The Ghavi-Helm Laboratory

Updated publications on PubMed

Alberti B, Vincent S, Stévant I, Lajoignie D, Tarayre H, Villoutreix P, Ghavi-Helm Y. Spatial reconstruction of single-cell enhancer activity in a multicellular organism. BioRxiv. https://doi.org/10.1101/2024.10.02.616294

 Nemoz-Billet L, Balland M, Gilquin L, Gillet B, Stévant I, Guillon E, Hughes S, Carpentier G, Vaganay E, Sohm F, Misiak V, Gonzalez-Melo M-J, Koch M, Ghavi-Helm Y, Bretaud S, Ruggiero F. ­­­­­­Dual topologies of myotomal collagen XV and tenascin C act in concert to guide and shape developing motor axons. PNAS. https://www.pnas.org/doi/10.1073/pnas.2314588121

Pollex T, Marco-Ferreres R, Ciglar L, Ghavi-Helm Y, Rabinowitz A, Rodriguez Viales R, Schaub C, Jankowski A, Girardot C, Furlong E. Chromatin gene-gene loops support the cross-regulation of genes with related function. Mol. Cell. https://doi-org.insb.bib.cnrs.fr/10.1016/j.molcel.2023.12.023

Balasubramanian D*, Borges Pinto P*, Grasso A*, Vincent S, Tarayre H, Lajoignie D, Ghavi-Helm Y. Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries. NAR. https://t.co/LtqJyX1RNV

Zhang J, Le Gras S, Pouxvielh K, Faure F, Fallone L, Kern N, Moreews M, Mathieu AL, Schneider R, Marliac Q, Jung M, Berton A, Hayek S, Vidalain PO, Marçais A, Dodard G, Dejean A, Brossay L, Ghavi-Helm Y, Walzer T. Sequential actions of EOMES and T-BET promote stepwise maturation of natural killer cells. Nat Commun. 2021 Sep 14;12(1):5446. doi: 10.1038/s41467-021-25758-2.

Akhtar J, Renaud Y, Albrecht S, Ghavi-Helm Y, Roignant JY, Silies M, Junion G. m6A RNA methylation regulates promoter proximal pausing of RNA Polymerase II. Mol Cell. 2021 Aug 19;81(16):3356-3367.e6. doi: 10.1016/j.molcel.2021.06.023.

Moretti C*, Stévant I*, Ghavi-Helm Y. 3D genome organisation in Drosophila. Brief Funct Genomics. 2020 Mar 23;19(2):92-100. doi: 10.1093/bfgp/elz029. (Review)

Ghavi-Helm Y. Functional consequences of chromosomal rearrangements on gene

expression: not so deleterious after all? J Mol Biol. 2020 doi: 10.1016/j.jmb.2019.09.010. (Review) Link

Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel J, Furlong EEM. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nature Genetics. 2019. doi:10.1038/s41588-019-0462-3

Schauer T, Ghavi-Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong EEM, Becker PB. Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. EMBO Rep. 2017 Aug 9. pii: e201744292.

Erceg J*, Pakozdi T*, Marco-Ferreres R*, Ghavi-Helm Y, Girardot C, Bracken AP, and Furlong EEM. Dual functionality of cis-regulatory elements as developmental enhancers and polycomb response elements. Genes and Development. 2017 Mar 15;31(6):590-602.

Seyres D, Ghavi-Helm Y, Junion G, Taghli-Lamalhem O, Guichard C, Roder L, Girardot C, Furlong EE, Perrin L. Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network. Development. 2016 Dec 1;143(23):4533-4542.

Ghavi-Helm Y, Zhao B, Furlong EE. Chromatin immunoprecipitation for analyzing transcription factor binding and histone modifications in Drosophila. Methods in Molecular Biology. 2016;1478:263-277.

Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W. FourCSeq: analysis of 4C sequencing data. Bioinformatics. 2015 Oct 1;31(19):3085-91.

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. Enhancer loops appear stable during development and are associated with paused polymerase. Nature. 2014 Aug 7;512(7512):96-100.

Pinskaya M, Ghavi-Helm Y, Mariotte-Labarre S, Morillon A, Soutourina J, Werner M. PHD and TFIIS-like domains of the Bye1 transcription factor determine its multivalent genomic distribution. PLoS One. 2014 Jul 16;9(7):e102464.

Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE. Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nature Genetics. 2012 Jan 8;44(2):148-56.

Carrière L, Graziani S, Alibert O, Ghavi-Helm Y, Boussouar F, Humbertclaude H, Jounier S, Aude JC, Keime C, Murvai J, Foglio M, Gut M, Gut I, Lathrop M, Soutourina J, Gérard M, Werner M. Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells. Nucleic Acids Research. 2012 Jan;40(1):270-83.

Ghavi-Helm Y, Furlong EE. Analyzing transcription factor occupancy during embryo development using ChIP-seq. Methods in Molecular Biology. 2012;786:229-45.

Ghavi-Helm Y, Michaut M, Acker J, Aude J-C, Thuriaux P, Werner M, Soutourina J. Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription. Genes and Development. 2008 Jul 15;22(14):1934-47.

Esnault C, Ghavi-Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, Holstege F and Werner M. Mediator-dependent recruitment of TFIIH modules in preinitiation complex. Molecular Cell. 2008 Aug 8;31(3):337-46.

Kwapisz M, Wery M, Després D, Ghavi-Helm Y, Soutourina J, Thuriaux P and Lacroute F. Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways. The EMBO Journal. 2008 Sep 17;27(18):2411-21.

Cazalet C, Jarraud S, Ghavi-Helm Y, Kunst F, Glaser P, Etienne J, Buchrieser C. Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species. Genome Research. 2008 Mar;18(3):431-41.