Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR10030100_1.fastq.gz | Fastqsanger.gz | |||
| SRR10030100_2.fastq.gz | Fastqsanger.gz | |||
| SRR10030101_1.fastq.gz | Fastqsanger.gz | |||
| SRR10030101_2.fastq.gz | Fastqsanger.gz |
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Project description:Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. Two examples of TEs that escape this regulation are the murine-specific intracisternal A particle (IAP) elements Avy and AxinFu, which exhibit inter-individual variability in methylation associated with phenotypic variation. To determine the frequency of this phenomenon, its underlying mechanisms, and its effects on gene expression, we previously conducted a screen identifying variably methylated IAPs (VM-IAPs). Here, we fully validate these elements, categorising VM-IAPs for the first time into those exhibiting tissue specificity (tsVM-IAPs) and those showing uniform methylation among tissues (constitutive- or cVM-IAPs) with both types having the potential to regulate the genome in cis. Using our validated set of VM-IAPs, we explore how variable methylation is established and identify sequences enriched within cVM-IAPs, implicating genetics as a determinant of variability. CTCF, a methylation-sensitive transcription factor known for its role in facilitating chromatin interactions, is enriched at VM-IAPs and we show that CTCF binding is inversely correlated with methylation at cVM-IAPs. We uncover dynamic physical interactions between lowly-methylated cVM-IAPs and other genomic loci, suggesting that VM-IAPs have the potential for long-range genomic regulation. Lastly, screening for variably methylated regions in other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We propose that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs has the potential to cause inter-individual variability in transcriptional outcomes with implications for phenotypic variation.
2021-03-02 | GSE159110 | GEO
Project description:Cell migration is an instrumental process that ensures cells are properly positioned to support the specification of distinct tissue types during development. To provide insight, we used fluorescence activated cell sorting (FACS) to isolate two migrating cell types from the Drosophila embryo: caudal visceral mesoderm (CVM) cells, precursors of longitudinal muscles of the gut, and hemocytes (HCs), the Drosophila equivalent of blood cells. ~350 genes were identified from each of the sorted samples using RNA-seq, and in situ hybridization was used to confirm expression within each cell type or, alternatively, within other interacting, co-sorted cell types. To start, the two gene expression profiling datasets were compared to identify cell migration regulators that are potentially generally-acting. 73 genes were present in both CVM cell and HC gene expression profiles, including the transcription factor zinc finger homeodomain-1 (zfh1). Comparisons with gene expression profiles of Drosophila border cells that migrate during oogenesis had a more limited overlap, with only the genes neyo (neo) and singed (sn) found to be expressed in border cells as well as CVM cells and HCs, respectively. Neo encodes a protein with Zona pellucida domain linked to cell polarity, while sn encodes an actin binding protein. Tissue specific RNAi expression coupled with live in vivo imaging was used to confirm cell-autonomous roles for zfh1 and neo in supporting CVM cell migration, whereas previous studies had demonstrated a role for Sn in supporting HC migration. In addition, comparisons were made to migrating cells from vertebrates. Seven genes were found expressed by chick neural crest cells, CVM cells, and HCs including extracellular matrix (ECM) proteins and proteases. In summary, we show that genes shared in common between CVM cells, HCs, and other migrating cell types can help identify regulators of cell migration. Our analyses show that neo in addition to zfh1 and sn studied previously impact cell migration. This study also suggests that modification of the extracellular milieu may be a fundamental requirement for cells that undergo cell streaming migratory behaviors.
2017-12-11 | GSE104420 | GEO