Fragile Nucleosome Journal Club
The Fragile Nucleosome Journal Club is a new project of the Fragile Nucleosome community where students and postdocs interested in chromatin and gene regulation can actively discuss recent papers in concordance with peers from around the world. The format of the Fragile Nucleosome Journal Club is very different from the Fragile Nucleosome Seminars. Participants will discuss a preprint or recent paper helped by an invited expert in the field. Unlike our seminars, the journal club will not be recorded and published to the public, allowing all participants to express their opinions freely. For this reason, we recommend any authors/members associated with the group of the corresponding author, to kindly not sign up when your paper is used for discussion 🙂
From 2021, we will gather the points discussed in the Journal Club and share it with the authors to help in their review process(following obtaining permission from the Expert of the respective journal club).
When: Thursdays, 9am Pacific time (5pm UK, 6pm Central Europe). The signup is open from Thursday the prior week.
Organisers: Jei Diwakar, Ulduz Afshar, Sandipan Brahma, Pallabi Mustafi, Nathan Gamarra with help from the seminars organisers Christine Cucinotta, Hanneke Vlaming, Pravrutha Raman and Vladimir Teif.
Proposed format:
Participants will discuss both positives and negatives of the paper.
We would like participants to introduce the figures to their peers prior to in depth discussion.
The trainee-led discussion will last for approximately 50 mins.
The Expert will then help to put the paper in context of the field.
Note for experts:
If any experts are interested in helping with one of these journal club sessions in the future, please email [email protected] (Senior Postdocs also encouraged to get in touch)
Upcoming Events
17
Mar 2022
Invited Expert – Ana Pombo
Paper: ‘Inversion of a topological domain leads to restricted changes in its gene expression and affects inter-domain communication’
Galupa et al. bioRxiv Jan 2022
10:00am (Pacific time), 6pm CET (US Daylight Saving)
MDC Berlin, Germany
28
April 2022
Invited Expert – Edda Schulz
Paper: TBC
9:00am (Pacific time)
MPI for Molecular Genetics, Germany
Past Events
23
June 2020
Invited Expert – Boyan Bonev
Paper: ‘Detailed temporal dissection of an enhancer cluster reveals two distinct roles for individual elements’
Thomas et al. bioRxiv, May 2020 https://doi.org/10.1101/2020.05.06.080564
9:00am (Pacific time)
Munich, Germany
30
June 2020
Invited Expert – Giacomo Cavalli
Paper: ‘CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response’
Stik et al. Nature Genetics June 2020 https://doi.org/10.1038/s41588-020-0643-0
9:00am (Pacific time)
CNRS, France
9
July 2020
Invited Expert: Alan Underhill
Paper: ‘An embryonic stem cell-specific heterochromatin state allows core histone exchange in the absence of DNA accessibility’
Navarro et al. bioRxiv, May 2020 https://www.biorxiv.org/content/10.1101/2020.05.22.110742v2
9:00am (Pacific time)
University of Alberta, Canada
16
July 2020
Invited Expert: Vijay Ramani
Paper: ‘Single molecule occupancy patterns of transcription factors reveal determinants of cooperative binding in vivo’
et al. bioRxiv, June 2020 https://doi.org/10.1101/2020.06.29.167155
9:00am (Pacific time)
USCF, USA
23
July 2020
Invited Expert: Stefan Schoenfelder
Paper: ‘Spatial Organisation of Transcribed Eukaryotic Genes’
Leidescher et al. bioRxiv, May 2020 https://www.biorxiv.org/content/10.1101/2020.05.20.106591v1
9:00am (Pacific time)
Babraham Institute, UK
30
July 2020
Invited Expert: Serena Sanulli
Paper: ‘Phase separation induced by cohesin SMC protein complexes’
Ryu et al. bioRxiv June 2020 https://doi.org/10.1101/2020.06.13.149716
9:00am (Pacific time)
Stanford University, USA
6
August 2020
Invited Expert – Maria Elena Torres-Padilla
Paper: ‘Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA’
Zhang et al. Mol Cell, June 2020
https://doi.org/10.1016/j.molcel.2020.06.001
9:00am (Pacific time)
Helmholtz Zentrum Munchen, Germany
13
