primiReference: a reference for analysis of primary-microRNA expression in single-nucleus sequencing data

Elias, Amy E.; Nuñez, Thomas A.; Kun, Bianca; Kreiling, Jill A.

doi:10.1016/j.jgg.2022.10.003

Cited by 2 publications

(2 citation statements)

References 81 publications

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“…In control cells that express Drosha protein, we mainly detect cleaved transcripts (Figure 4A, above). This is consistent with previous observations that cleaved pri-miRNAs remain in the chromatin for some time after processing (Conrad et al 2014), and also pri-miRNAs have previously been reported in sequencing of single nuclei (Elias et al 2023), where they are located. The paucity of full-length pri-miRNAs in the control cells further suggests that pri-miRNA are cleaved relatively fast after being transcribed in mouse embryonic stem cells.…”

Section: Resultssupporting

confidence: 93%

Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells

Tarbier,

Mackowiak,

Sekar

et al. 2024

Preprint

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MicroRNAs are small RNA molecules that can repress the expression of protein coding genes post-transcriptionally. Previous studies have shown that microRNAs can also have alternative functions including target noise buffering and co-expression, but these observations have been limited to a few microRNAs. Here we systematically study microRNA alternative functions in mouse embryonic stem cells, by genetically deleting Drosha - leading to global loss of microRNAs. We apply complementary single-cell RNA-seq methods to study the variation of the targets and the microRNAs themselves, and transcriptional inhibition to measure target half-lives. We find that microRNAs form four distinct co-expression groups across single cells. In particular the mir-290 and the mir-182 clusters are abundantly, variably and inversely expressed. Intriguingly, some cells have global biases towards specific miRNAs originating from either end of the hairpin precursor, suggesting the presence of unknown regulatory cofactors. We find that miRNAs generally increase variation and covariation of their targets at the RNA level, but we also find miRNAs such as miR-182 that appear to have opposite functions. In particular, miRNAs that are themselves variable in expression, such as miR-291a, are more likely to induce covariations. In summary, we apply genetic perturbation and multi-omics to give the first global picture of microRNA dynamics at the single cell level.

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Section: Resultssupporting

confidence: 93%

Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells

Tarbier,

Mackowiak,

Sekar

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…In future, as more nascent transcriptome single cell profiles become available, better capture of miRNA gene expression levels could be achieved. Among existing data, scRNA-seq profiles generated from nuclei already provide higher capture of intronic reads 47 that will improve miRNA gene detection 48 . As the signal within pri-miRNA gene loci in standard scRNA-seq libraries can arise from random priming at unspliced introns or polyA-based capture of incompletely processed primary transcripts, we chose to base the miRNA gene annotation on integrated GRO-, CAGE- and ChIP-seq 9 and Drosha knockout (KO) profiles 49 , extending here to cover both human and mouse genomes.…”

Section: Discussionmentioning

confidence: 99%

Cell-type-specific characterization of miRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution

de Sande,

Turunen,

Bouvy-Liivrand

et al. 2023

Preprint

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MicroRNAs (miRNAs) are a class of regulatory non-coding RNAs that finetune cellular functions by modulating the stability and abundance of their target mRNAs, thereby contributing to regulation of tissue homeostasis. MiRNA genes are transcribed similarly to protein-coding genes and recent studies have enabled their annotation and quantification genome-wide from bulk nascent transcriptomes. Here, we developed an approach to quantify and integrate miRNA gene signatures into single-cell studies. To characterize miRNA gene expression dynamics, we first compared the suitability of droplet and plate-based single-cell RNA-sequencing (scRNA-seq) platforms using the matched datasets provided by the Tabula Muris Senis and Tabula Sapiens consortiums. We found high concordance between the platforms and with cell type-specific bulk expression data. Based on the comprehensive aging profiles, our analysis comparing spleen immune cells between young and old mice revealed a concordant regulation of miRNAs involved in senescence and inflammatory pathways in multiple immune cell types, including up-regulation of mmu-mir-146a, mmu-mir-101a and mmu-mir-30 family genes. To study the aberrant regulation of immune cell homeostasis and tissue inflammation that pre-dispose to aging-related disease development, we collected transcriptome profiles from atherosclerosis development in LDLR-/-ApoB100/100mice. We found an elevated myeloid cell proportion in the adipose tissue and further characterized the cell subtypes based on reproducible transcriptome clusters. We then compared miRNA gene expression in early versus late disease and upon inflammatory challenge to monitor different stages during disease progression. At atherosclerotic stage, pro-inflammatory mmu-mir-511 expression increased in several macrophage subtypes, while immunosuppressive mmu-mir-23b∼mir-24-2∼mir-27b up-regulation was specific to Trem2+ lipid-associated macrophages. The infiltrating monocytes up-regulated mmu-mir-1938 and mmu-mir-22 expression and in classical monocytes maturation further increased mmu-mir-221∼222, mmu-mir-511 and mmu-mir-155 expression. To validate that these changes detected from single cell profiles represent miRNA gene transcriptional regulation, we used nascent transcriptomics data fromex vivomacrophage cultures with pro-inflammatory stimulation, confirming both rapid and long-lasting transcriptional activation of the miRNA loci studied. Collectively, our work enables integrating miRNA gene analysis to current single cell genomics pipelines and facilitates characterization of miRNA regulatory networks during aging and disease development.

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primiReference: a reference for analysis of primary-microRNA expression in single-nucleus sequencing data

Cited by 2 publications

References 81 publications

Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells

Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells

Cell-type-specific characterization of miRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution

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