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Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Blastomeres]

ABSTRACT: Gene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize for the widely used model system C. elegans. By using a new method based on in vivo covalent modification of DNA by RNA polymerases, we determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. Additionally, this method can be fully performed in a single laboratory by using third generation sequencing methods (ONT).

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE157415 | GEO | 2020/10/28

REPOSITORIES: GEO

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Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Young adult]

Project description:Gene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize for the widely used model system C. elegans. By using a new method based on in vivo covalent modification of DNA by RNA polymerases, we determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. Additionally, this method can be fully performed in a single laboratory by using third generation sequencing methods (ONT).

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Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Blastomeres]

Project description:Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Blastomeres]

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Young adult]

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Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in <i>Caenorhabditis elegans</i>.

Project description: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.

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Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans

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