Tissue-Specific Transcription Footprinting Using NoI Dam (RAPID) in .
Fiche publication
Date publication
octobre 2020
Journal
Genetics
Auteurs
Membres identifiés du Cancéropôle Est :
Dr JARRIAULT Sophie
Tous les auteurs :
Gómez-Saldivar G, Osuna-Luque J, Semple JI, Glauser DA, Jarriault S, Meister P
Lien Pubmed
Résumé
Differential gene expression across cell types underlies the development and cell physiology in multicellular organisms. is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates, however, to the difficulty to obtain comprehensive tissue-specific gene transcription data, since available methods are still challenging to execute and/or require large worm populations. Here, we introduce the Nol Dam (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit in order to create transcriptional footprints methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, sorted embryonic blastomeres and in different tissues from intact young adults by driving Dam fusion expression tissue-specifically. We obtained meaningful transcriptional footprints in line with RNA-seq studies in whole animals or specific tissues. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX neuroendocrine cells, representing 0.2% of the somatic cell content of the animals. We identified 2362 candidate genes with putatively active transcription in XXX cells, among which the few known markers for these cells. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were expressed in XXX and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of polymerase footprints in specific tissues of without the need for cell sorting or RNA tagging.
Mots clés
C. elegans, DNA methyltransferase identification, RNA polymerase footprinting, tissue-specific gene expression
Référence
Genetics. 2020 Oct 9;: