISSN 2575-1077
Éditeur: Life science alliance
DOI: 10.26508/lsa.202302244

Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression.

Auteurs: 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
Publié dans: Molecular Cell, Numéro 81, 15, 2021, Page(s) 3082-3095, ISSN 1097-2765
Éditeur: Cell Press
DOI: 10.1016/j.molcel.2021.06.008

Prediction of chromatin looping using deep hybrid learning (DHL)

Auteurs: Mateusz Chiliński, Anup Kumar Halder, Dariusz Plewczynski
Publié dans: Quantitative Biology, Numéro 11(2), 2023, Page(s) 155-162, ISSN 2095-4689
Éditeur: Higher Education Press
DOI: 10.15302/j-qb-022-0315

GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks

Auteurs: 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.
Publié dans: Molecular Systems Biology, Numéro 19: e11627, 2023, ISSN 1744-4292
Éditeur: Nature Publishing Group
DOI: 10.15252/msb.202311627

Hematopoietic stem cells undergo a lymphoid to myeloid switch in early stages of emergency granulopoiesis

Auteurs: 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
Publié dans: EMBO Journal, Numéro 42, 2023, Page(s) e113527, ISSN 1460-2075
Éditeur: Wiley Blackwell
DOI: 10.15252/embj.2023113527

Current challenges in understanding the role of enhancers in disease

Auteurs: 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
Publié dans: Nature Structural & Molecular Biology, Numéro 29, 2022, Page(s) 1148–1158 (2022), ISSN 1545-9985
Éditeur: 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

Auteurs: Tomas Pachano; Alvaro Rada-Iglesias
Publié dans: STAR Protocols, 2022, Page(s) 3(3): 101492, ISSN 2666-1667
Éditeur: 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.

Auteurs: Mateusz Chiliński, Kaustav Sengupta, Dariusz Plewczynski
Publié dans: Seminars in cell & developmental biology, Numéro Vol. 121, 2022, Page(s) 171-185, ISSN 1096-3634
Éditeur: 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

Auteurs: Sarah Robert, Alvaro Rada-Iglesias
Publié dans: BioEssays : news and reviews in molecular, cellular and developmental biology, Numéro Vol. 45 (10), 2023, Page(s) e2300038, ISSN 1521-1878
Éditeur: Wiley
DOI: 10.1002/bies.202300038

Multi-scale phase separation by explosive percolation with single-chromatin loop resolution

Auteurs: Kaustav Sengupta, Michał Denkiewicz, Mateusz Chiliński, Teresa Szczepińska, Ayatullah Faruk Mollah, Sevastianos Korsak, Raissa D'Souza, Yijun Ruan, Dariusz Plewczynski
Publié dans: Computational and structural biotechnology journal, Numéro 20, 2022, Page(s) 3591-3603, ISSN 2001-0370
Éditeur: 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

Auteurs: 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
Publié dans: Nature Structural Molecular Biology, Numéro 29, 2022, Page(s) 563–574, ISSN 1545-9993
Éditeur: Nature Publishing Group
DOI: 10.1038/s41594-022-00787-7

Chronic inflammation decreases HSC fitness by activating the druggable Jak/Stat3 signaling pathway

Auteurs: 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
Publié dans: EMBO reports, Numéro 24 (1), 2022, Page(s) e54729, ISSN 1469-3178
Éditeur: Wiley Blackwell
DOI: 10.15252/embr.202254729

The dynamic role of cohesin in maintaining human genome architecture

Auteurs: Agarwal A; Korsak S; Choudhury A; Plewczynski D;
Publié dans: BioEssays : news and reviews in molecular, cellular and developmental biology, Numéro Vol. 45 (10), 2023, Page(s) e2200240, ISSN 1521-1878
Éditeur: Wiley
DOI: 10.1002/bies.202200240

Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells

Auteurs: 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
Publié dans: Nature Communications, Numéro 4, 2023, Page(s) 180, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-35859-9

Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions

Auteurs: Mateusz Chiliński, Jakub Lipiński, Abhishek Agarwal, Yijun Ruan & Dariusz Plewczynski
Publié dans: Scientific Reports, Numéro 13(1), 2023, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-023-38865-5

Enhancer-gene specificity in development and disease

Auteurs: Tomás Pachano; Endika Haro; Alvaro Rada-Iglesias
Publié dans: Development, Numéro 149 (11), 2022, ISSN 1477-9129
Éditeur: The Company of Biologists
DOI: 10.1242/dev.186536

cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling.

