Molecular basis of human enhanceropathies

Risultati finali

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

Pubblicazioni

Targeted Chromosome Conformation Capture (HiCap)

Autori: Artemy Zhigulev & Pelin Sahlén
Pubblicato in: Methods in molecular biology, Numero 2532, 2022, Pagina/e 75-94, ISSN 1940-6029
Editore: Humana Press
DOI: 10.1007/978-1-0716-2497-5_5

Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription

Autori: 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
Pubblicato in: Genes and Development, Numero Vol. 37 (21-24), 2023, Pagina/e 1017-1040, ISSN 1549-5477
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.351057.123

Chromatin modules and their implication in genomic organization and gene regulation

Autori: van Mierlo, G., Pushkarev, O., Kribelbauer, J. F., & Deplancke, B.
Pubblicato in: Trends in Genetics, Numero Volume 39, Numero 2, 2023, Pagina/e 140-153, ISSN 0168-9525
Editore: Elsevier BV
DOI: 10.1016/j.tig.2022.11.003

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

Autori: Juliette Malfait, Jing Wan, Salvatore Spicuglia
Pubblicato in: BioEssays : news and reviews in molecular, cellular and developmental biology, Numero Vol. 45 (10), 2023, Pagina/e e2300012, ISSN 1521-1878
Editore: 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

Autori: Michal Wlasnowolski, Michal Kadlof, Kaustav Sengupta, Dariusz Plewczynski
Pubblicato in: Nucleic Acids Research, Numero Vol. 51 (W1), 2023, Pagina/e W5-W10, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkad354

Chronic inflammation promotes cancer progression as a second hit

Autori: Monika Burocziova, Srdjan Grusanovic, Karolina Vanickova, Sladjana Kosanovic, Meritxell Alberich-Jorda
Pubblicato in: Experimental Hematology, Numero 128, 2023, Pagina/e 30–37, ISSN 1873-2399
Editore: Elsevier Science
DOI: 10.1016/j.exphem.2023.09.002

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

Autori: Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski
Pubblicato in: BMC Bioinformatics, Numero 22(1), 2021, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-021-03984-1

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

Autori: Teresa Szczepińska, Ayatullah Faruk Mollah, Dariusz Plewczynski
Pubblicato in: International Journal of Molecular Sciences, Numero Vol. 22 (21), 2022, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222111591

Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression

Autori: Artemy Zhigulev, Zandra Norberg, Julie Cordier, Rapolas Spalinskas, Hassan Bassereh, Niclas Björn, Sailendra Pradhananga, Henrik Gréen, Pelin Sahlén
Pubblicato in: Life science alliance, Numero Vol. 7 (3), 2024, ISSN 2575-1077
Editore: Life science alliance
DOI: 10.26508/lsa.202302244

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

Autori: 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
Pubblicato in: Molecular Cell, Numero 81, 15, 2021, Pagina/e 3082-3095, ISSN 1097-2765
Editore: Cell Press
DOI: 10.1016/j.molcel.2021.06.008

Prediction of chromatin looping using deep hybrid learning (DHL)

Autori: Mateusz Chiliński, Anup Kumar Halder, Dariusz Plewczynski
Pubblicato in: Quantitative Biology, Numero 11(2), 2023, Pagina/e 155-162, ISSN 2095-4689
Editore: Higher Education Press
DOI: 10.15302/j-qb-022-0315

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

Autori: 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.
Pubblicato in: Molecular Systems Biology, Numero 19: e11627, 2023, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.202311627

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

Autori: 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
Pubblicato in: EMBO Journal, Numero 42, 2023, Pagina/e e113527, ISSN 1460-2075
Editore: Wiley Blackwell
DOI: 10.15252/embj.2023113527

Current challenges in understanding the role of enhancers in disease

Autori: 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
Pubblicato in: Nature Structural & Molecular Biology, Numero 29, 2022, Pagina/e 1148–1158 (2022), ISSN 1545-9985
Editore: 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

Autori: Tomas Pachano; Alvaro Rada-Iglesias
Pubblicato in: STAR Protocols, 2022, Pagina/e 3(3): 101492, ISSN 2666-1667
Editore: 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.

Autori: Mateusz Chiliński, Kaustav Sengupta, Dariusz Plewczynski
Pubblicato in: Seminars in cell & developmental biology, Numero Vol. 121, 2022, Pagina/e 171-185, ISSN 1096-3634
Editore: 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

Autori: Sarah Robert, Alvaro Rada-Iglesias
Pubblicato in: BioEssays : news and reviews in molecular, cellular and developmental biology, Numero Vol. 45 (10), 2023, Pagina/e e2300038, ISSN 1521-1878
Editore: Wiley
DOI: 10.1002/bies.202300038

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

Autori: Kaustav Sengupta, Michał Denkiewicz, Mateusz Chiliński, Teresa Szczepińska, Ayatullah Faruk Mollah, Sevastianos Korsak, Raissa D'Souza, Yijun Ruan, Dariusz Plewczynski
Pubblicato in: Computational and structural biotechnology journal, Numero 20, 2022, Pagina/e 3591-3603, ISSN 2001-0370
Editore: 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

