Molecular basis of human enhanceropathies

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Detailed plan of dissemination and communication actions

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

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)

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

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

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

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

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

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

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

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

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