August 2020
Invited Expert РEva H̦rmanseder
Paper: ‘Epigenetic regulations follow cell cycle progression during differentiation of human pluripotent stem cells’
Madrigal et al. bioRxiv, June 2020 https://doi.org/10.1101/2020.06.26.173211
9:00am (Pacific time)
Helmholtz Zentrum Munchen, Germany
20
August 2020
Invited Expert- Robert Illingworth
Paper: ‘Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation’
Kraft et al. bioRxiv, July 2020
https://doi.org/10.1101/2020.07.27.223438
9:00am (Pacific time)
University of Edinburgh, UK
3
September 2020
Invited Expert – Tolga Emre
Paper: ”H3 K27M and EZHIP impede H3K27-methylation spreading by inhibiting allosterically stimulated PRC2′
Jain et al. bioRxiv, August 2020 https://doi.org/10.1101/2020.08.05.236737
9:00am (Pacific time)
Boğaziçi University, Istanbul
17
September 2020
Invited Expert- Lothar Schermelleh
Paper: ‘RNA promotes the formation of spatial compartments in the nucleus’
Quinodoz et al. bioRxiv, August 2020
https://doi.org/10.1101/2020.08.25.267435
9:00am (Pacific time)
University of Oxford, UK
1
October 2020
Invited Expert – Argyis Papantonis
Paper: ‘ Homeotic Regulation of Olfactory Receptor Choice via NFI-dependent Heterochromatic Silencing and Genomic Compartmentalization ‘
Bashkirova et al. bioRxiv, August 2020 https://doi.org/10.1101/2020.08.30.274035
9:00am (Pacific time)
University of Göttingen, Germany
15
October 2020
Invited Expert – Sheila Teves
Paper: ‘Nanobody-mediated control of gene expression and epigenetic memory’
Van et al. bioRxiv, September 2020 https://doi.org/10.1101/2020.09.09.290015
9:00am (Pacific time)
University of British Columbia, Canada
29
October 2020
Invited Expert – Hamed Najafabadi
Paper: ‘Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors’
Cusack et al. Genome Research, August 2020
https://genome.cshlp.org/content/30/10/1393.short?rss=1
9:00am (Pacific time)
McGill University, Canada
12
November 2020
Invited Expert – Michelle Percharde
Paper: ‘Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency’
Mehdipour et al. Nature, October 2020
https://www.nature.com/articles/s41586-020-2844-1
9:00am (Pacific time)
Imperial College London/ MRC LMS, UK
26
November 2020
Invited Expert – Tuncay Baubec
Paper : ‘High-throughput discovery and characterization of human transcriptional effectors’
Tycko et al. bioRxiv September 2020
https://doi.org/10.1101/2020.09.09.288324
9:00am (Pacific time)
University of Zurich, Switzerland
14
January 2021
Invited Expert – Maxim Greenberg
Paper: ‘De novo DNA methylation suppresses aberrant fate determination during pluripotency transition’
Kinoshita et al. bioRxiv, December 2020
https://doi.org/10.1101/2020.12.20.423404
9:00am (Pacific time)
Institut Jacques Monod, France
21
January 2021
Invited Expert – Anders Sejr Hansen
Paper : ‘Spatio-Temporal Coordination of Transcription Preinitiation Complex Assembly in Live Cells’
Nguyen et al. bioRxiv, December 2020
https://doi.org/10.1101/2020.12.30.424853
9:00am (Pacific time)
MIT, USA
4
February 2021
Invited Expert – Gabriella Ficz
Paper: ‘Multi-omic rejuvenation of human cells by maturation phase transient reprogramming’
Gill et al. bioRxiv, January 2021
https://doi.org/10.1101/2021.01.15.426786
9:00am (Pacific time)
Barts Cancer Institute, UK
18
February 2021
Invited Expert – Raffaella Santoro
Paper : ‘B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells’
Yu et al. bioRxiv, Jan 2021
https://doi.org/10.1101/2021.01.03.425167
9:00am (Pacific time)
University of Zurich, Switzerland
4
March 2021
Invited Expert – Tamer Onder
Paper: ‘Permissive epigenomes endow reprogramming competence to transcriptional regulators’
Kim et al. Nature Chemical Biology, Aug 2020
https://doi.org/10.1038/s41589-020-0618-6
9:00am (Pacific time)
Koç Üniversitesi, Turkey
18
March 2021
Invited Expert – Jesse Engreitz
Paper : ‘Genomic environments scale the activities of diverse core promoter’
Hong et al. bioRxiv March 2021
https://doi.org/10.1101/2021.03.08.434469
9:00am (Pacific time)
Stanford University, USA
15
April 2021
Thomas Schwarz-Romond- Special Session