Autori: 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
Pubblicato in: Nature Structural Molecular Biology, Numero 29, 2022, Pagina/e 563–574, ISSN 1545-9993
Editore: Nature Publishing Group
DOI: 10.1038/s41594-022-00787-7

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

Autori: 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
Pubblicato in: EMBO reports, Numero 24 (1), 2022, Pagina/e e54729, ISSN 1469-3178
Editore: Wiley Blackwell
DOI: 10.15252/embr.202254729

The dynamic role of cohesin in maintaining human genome architecture

Autori: Agarwal A; Korsak S; Choudhury A; Plewczynski D;
Pubblicato in: BioEssays : news and reviews in molecular, cellular and developmental biology, Numero Vol. 45 (10), 2023, Pagina/e e2200240, ISSN 1521-1878
Editore: Wiley
DOI: 10.1002/bies.202200240

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

Autori: 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
Pubblicato in: Nature Communications, Numero 4, 2023, Pagina/e 180, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-35859-9

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

Autori: Mateusz Chiliński, Jakub Lipiński, Abhishek Agarwal, Yijun Ruan & Dariusz Plewczynski
Pubblicato in: Scientific Reports, Numero 13(1), 2023, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-023-38865-5

Enhancer-gene specificity in development and disease

Autori: Tomás Pachano; Endika Haro; Alvaro Rada-Iglesias
Pubblicato in: Development, Numero 149 (11), 2022, ISSN 1477-9129
Editore: The Company of Biologists
DOI: 10.1242/dev.186536

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

Autori: Michal Wlasnowolski, Pawel Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski
Pubblicato in: Bioinformatics, Numero Volume 39, Numero 10, 2023, ISSN 1367-4811
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btad588

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

Autori: Mateusz Chiliński, Dariusz Plewczynski
Pubblicato in: Bioinformatics, Numero Volume 38, Numero 24, 2022, Pagina/e 5440-5442, ISSN 1367-4811
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btac709

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

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

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

Autori: Víctor Sánchez-Gaya; Álvaro Rada-Iglesias
Pubblicato in: Nucleic Acids Research, Numero 51(9): e54, 2023, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad225

Transcription factors: Bridge between cell signaling and gene regulation

Autori: Paula Weidemüller, Maksim Kholmatov, Evangelia Petsalaki, Judith B Zaugg
Pubblicato in: PROTEOMICS, 2021, Pagina/e 2021 Dec;21(23-24):e2000034, ISSN 1615-9853
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202000034

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

Autori: 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
Pubblicato in: Nature Communications, 2021, Pagina/e 18;12(1):6660, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-26861-0

Interplay between regulatory elements and chromatin topology in cellular lineage determination

Autori: V. Shukla, A. Cetnarowska, M. Hyldahl, S. Mandrup
Pubblicato in: Trends in genetics, Numero 38 (10), 2022, Pagina/e 1048-1061, ISSN 0168-9525
Editore: Elsevier BV
DOI: 10.1016/j.tig.2022.05.011

Context transcription factors establish cooperative environments and mediate enhancer communication

Autori: Kribelbauer, J. F., Pushkarev, O., Gardeux, V., Russeil, J., van Mierlo, G., & Deplancke, B.
Pubblicato in: bioRxiv, 2023, ISSN 1552-2466
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.05.05.539543

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

Autori: Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B.
Pubblicato in: bioRxiv, 2023, ISSN 1552-2466
Editore: 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

Autori: Anup Kumar Halder, Abhishek Agarwal, Sevastianos Korsak, Karolina Jodkowska & Dariusz Plewczynski
Pubblicato in: Pattern Recognition and Machine Intelligence, Numero LNCS,volume 14301, 2023, ISBN 978-3-031-45169-0
Editore: Springer Nature
DOI: 10.1007/978-3-031-45170-6_91

The role of rare enhancer variants in bicuspid aortic valve pathology

Autori: A. Zhigulev, K. Lång, S. Pradhananga, R. Spalinskas, A. Franco-Cereceda, H. Björck, P. Eriksson, P. Sahlén
Pubblicato in: Atherosclerosis, Numero 355, 2022, ISSN 0021-9150
Editore: 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

Autori: Robert Baber, Mahsan Banijamali, Pontus Höjer, Afshin Ahmadian, and Aurélie Vigne
Pubblicato in: Proceedings of the 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021, 2021, Pagina/e 1767-1768
Editore: 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

Autori: Mateusz Chiliński, Sachin Gadakh, Kaustav Sengupta, Karolina Jodkowska, Natalia Zawrotna, Jan Gawor, Michal Pietal & Dariusz Plewczynski
Pubblicato in: Numero 404, 2022, Pagina/e 41–49
Editore: Springer
DOI: 10.1007/978-981-19-0105-8_5

Understanding enhancer function to understand human disease.

Autori: Salvatore Spicuglia, Alvaro Rada-Iglesias
Pubblicato in: BioEssays : news and reviews in molecular, cellular and developmental biology, Numero Vol. 45 (10), 2023, Pagina/e e2300149, ISSN 1521-1878
Editore: Wiley
DOI: 10.1002/bies.202300149

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