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 post feedback on the preprint on meno.science for the benefit of the authors (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 CucinottaHanneke 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

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: TBC

9:00am (Pacific time)

NCI, USA

14

Oct 2021

Invited Expert – Axel Imhof

Paper: TBC

9:00am (Pacific time)

BMC Munich, Germany

11

Nov 2021

Invited Expert – Effie Apostolou

Paper: TBC

9:00am (Pacific time)

Cornell , USA

25

Nov 2021

Invited Expert – Julie Ahringer

Paper: TBC

9:00am (Pacific time)

Gurdon Institute, UK

9

Dec 2021

Invited Expert – Nick Gilbert

Paper: TBC

9:00am (Pacific time)

MRC Edinburgh , UK

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’

Sönmezer 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