Title : "STING is a central rheostat of metabolic and inflammatory homeostasis" 
Contact : etienne.schwob@igmm.cnrs.fr

Title : "SALL4 controls cell fate in response to DNA base composition "
Contact : jean-christophe.andrau@igmm.cnrs.fr
 
Mammalian genomes are divided into large domains characterised by distinct compositions of A/T versus G/C nucleotides. While these genomic features are evolutionarily conserved, their functional relevance remains unknown. We identified SALL4 as a top hit in a DNA-pulldown/mass spectrometry screen for AT-binding proteins in mouse embryonic stem cells (ESCs). We uncovered a specific zinc-finger cluster responsible for binding to short AT-rich motifs (ZFC4) and hypothesised that this domain could mediate regulation of gene expression dependent on DNA base composition. Mutation of ZFC4, but not other zinc-fingers, drastically reduced SALL4 genome occupancy in ESCs. In agreement with our predictions, RNA-seq analyses revealed that SALL4 represses the expression of differentiation-associated genes in proportion to the AT-content across the body of these genes. Importantly, ZFC4 mutation mimicked defects seen in Sall4knockout, including abnormal neuronal differentiation and early embryonic lethality. This work provided the first demonstration that a protein (SALL4) can control gene expression and cell fate by reading DNA base composition. Our current efforts aim at validating our working model, in which SALL4 represses the expression of AT-rich genes by recruiting the NuRD co-repressor complex. 

Title : "Dynamics of Histone and RNA Polymerase II Modifications in Living Cells"
Contact : mounia.lagha@igmm.cnrs.fr
 

Posttranslationalmodifications of histones and RNA polymerase II (RNAP2) play a critical role ingene regulation during development and differentiation. To understand how genesare regulated in chromatin context in living cells, we have developedmodification-specific antibody-based fluorescent probes, such as dye-labeledFabs and fluorescent protein-tagged single-chain variable fragments. Usingthese probes, we have revealed the critical role of H3K27 acetylation intranscription activation in response to external and internal stimuli,including steroid hormone stimulation, heat shock stress, and zygotic genomeactivation. We have also detected the different behavior of transcriptioninitiation and elongation foci using RNAP2 Ser5ph- and Ser2ph-specific probes.In addition, we have also developed low-input epigenome profiling techniques,including a single-cell multi-target analysis. I will present our recent datafor spatiotemporal dynamics of chromatin and transcription.

References

Ohishi etal. STREAMING-tag system reveals spatiotemporal relationships betweentranscriptional regulatory factors and transcriptional activity. bioRxiv 2022.01.06.472721.

Kimura andSato (2022) Imaging transcription elongation dynamics by new technologiesunveils the organization of initiation and elongation in transcriptionfactories. Curr Opin Cell Biol 74, 71-79.

Uchino etal. (2022) Live imaging of transcription sites using an elongating RNA polymeraseII–specific probe. J Cell Biol 221, e202104134.

Tjalsma etal. (2021) H4K20me1 and H3K27me3 are concurrently loaded onto the inactive Xchromosome but dispensable for inducing gene silencing. EMBO Rep 22, e51989.

Sato et al.(2019) Histone H3K27 acetylation precedes active transcription during zebrafishzygotic genome activation as revealed by live-cell analysis. Development 146,dev179127.

Harada etal. (2018) A chromatin integration labelling method enables epigenomicprofiling with lower input. Nat Cell Biol 21, 287-296.

Modeling microvillus atrophy andregeneration: from C. elegans and mouse intestinal organoidsto patients

Intestinal microvillus atrophy is amajor cause of enteropathies such as idiopathic or congenital diarrhea,that are often associated with severe morbidity. It can be caused bygenetic disorders, inflammatory diseases such as Crohn’s andceliac diseases, or pathogens. In particular genetic microvillus atrophycan be triggered by mutations in MYO5B, STX3 or MUNC18.2 whichalter epithelial polarity by affecting apical trafficking inintestinal epithelial cells.

Using live super-resolution microscopy and endogenouslyexpressed probes we first described microvillus growth and dynamicsthroughout embryonic and larval development in C. elegans. We nextestablished a genetic worm model of an inherited disorder leading tomicrovillus atrophy by depleting the V0 domain of the V-ATPase. Wethen transposed this model to mouse intestinal organoids where italso triggers a very severe microvillus atrophy. We are now integratingthe function of this new factor in the broader framework of apical traffickingand inherited microvillus atrophy.

By combining a genetically tractable model,intestinal organoids and observations in patients, we aim to propose newtherapeutic options to treat microvillus atrophy and trigger theirregeneration. Indeed, while regeneration is essential for life, it ismostly investigated at the tissue or organ level; microvilli regrowthprovides a unique model for subcellular regeneration which could be usefulto treat not only genetic disorders but also all the other causes ofmicrovillus atrophy.
 
Selected publications
Bidaud-Meynard A, Demouchy F, Nicolle O, Pacquelet A, Suman SK, Plancke C, Robin F, Michaux G.
High resolution dynamic mapping of the C. elegans intestinal brush border.
2021, Development, 148, dev200029.

Bidaud-Meynard A, Nicolle O, Heck M, Michaux G.
V0-ATPase-dependent apical trafficking maintains the polarity of the intestinal absorptive membrane.
2019, Development, 146, dev174508.

Mosa MH, Nicolle O, Maschalidi S, Sepulveda FE, Bidaud-Meynard A, Menche C, Michels BE, Michaux G, de Saint Basile G and Farin HF.
Dynamic formation of microvillus inclusions during enterocyte differentiation in Munc18-2 deficient intestinal organoids.
2018, Cell Mol Gastroenterol Hepatol, 6, 477-493.

Michaux G, Massey-Harroche D, Nicolle O, Rabant M, Brousse N, Goulet O, Le Bivic A, Ruemmele FM.
The localisation of the apical Par/Cdc42 polarity module is specifically affected in microvillus inclusion disease.
2016, Biology of the Cell, 108, 19-28.

Shafaq-Zadah M, Brocard L, Solari F, Michaux G.
AP-1 is required for the maintenance of apico-basal polarity in the C. elegans intestine.
2012, Development, 139, 2061-2070. 
Contact claude.prigent@crbm.cnrs.fr