Publications

2022

  • Nickels JF*, Della-Rosa ME*, Miguelez Goyeneche I, Charlton SJ, Sneppen K, Thon G (2022) The transcription factor Atf1 lowers the transition barrier for nucleosome-mediated establishment of heterochromatin. Cell Rep. May 17;39(7):110828.
    doi: 10.1016/j.celrep.2022.110828 (*these authors contributed equally). Pubmed
  • Hita A, Brocart G, Fernandez A, Rehmsmeier M, Alemany A, Schvartzman S (2022)

    MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts. BMC Bioinformatics. Jan 14;23(1):39. doi: 10.1186/s12859-021-04544-3. Pubmed

2021

  • Mazzocca M*, Colombo E*, Callegari A and Mazza D (2021) Transcription factor binding kinetics and transcriptional bursting: What do we really know? Curr Opin Struct Biol. Dec;71:239-248. doi: 10.1016/j.sbi.2021.08.002. Epub 2021 Sep 1. (*these authors equally contributed to this work). Pubmed
  • Steffen PA, Altmutter C, Dworschak E, Junttila S, Gyenesei A, Zhu X, Kockmann T, Ringrose L (2021) 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. Chromosoma. Sep;130(2-3):215-234. doi: 10.1007/s00412-021-00762-z. Epub 2021 Jul 31. Pubmed
  • Mazzocca M, Fillot T, Loffreda A, Gnani D and Mazza D (2021) The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes. Biochem Soc Trans. Jun 30;49(3):1121-1132. doi: 10.1042/BST20200709. Pubmed
  • Nickels JF*, Edwards AK*, Charlton SJ*, Møller Mortensen A, Lykke Hougaard SC, Trusina A, Sneppen K and Thon G (2021) Establishment of heterochromatin in domain-size-dependent bursts. PNAS. Apr 13;118(15):e2022887118.
    doi: 10.1073/pnas.2022887118 (*these authors contributed equally). Pubmed
  • Riba A, Oravecz A, Durik M, Jiménez S, Alunni V, Cerciat M, Jung M, Keime C, Keyes WM and Molina N (2021) Cell cycle gene regulation dynamics revealed by RNA velocity and deep-learning. bioRxiv preprint, version posted March 19. doi: https://doi.org/10.1101/2021.03.17.435887
  • Oliveira GM, Oravecz A,, Kobi D, Maroquenne M, Bystricky K, Sexton T and Molina N (2021) Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes. bioRxiv preprint, version posted March 17. doi: https://doi.org/10.1101/2021.03.16.435699
  • Uzun U, Brown T, Fischl HJ, Angel A and Mellor J (2021) Spt4 Facilitates the Movement of RNA Polymerase II through the +2 Nucleosomal Barrier. bioRxiv preprint, version posted March 4. doi: https://doi.org/10.1101/2021.03.03.433772
  • Chiariello* AM, Bianco* S, Esposito A, Fiorillo L, Conte M, Irani E, Musella F, Abraham A, Prisco A and Nicodemi M (2021) Physical mechanisms of chromatin spatial organization. FEBS J. Feb 14. doi: 10.1111/febs.15762. Online ahead of print
     Pubmed

2020

  • Reinig* J, Ruge* F, Howard M and Ringrose L (2020) A theoretical model of Polycomb/Trithorax action unites stable epigenetic memory and dynamic regulation. Nat Commun. Sep 22;11(1):4782. doi: 10.1038/s41467-020-18507-4.
     Pubmed
  • Zambrano1,2,* S, Loffreda A, Carelli E, Stefanelli G, Colombo F, Bertrand E, Tacchetti C, Agresti A, Bianchi ME, Molina* N and Mazza 2,* D (2020) First responders shape a prompt and sharp NF-κB –mediated transcriptional response to TNF-α. iScience. Sep 4;23(9):101529. doi: 10.1016/j.isci.2020.101529. eCollection 2020 Sep 25. (1 Lead contact, 2 These authors contributed equally, *corresponding authors) Pubmed
  • Zambrano1,2,* S, Loffreda A, Carelli E, Stefanelli G, Colombo F, Bertrand E, Tacchetti C, Agresti A, Bianchi ME, Molina* N and Mazza 2,* D (2020) First responders shape a prompt and sharp NF-κB–mediated transcriptional response to TNF-α. BioRxiv preprint, version posted June 29. (1 Lead contact, 2 These authors contributed equally, *corresponding authors). doi: https://doi.org/10.1101/2020.06.27.174995.