‘Adept manuscript reading – an ‘ask anything’ session to more efficiently dissect preprints!‘
Previous Senior Scientific Editor at EMBO
Current Director of Operations at Helmholtz Pioneer Campus
9:00am (Pacific time)
Munich, Germany
29
April 2021
Invited Expert – Arnaud Krebs
Paper: ‘Sequence determinants of human gene regulatory elements’
Sahu et al. bioRxiv, March 2021
https://doi.org/10.1101/2021.03.18.435942
9:00am (Pacific time)
EMBl Heidelberg, Germany
13
May 2021
Invited Expert – Kami Ahmad
Paper: ‘PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency’
Dobrinic et al. bioRxiv Oct 2020 https://doi.org/10.1101/2020.10.09.333294
9:00am (Pacific time)
Fred Hutch, USA
27
May 2021
Invited Expert – Luca Giorgetti
Paper: ‘Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer’
Rouco et al. bioRxiv, March 2021
https://doi.org/10.1101/2021.03.10.434611
9:00am (Pacific time)
FMI, Switzerland
10
June 2021
Invited Expert – Tineke Lenstra
Paper: ‘Nonlinear control of transcription through enhancer-promoter interactions’
Zuin et al. bioRxiv, April 2021
https://doi.org/10.1101/2021.04.22.440891
9:00am (Pacific time)
NCI , Netherlands
24
June 2021
Invited Expert – Elphege Nora
Paper: Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at the Xist locus’
Gjaltema et al. bioRxiv, March 2021
https://doi.org/10.1101/2021.03.29.437476
9:00am (Pacific time)
UCSF, USA
08
July 2021
Invited Expert – Maria Christophorou
Paper: ‘Signals Secreted by Infection Induce Transcriptional and Epigenetic Changes in Neurons’
Tedford et al. bioRxiv, Nov 2020
https://doi.org/10.1101/2020.11.26.399345
9:00am (Pacific time)
Babraham Institute , UK
22
July 2021
Invited Expert РGenevi̬ve Almouzni
Paper: ‘Horizontal Transfer of Histone H3 by Mammalian Cells’
Sulkowski et al. bioRxiv June 2021
https://doi.org/10.1101/2021.06.30.450524
9:00am (Pacific time)
Institut Curie, France
2
Sept 2021
Invited Expert – Benoit Bruneau
Paper: ‘Sequential in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster’
Amandio et al. bioRxiv, Aug 2020
https://doi.org/10.1101/2021.08.13.456193
9:00am (Pacific time)
Gladstone Institute, USA
23
Sept 2021
Invited Expert – Ezgi Karaca
Paper: ‘Structures and implications of TBP–nucleosome complexes’
Wang et al. PNAS July 2021
https://doi.org/10.1073/pnas.2108859118
9:00am (Pacific time)
Izmir Biomedicine and Genome Center, Turkey
30
Sept 2021
Invited Expert – Payel Sen
Paper: ‘Reversible reprogramming of cardiomyocytes to a fetal state drives heart regeneration in mice’
Chen et al. Science Sept 2021
https://www.science.org/doi/10.1126/science.abg5159
9:00am (Pacific time)
NCI, USA
14
Oct 2021
Invited Expert – Axel Imhof
Paper: ‘Centromere formation remodels chromatin fibre structure’
Naughton et al. bioRxiv Aug 2021
https://doi.org/10.1101/2021.08.01.454615
9:00am (Pacific time)
BMC Munich, Germany
11
Nov 2021
Invited Expert – Effie Apostolou
Paper: ‘Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1’
Hsieh et al. bioRxiv July 2021
https://doi.org/10.1101/2021.07.14.452365
9:00am (Pacific time)
Cornell , USA
25
Nov 2021
Invited Expert – Julie Ahringer
Paper: ‘DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers’
de Almeida et al. bioRxiv Oct 2021
https://doi.org/10.1101/2021.10.05.463203
9:00am (Pacific time)
Gurdon Institute, UK
9
Dec 2021
Invited Expert – Nick Gilbert
Paper: ‘Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH’
Hung et al. bioRxiv Nov 2021
https://doi.org/10.1101/2021.11.28.470285
9:00am (Pacific time)
MRC Edinburgh , UK
20
Jan 2022
Invited Expert – Steven Hahn
Paper: ‘The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication’
Karr et al. Gene & Dev Jan 2022 http://www.genesdev.org/cgi/doi/10.1101/gad.349160.121.
9:00am (Pacific time)
CNRS, France
3
Mar 2022
Invited Expert – Brian Hendrich
Paper: ‘Transcriptional regulation and chromatin architecture maintenance are decoupled modular function at the Sox2 locus’
Taylor,et al. bioRxiv, Feb 2022
https://doi.org/10.1101/2022.02.09.479674
9:00am (Pacific time)
MRC Cambridge Stem Cell Institute, UK