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My research activities

 

My research interests lie in the field of chromatin biology and the epigenetic regulation of nuclear functions in mammals. During my PhD-thesis (2008 – 2012, ENS de Lyon, France), I studied the links between chromatin topology and DNA replication (1, 2). During my post-doc (2012 – 2016, Oxford, UK), I made use of a genetic loss-of-function screen in mouse embryonic stem cells to identify and characterize novel factors required for X-chromosome inactivation (3-5).

In September 2016, I was recruited as a Lecturer by the Paris-Sud / Paris-Saclay University and joined the Noordermeer lab (I2BC, Gif-sur-Yvette, France). I now study the contribution of the 3D-genome organization in the mono-allelic expression of genes subjected to genomic imprinting. A first preprint of our work is now hosted on BioRxiv (6).

 

Genomic imprinting -- Introduction

Genomic imprinting is a physiological process in mammals whereby the expression of an allele depends on its parental origin (7). The mono-allelic expression is largely determined by differentially methylation regions (DMR) that carry germline-acquired allelic DNA methylation (8). The Igf2 – H19 and Dlk1 – Dio3 domains both contain allele-specific CTCF binding site at the DMR or close to the DMR (9, 10). CTCF being one of the key 3D-genome organizers in mammals, I am combining different genomics-based approaches to comprehend the functional importance of the allelic chromatin 3D-organization for correct imprinting.

Dlk1-Dio3 and CTCF
Figure -- CTCF binding sites within the Dlk1-Dio3 domain, as determined by ChIP-seq in mono-parental mouse embryonic stem cells.

 

Genomic imprinting -- Our work

Using 4C-seq, our work demonstrates that the two alleles of the Igf2 – H19 and Dlk1 – Dio3 domains have pronouncedly different sub-TAD organization, due to the presence of maternal-specific CTCF binding sites that redistribute the 3D-contacts. The definite 3D-organization of the maternal allele is essential to prevent the activation of the paternally-expressed genes from the maternal chromosome. Altogether, this highlights the importance of allele-specific 3D domain organization to ensure correct mono-allelic expression. A preprint of this work, in collaboration with the lab of Robert Feil, is now hosted on BioRxiv (6).

Dlk1-Dio3 and 4C-seq
Figure -- 4C-seq profiles within the Dlk1-Dio3 domain, using the the main DMR of the locus (IGDMR) as a viewpoint. The ratio maternal/paternal is provided in-between. The CTCF Chip-seq signal is indicated below the 4C profiles. Coordinates are based on mm10.

 

Collaboration

This work is done in collaboration with the lab of Robert Feil.

 

Selected References

  • 1. Baker,A., Audit,B., Chen,C.-L., Moindrot,B., Leleu,A., Guilbaud,G., Rappailles,A., Vaillant,C., Goldar,A., Mongelard,F., et al. (2012) Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines. PLoS Comput Biol, 8, e1002443.
  • 2. Moindrot,B., Audit,B., Klous,P., Baker,A., Thermes,C., De Laat,W., Bouvet,P., Mongelard,F. and Arneodo,A. (2012) 3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res., 40, 9470–9481.
  • 3. Moindrot,B., Cerase,A., Coker,H., Masui,O., Grijzenhout,A., Pintacuda,G., Schermelleh,L., Nesterova,T.B. and Brockdorff,N. (2015) A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing. Cell Rep, 12, 562–572.
  • 4. Pintacuda,G., Wei,G., Roustan,C., Kirmizitas,B.A., Solcan,N., Cerase,A., Castello,A., Mohammed,S., Moindrot,B., Nesterova,T.B., et al. (2017) hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing. Mol. Cell, 68, 955–969.e10.
  • 5. Nesterova,T.B., Wei,G., Coker,H., Pintacuda,G., Bowness,J.S., Zhang,T., Almeida,M., Bloechl,B., Moindrot,B., Carter,E.J., et al. (2019) Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation. Nat Commun, 10, 3129.
  • 6. Llères,D., Moindrot,B., Pathak,R., Piras,V., Matelot,M., Pignard,B., Marchand,A., Poncelet,M., Perrin,A., Tellier,V., et al. (2019) CTCF controls imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains by modulating allele-specific sub-TAD structure. bioRxiv.
  • 7. Ferguson-Smith,A.C. (2011) Genomic imprinting: the emergence of an epigenetic paradigm. Nat. Rev. Genet., 12, 565–575.
  • 8. Kelsey,G. and Feil,R. (2013) New insights into establishment and maintenance of DNA methylation imprints in mammals. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 368, 20110336.
  • 9. Bell,A.C. and Felsenfeld,G. (2000) Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature, 405, 482–485.
  • 10. Rosa,A.L., Wu,Y.-Q., Kwabi-Addo,B., Coveler,K.J., Reid Sutton,V. and Shaffer,L.G. (2005) Allele-specific methylation of a functional CTCF binding site upstream of MEG3 in the human imprinted domain of 14q32. Chromosome Res., 13, 809–818.


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