  • Beagrie RA*, Thieme* CJ, Annunziatella* C, Baugher C, Zhang Y, Schueler M, Kramer DCA, Chiariello AM, Bianco S, Kukalev A, Li Y, Kempfer R, Scialdone A,  Welch‡ LR, Nicodemi‡ M and Pombo‡ A (2020) Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C. BioRxiv preprint, version posted July 31. (*joint first authors, ‡ joint corresponding authors).
    doi: https://doi.org/10.1101/2020.07.31.230284.

  • Pacini G, Dunkel I, Mages N, Mutzel V, Timmermann B, Marsico A and Schulz EG (2020) Integrated analysis of Xist upregulation and gene silencing at the onset of random X-chromosome inactivation at high temporal and allelic resolution. bioRxiv preprint, version posted July 21. doi: https://doi.org/10.1101/2020.07.20.211573.

  • Conte M, Fiorillo L, Bianco S, Chiariello AM, Esposito A and Nicodemi M (2020) Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation. Nat Commun. Jul 3;11(1):3289.
    doi: 10.1038/s41467-020-17141-4. Pubmed
  • Feltham JE, Xi S, Murray SC, Wouters M, Urdiain-Arraiza J, Heilig R, George C, Townley AF, Roberts E, Kessler BM, Liberatori S, Charles PD, Angel A, Fischer R and Mellor J (2020) Transcriptional changes are regulated by metabolic pathway dynamics but decoupled from protein levels. bioRxiv preprint, version posted June 10.
    doi: https://doi.org/10.1101/833921.
  • Bianco S, Chiariello AM, Conte M, Esposito A, Fiorillo L, Musella F and Nicodemi M (2020) Computational approaches from polymer physics to investigate chromatin folding. Curr Opin Cell Biol. Jun;64:10-17. doi: 10.1016/j.ceb.2020.01.002. Pubmed
  • Conte M, Fiorillo L, Bianco S, Chiariello AM, Esposito A and Nicodemi M (2020) Chromatin folding variability across single-cells results from state degeneracy in phase-separation. bioRxiv preprint, version posted May 16.
    doi: https://doi.org/10.1101/2020.05.16.099275. 

  • Mutzel V and  Schulz EG (2020) Dosage Sensing, Threshold Responses, and Epigenetic Memory: A Systems Biology Perspective on Random X-Chromosome Inactivation. Bioessays. Apr;42(4):e1900163. doi: 10.1002/bies.201900163. Pubmed

  • Fiorillo* L, Musella* F, Kempfer R, Chiariello AM, Bianco S, Kukalev A, Irastorza-Azcarate I, Esposito A, Conte M, Prisco A, Pombo A and Nicodemi M (2020) Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin. BioRxiv preprint, version posted April 25. (*these authors contributed equally).
    doi: https://doi.org/10.1101/2020.04.24.059915.

2019

  • Barros de Andrade E Sousa L, Jonkers I, Syx L, Dunkel I, Chaumeil J, Picard C, Foret B, Chen CJ, Lis* JT, Heard* E, Schulz* EG and Marsico* A (2019) Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features. Genome Res. Jul;29(7):1087-1099. doi: 10.1101/gr.245027.118.
    Epub 2019 Jun 7. (* corresponding authors) Pubmed
  • Dellino GI, Palluzzi F, Chiariello AM, Piccioni R, Bianco S, Furia L, De Conti G, Bouwman BAM, Melloni G, Guido D, Giacò L, Luzi L, Cittaro D, Faretta M, Nicodemi M, Crosetto N and Pelicci PG (2019) Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations. Nat Genet. Jun;51(6):1011-1023. doi: 10.1038/s41588-019-0421-z. Epub 2019 May 20. Pubmed
  • Mutzel V, Okamoto I, Dunkel I, Saitou M, Giorgetti L, Heard E and Schulz EG (2019) A symmetric toggle switch explains the onset of random X inactivation in different mammals. Nat Struct Mol Biol. May;26(5):350-360.
    doi: 10.1038/s41594-019-0214-1. Epub 2019 Apr 8. Pubmed
  • Sneppen K and Ringrose L (2019) Theoretical Analysis of Polycomb-Trithorax Systems Predicts That Poised Chromatin Is Bistable and Not Bivalent. Nat Commun.
    May 13;10(1):2133.doi: 10.1038/s41467-019-10130-2. Pubmed

2018

  • Brown T, Howe FS, Murray SC, Wouters M, Lorenz P, Seward E, Rata S, Angel A and  Mellor J (2018) Antisense transcription-dependent chromatin signature modulates sense transcript dynamics. Mol Syst Biol. Feb 12;14(2):e8007.
    doi: 10.15252/msb.20178007. Pubmed