Predictive Epigenetics: Fusing Theory and Experiment

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Publications

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

Auteurs: Govind Menon, Eduardo Mateo Bonmati, Svenja Reeck, Robert Maple, Zhe Wu, Robert Ietswaart, Caroline Dean, Martin Howard
Publié dans: BioRxiv, 2023
Éditeur: 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

Auteurs: 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
Publié dans: Numéro 1, 2020
Éditeur: 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

Auteurs: 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
Publié dans: BioRxiv, 2022
Éditeur: Cold Spring Harbor Laboratories (CSHL)
DOI: 10.1101/2022.08.02.502458

Chromatin organization drives the exploration strategy of nuclear factors

Auteurs: 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
Publié dans: BioRxiv, 2022
Éditeur: 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

Auteurs: 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,
Publié dans: BioRxiv, 2020
Éditeur: Cold Spring Harbor Laboratory (CSHL)
DOI: 10.1101/833921

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

Auteurs: Cecilia Lovkvist, Pawel Mikulski, Svenja Reeck, Matthew Hartley, Caroline Dean, Martin Howard
Publié dans: eLife, 2021, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.66454

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

Auteurs: Mattia Conte, Luca Fiorillo, Simona Bianco, Andrea M. Chiariello, Andrea Esposito, Mario Nicodemi
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-17141-4

Establishment of heterochromatin in domain-size-dependent bursts

Auteurs: Jan Fabio Nickels, Ashleigh Katrine Edwards, Sebastian Jespersen Charlton, Amanda Møller Mortensen, Sif Christine Lykke Hougaard, Ala Trusina, Kim Sneppen, Geneviève Thon
Publié dans: Proceedings of the National Academy of Sciences, Numéro 118/15, 2021, Page(s) e2022887118, ISSN 0027-8424
Éditeur: 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

Auteurs: Gemma Noviello, Rutger AF Gjaltema, Edda G Schulz
Publié dans: Nature Communications, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group

Cohesin and CTCF control the dynamics of chromosome folding

Auteurs: 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
Publié dans: Nature Genetics, Numéro 54, 2022, ISSN 1061-4036
Éditeur: 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

Auteurs: Philipp A. Steffen; Christina Altmutter; Eva Dworschak; Sini Junttila; Attila Gyenesei; Xinzhou Zhu; Tobias Kockmann; Leonie Ringrose
Publié dans: Chromosoma, Numéro 1, 2021, ISSN 0009-5915
Éditeur: 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

Auteurs: Mattia Conte, Ehsan Irani, Andrea M. Chiariello, Alex Abraham, Simona Bianco, Andrea Esposito & Mario Nicodemi
Publié dans: Nature Communications, Numéro 13, 4070, 2022, ISSN 2041-1723
Éditeur: 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

Auteurs: Matteo Mazzocca, Tom Fillot, Alessia Loffreda, Daniela Gnani, Davide Mazza
Publié dans: Biochemical Society Transactions, 2021, ISSN 0300-5127
Éditeur: Portland Press, Ltd.
DOI: 10.1042/bst20200709

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

Auteurs: Kim Sneppen, Leonie Ringrose
Publié dans: Nature Communications, Numéro 10/1, 2019, ISSN 2041-1723
Éditeur: 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

Auteurs: Andrea Hita, Gilles Brocart, Ana Fernandez, Marc Rehmsmeier, Anna Alemany and Sol Schvartzman
Publié dans: BMC Bioinformatics, 2022, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-021-04544-3

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

Auteurs: Nickels, J. F., Della-Rosa, M. E., Goyeneche, I. M., Charlton, S. J., Sneppen, K., & Thon, G.
Publié dans: Cell Reports, Numéro 39(7), 110828, 2022, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2022.110828

Integrating analog and digital modes of gene expression at Arabidopsis FLC

Auteurs: 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
Publié dans: eLife, Numéro 12, e79743, 2023, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.1101/2022.07.04.498694

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