Predictive Epigenetics: Fusing Theory and Experiment

Resultado final

Report on whether additional statistically weak PREs in the fly could be identified (UBER), Presentation of TF mitotic bookmarking in an international conference (CERBM).

Presentation of WP3 results at meetings

ESR13 Poster on Technology development for single-cell small non-coding RNA-seq analysis (DIAGENODE), ESR14 Poster on Novel computational tools to quantify NGS data for total RNA-seq (DIAGENODE)

Manuscripts describing WP1 results

Paper that describes, validates and explores the Polycomb memory model (UCPH), Manuscript of PcG/TrxG residence times in live Drosophila chromatin (UBER), Manuscript describing and validating FLC transcriptional dynamics model (JIC), Manuscript on antisense-mediated bistable switch in X-chromosome inactivation (MPG)

Manuscripts describing WP2 results

A review article based on the introduction to the thesis (OSR), Manuscript on TF mitotic bookmarking (CERBM), Manuscript of high-throughput reporter assay for predicted mammalian PREs (UBER), Manuscript on Polycomb targeting in flies (UBER).

Final Conference

WP5 Task 5.2, event 6

Manuscripts describing WP3 results

Article on chromatin architecture of selected specific loci and genome-wide (NAPOLI), Article comparing chromatin contact between ES and mouse embryos (MDC), ESR 11 Review article based on the introduction to the thesis (UOXF), ESR 15 Review article based on the introduction to the thesis (UOXF).

Network logo designed

WP6 Task 6.1 logo

Presentation of WP1 results at meetings

Presentation on 3D single cell chromosome organisation (FMI), Poster of Polycomb cellular memory model (UCPH), Presentation describing a model for FLC transcriptional dynamics (JIC)

Network information flyer complete

WP6 Task 6.1 flyer

Strasbourg Summer School

WP5 Task 5.2, event 3

Network website online

WP6 Task 6.1 website

Publicaciones

Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing

Autores: Govind Menon, Eduardo Mateo Bonmati, Svenja Reeck, Robert Maple, Zhe Wu, Robert Ietswaart, Caroline Dean, Martin Howard
Publicado en: BioRxiv, 2023
Editor: Cold Spring Harbor Laboratories (CSHL)
DOI: 10.1101/2023.07.06.547969

Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin

Autores: Francesco Musella; Ana Pombo; Rieke Kempfer; Antonella Prisco; Andrea Esposito; Andrea M. Chiariello; Luca Fiorillo; Mattia Conte; Mario Nicodemi; Ibai Irastorza-Azcarate; Simona Bianco; Alexander Kukalev
Publicado en: Edición 1, 2020
Editor: bioRxiv
DOI: 10.1101/2020.04.24.059915

GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of a distal enhancer element

Autores: Liat Ravid Lustig, Abhishek Sampath Kumar, Till Schwämmle, Ilona Dunkel, Gemma Noviello, Raha Weigert, Guido Pacini, Rene Buschow, Afrah Ghauri, Maximilian Stoetzel, Lars Wittler, Alexander Meissner, Edda G Schulz
Publicado en: BioRxiv, 2022
Editor: Cold Spring Harbor Laboratories (CSHL)
DOI: 10.1101/2022.08.02.502458

Chromatin organization drives the exploration strategy of nuclear factors

Autores: Matteo Mazzocca, Alessia Loffreda, Emanuele Colombo, Tom Fillot, Daniela Gnani, Paola Falletta, Emanuele Monteleone, Serena Capozi, Edouard Bertrand, Gaelle Legube, Zeno Lavagnino, Carlo Tacchetti, Davide Mazza
Publicado en: BioRxiv, 2022
Editor: Cold Spring Harbor Laboratories (CSHL)
DOI: 10.1101/2022.12.29.522193

Transcriptional changes are regulated by metabolic pathway dynamics but decoupled from protein levels

Autores: Jack E. Feltham, Shidong Xi, Struan C. Murray, Meredith Wouters, Julian Urdiain-Arraiza, Raphael Heilig, Charlotte George, Anna F. Townley, Emile Roberts, Benedikt M. Kessler, Sabrina Liberatori, Philip D. Charles, Andrew Angel, Roman Fischer,
Publicado en: BioRxiv, 2020
Editor: Cold Spring Harbor Laboratory (CSHL)
DOI: 10.1101/833921

Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory

Autores: Cecilia Lovkvist, Pawel Mikulski, Svenja Reeck, Matthew Hartley, Caroline Dean, Martin Howard
Publicado en: eLife, 2021, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.66454

Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

Autores: Mattia Conte, Luca Fiorillo, Simona Bianco, Andrea M. Chiariello, Andrea Esposito, Mario Nicodemi
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-17141-4

Establishment of heterochromatin in domain-size-dependent bursts

Autores: Jan Fabio Nickels, Ashleigh Katrine Edwards, Sebastian Jespersen Charlton, Amanda Møller Mortensen, Sif Christine Lykke Hougaard, Ala Trusina, Kim Sneppen, Geneviève Thon
Publicado en: Proceedings of the National Academy of Sciences, Edición 118/15, 2021, Página(s) e2022887118, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2022887118

CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression

Autores: Gemma Noviello, Rutger AF Gjaltema, Edda G Schulz
Publicado en: Nature Communications, 2023, ISSN 2041-1723
Editor: Nature Publishing Group

Cohesin and CTCF control the dynamics of chromosome folding

Autores: Pia Mach, Pavel I. Kos, Yinxiu Zhan, Julie Cramard, Simon Gaudin, Jana Tünnermann, Edoardo Marchi, Jan Eglinger, Jessica Zuin, Mariya Kryzhanovska, Sebastien Smallwood, Laurent Gelman, Gregory Roth, Elphège P. Nora, Guido Tiana & Luca Giorgetti
Publicado en: Nature Genetics, Edición 54, 2022, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/s41588-022-01232-7

The Trithorax group protein ASH1 requires a combination of BAH domain and AT hooks, but not the SET domain, for mitotic chromatin binding and survival

Autores: Philipp A. Steffen; Christina Altmutter; Eva Dworschak; Sini Junttila; Attila Gyenesei; Xinzhou Zhu; Tobias Kockmann; Leonie Ringrose
Publicado en: Chromosoma, Edición 1, 2021, ISSN 0009-5915
Editor: Springer Verlag
DOI: 10.3929/ethz-b-000500204

Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding

Autores: Mattia Conte, Ehsan Irani, Andrea M. Chiariello, Alex Abraham, Simona Bianco, Andrea Esposito & Mario Nicodemi
Publicado en: Nature Communications, Edición 13, 4070, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-31856-6

The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes

Autores: Matteo Mazzocca, Tom Fillot, Alessia Loffreda, Daniela Gnani, Davide Mazza
Publicado en: Biochemical Society Transactions, 2021, ISSN 0300-5127
Editor: Portland Press, Ltd.
DOI: 10.1042/bst20200709

Theoretical analysis of Polycomb-Trithorax systems predicts that poised chromatin is bistable and not bivalent

Autores: Kim Sneppen, Leonie Ringrose
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-10130-2

MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts

Autores: Andrea Hita, Gilles Brocart, Ana Fernandez, Marc Rehmsmeier, Anna Alemany and Sol Schvartzman
Publicado en: BMC Bioinformatics, 2022, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-021-04544-3

The transcription factor Atf1 lowers the transition barrier for nucleosome-mediated establishment of heterochromatin

Autores: Nickels, J. F., Della-Rosa, M. E., Goyeneche, I. M., Charlton, S. J., Sneppen, K., & Thon, G.
Publicado en: Cell Reports, Edición 39(7), 110828, 2022, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2022.110828

Integrating analog and digital modes of gene expression at Arabidopsis FLC

Autores: Rea L. Antoniou-Kourounioti, Anis Meschichi, Svenja Reeck, Scott Berry, Govind Menon, Yusheng Zhao, John A. Fozard, Terri L. Holmes, Huamei Wang, Matthew Hartley, Caroline Dean, Stefanie Rosa, Martin Howard
Publicado en: eLife, Edición 12, e79743, 2023, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.1101/2022.07.04.498694

Resultado final

Publicaciones

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