Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans

Gomez-Saldivar, Georgina; Osuna-Luque, Jaime; Semple, Jennifer I.; Glauser, Dominique A.; Jarriault, Sophie; Meister, Peter (2020). Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics, 216(4), pp. 931-945. Genetics Society of America 10.1534/genetics.120.303774

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Differential gene expression across cell types underlies development and cell physiology in multicellular organisms. Caenorhabditis elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates 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 RNA Polymerase DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit to create transcriptional footprints via methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, in sorted embryonic blastomeres and in different tissues from intact young adults by driving tissue-specific Dam fusion expression. We obtained meaningful transcriptional footprints in line with RNA-sequencing (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 3901 candidate genes with putatively active transcription in XXX cells, including the few previously 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 cells and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of RNA polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Cell Biology

UniBE Contributor:

Osuna Luque, Jaime; Semple, Jennifer Isabel and Meister, Pierre

Subjects:

500 Science > 570 Life sciences; biology

ISSN:

0016-6731

Publisher:

Genetics Society of America

Funders:

[4] Swiss National Science Foundation ; [18] European Research Council ; [152] European Cooperation in Science and Technology

Language:

English

Submitter:

Pierre Meister

Date Deposited:

08 Jan 2021 16:31

Last Modified:

08 Jan 2021 16:31

Publisher DOI:

10.1534/genetics.120.303774

PubMed ID:

33037050

BORIS DOI:

10.48350/148901

URI:

https://boris.unibe.ch/id/eprint/148901

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