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Gene Expression and Chromatin Accessibility of Nephron Progenitor Cells in Mice

ABSTRACT: We report the use of high-throughput sequencing, including RNA-seq and ATAC-seq, to compare the gene expression patterns and chromatin accessibility in uninduced (mK3) and epithelial-differentiated (mK4) metanephric mesenchymal cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE245355 | GEO | 2023/10/18

REPOSITORIES: GEO

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Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development [ATAC-Seq]

Project description:Mammalian nephron progenitors undergo transcriptional changes over the course of nephrogenesis that sensitize them to signals for differentiation over time. This increases the rate at which they exit their multipotent, self-renewing mesenchymal state and become differentiated epithelial cells, ultimately depleting the progenitor population and leading to the cessation of nephrogenesis. We hypothesized that changes in chromain accessibility and miRNA expression would accompany these transcriptional changes, and that regions of changing chromatin accessibiltiy could reveal chaning regulatory features such as enhancers, including some that affect miRNA expression. To test this, we pooled kidneys from wild-type mouse litters sacrificed at embryonic day 14.5 (E14.5) and post-natal day zero (P0) using positive selection for the surface protein Integrin alpha 8 (Itga8), then sequenced the assay for transposase-accessible chromatin (ATAC-seq) using 50,000 cells, and used the remaining cells for small RNA sequencing (smRNA-seq). ATAC-seq libraries were generated using the Nextera DNA Flex Library Prep Kit (Illumina FC-121-1030) with modifications according to a previously published method (Buenrostro et al., 2013), and all sequencing was performed using an Illumina NextSeq500 by the Health Sciences Sequencing Core at UPMC Children's Hospital of Pittsburgh.

2023-03-04 | GSE168339 | GEO

Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development [miRNA-Seq]

Project description:Mammalian nephron progenitors undergo transcriptional changes over the course of nephrogenesis that sensitize them to signals for differentiation over time. This increases the rate at which they exit their multipotent, self-renewing mesenchymal state and become differentiated epithelial cells, ultimately depleting the progenitor population and leading to the cessation of nephrogenesis. We hypothesized that changes in chromain accessibility and miRNA expression would accompany these transcriptional changes, and that regions of changing chromatin accessibiltiy could reveal chaning regulatory features such as enhancers, including some that affect miRNA expression. To test this, we pooled kidneys from wild-type mouse litters sacrificed at embryonic day 14.5 (E14.5) and post-natal day zero (P0) using positive selection for the surface protein Integrin alpha 8 (Itga8), then sequenced the assay for transposase-accessible chromatin (ATAC-seq) using 50,000 cells, and used the remaining cells for small RNA sequencing (smRNA-seq). smRNA-seq libraries were generated using the QIAseq miRNA library preparation kit (Qiagen 331502), and all sequencing was performed using an Illumina NextSeq500 by the Health Sciences Sequencing Core at UPMC Children's Hospital of Pittsburgh.

2023-03-04 | GSE168342 | GEO

Genome-wide chromatin accessibility (ATAC-Seq) of primary murine nephron progenitor cells.

Project description:This series contains ATAC-Seq data generated from mouse nephron progenitor cells (NPCs) isolated from different strains/mutants and developmental timepoints as indicated.

2024-03-21 | GSE224324 | GEO

Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development.

Project description: Not available

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Mapping open chromatin in mouse nephron progenitor cells

Project description:To delineate the epigenomic profile of the Six2+ mouse nephron progenitor cells, we mapped open chromatin using ATAC-Seq in Six2+ cells from E16.5 mouse kidneys.

2018-01-18 | GSE108424 | GEO

Genome-wide chromatin accessibility (ATAC-Seq) of primary murine nephron progenitor cells.

Project description:Genome-wide chromatin accessibility (ATAC-Seq) of primary murine nephron progenitor cells.

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The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in mice.

Project description: Not available

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Nephron progenitor commitment is a stochastic process influenced by cell migration.

Project description:Kidney development depends on a balance of nephron progenitor self-renewal and commitment. Here we examine how cells shift from a motile progenitor state to a static committed state during nephrogenesis. Cells that express Wnt4, an early marker of commitment, give rise to both the nephron lineage and a migrating sub-population that may re-enter the progenitor pool. Single cell transcriptional profiling reveals Wnt4-lineage cells across a range of transcriptional states, including cells that return to an uninduced progenitor state.

2019-01-31 | GSE118486 | GEO

LGR6 marks nephron progenitor cells.

Project description: Not available

| S-EPMC8597161 | biostudies-literature

LGR6 marks nephron progenitor cells

Project description:Background: Nephron progenitor cells (NPCs) undergo a stepwise process to generate all mature nephron structures. Mesenchymal to epithelial transition (MET) is considered a multi-step process of NPC differentiation to ensure progressive establishment of new nephrons. However, despite this important role, to date, no marker for NPCs undergoing MET in the nephron exists. Results: Here, we identify LGR6 as a NPC marker, expressed in very early cap mesenchyme, pre-tubular aggregates, renal vesicles and in segments of S-shaped bodies, following the trajectory of MET. By using a lineage tracing approach in embryonic explants in combination with confocal imaging and single-cell RNA sequencing, we provide evidence for the multiple fates of LGR6+ cells during embryonic nephrogenesis. Moreover, by using long-term in vivo lineage tracing, we show that postnatal LGR6+ cells are capable of generating the multiple lineages of the nephrons. Conclusion: Given the profound early mesenchymal expression and MET signature of LGR6+ cells, together with the lineage tracing of mesenchymal LGR6+ cells, we conclude that LGR6+ cells contribute to all nephrogenic segments by undergoing MET. LGR6+ cells can therefore be considered an early committed NPC population during embryonic and postnatal nephrogenesis with potential regenerative capability.

2021-05-25 | GSE164795 | GEO

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