Auteurs: Michal Wlasnowolski, Pawel Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski
Publié dans: Bioinformatics, Numéro Volume 39, Numéro 10, 2023, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btad588

ConsensuSV—from the whole-genome sequencing data to the complete variant list

Auteurs: Mateusz Chiliński, Dariusz Plewczynski
Publié dans: Bioinformatics, Numéro Volume 38, Numéro 24, 2022, Page(s) 5440-5442, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btac709

Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy

Auteurs: Zofia Parteka-Tojek, Jacqueline Jufen Zhu, Byoungkoo Lee, Karolina Jodkowska, Ping Wang, Jesse Aaron, Teng-Leong Chew, Krzysztof Banecki, Dariusz Plewczynski, Yijun Ruan
Publié dans: Scientific Reports, Numéro 12(1), 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-12568-9

POSTRE: a tool to predict the pathological effects of human structural variants

Auteurs: Víctor Sánchez-Gaya; Álvaro Rada-Iglesias
Publié dans: Nucleic Acids Research, Numéro 51(9): e54, 2023, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad225

Transcription factors: Bridge between cell signaling and gene regulation

Auteurs: Paula Weidemüller, Maksim Kholmatov, Evangelia Petsalaki, Judith B Zaugg
Publié dans: PROTEOMICS, 2021, Page(s) 2021 Dec;21(23-24):e2000034, ISSN 1615-9853
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202000034

Epromoters function as a hub to recruit key transcription factors required for the inflammatory response

Auteurs: 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
Publié dans: Nature Communications, 2021, Page(s) 18;12(1):6660, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-26861-0

Interplay between regulatory elements and chromatin topology in cellular lineage determination

Auteurs: V. Shukla, A. Cetnarowska, M. Hyldahl, S. Mandrup
Publié dans: Trends in genetics, Numéro 38 (10), 2022, Page(s) 1048-1061, ISSN 0168-9525
Éditeur: Elsevier BV
DOI: 10.1016/j.tig.2022.05.011

Context transcription factors establish cooperative environments and mediate enhancer communication

Auteurs: Kribelbauer, J. F., Pushkarev, O., Gardeux, V., Russeil, J., van Mierlo, G., & Deplancke, B.
Publié dans: bioRxiv, 2023, ISSN 1552-2466
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.05.05.539543

Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

Auteurs: Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B.
Publié dans: bioRxiv, 2023, ISSN 1552-2466
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.10.11.561870

ccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model

Auteurs: Anup Kumar Halder, Abhishek Agarwal, Sevastianos Korsak, Karolina Jodkowska & Dariusz Plewczynski
Publié dans: Pattern Recognition and Machine Intelligence, Numéro LNCS,volume 14301, 2023, ISBN 978-3-031-45169-0
Éditeur: Springer Nature
DOI: 10.1007/978-3-031-45170-6_91

The role of rare enhancer variants in bicuspid aortic valve pathology

Auteurs: A. Zhigulev, K. Lång, S. Pradhananga, R. Spalinskas, A. Franco-Cereceda, H. Björck, P. Eriksson, P. Sahlén
Publié dans: Atherosclerosis, Numéro 355, 2022, ISSN 0021-9150
Éditeur: 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

Auteurs: Robert Baber, Mahsan Banijamali, Pontus Höjer, Afshin Ahmadian, and Aurélie Vigne
Publié dans: Proceedings of the 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021, 2021, Page(s) 1767-1768
Éditeur: 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

Auteurs: Mateusz Chiliński, Sachin Gadakh, Kaustav Sengupta, Karolina Jodkowska, Natalia Zawrotna, Jan Gawor, Michal Pietal & Dariusz Plewczynski
Publié dans: Numéro 404, 2022, Page(s) 41–49
Éditeur: Springer
DOI: 10.1007/978-981-19-0105-8_5

Understanding enhancer function to understand human disease.

Auteurs: Salvatore Spicuglia, Alvaro Rada-Iglesias
Publié dans: BioEssays : news and reviews in molecular, cellular and developmental biology, Numéro Vol. 45 (10), 2023, Page(s) e2300149, ISSN 1521-1878
Éditeur: Wiley
DOI: 10.1002/bies.202300149

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