Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Beta cell 5’-shifted isomiRs are candidate regulatory hubs in type 2 diabetes

ABSTRACT: We performed deep sequencing of small RNA from mouse insulinoma (MIN6) cells cultured in 25mM glucose. We then developed and implemented an in-house short-read mapping strategy to analyze isomiR diversity. Profile of miRNA expression in MIN6 cells cultured in 25mM glucose.

ORGANISM(S): Mus musculus

SUBMITTER: Jeanette Baran-Gale

PROVIDER: E-GEOD-44262 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes.

Baran-Gale Jeanette J Fannin Emily E EE Kurtz C Lisa CL Sethupathy Praveen P

PloS one 20130909 9

Next-generation deep sequencing of small RNAs has unveiled the complexity of the microRNA (miRNA) transcriptome, which is in large part due to the diversity of miRNA sequence variants ("isomiRs"). Changes to a miRNA's seed sequence (nucleotides 2-8), including shifted start positions, can redirect targeting to a dramatically different set of RNAs and alter biological function. We performed deep sequencing of small RNA from mouse insulinoma (MIN6) cells (widely used as a surrogate for the study o ...[more]

PMID: 24039891

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Project description:Human embryonic stem cells share identical genomic sequences with other lineage-committed cells yet possess the remarkable properties of self-renewal and pluripotency. It has been proposed that epigenetic regulatory mechanisms, involving DNA methylation and various chromatin modifications, are at least partly responsible for the distinct cellular properties between different cell types. Previous studies focusing largely on gene promoters and CpG islands have identified close association between several chromatin modifications and DNA methylation, but revealed a relatively small degree of differences between pluripotent and lineage-committed cells. Here, we examine the association between 11 chromatin modifications and DNA methylation at high resolution throughout the genome in the human embryonic stem cells and primary fetal lung fibroblasts. We observe a new set of relationships between chromatin modifications and DNA methylation occurring outside of the promoter regions. We also find that epigenomic landscapes are drastically different between the ES cells and fibroblasts. In particular, over 40% of the human genome differs in their chromatin structure between the two cell types. Most of the changes come from a dramatic redistribution of the repressive H3K9me3 and H3K27me3 marks, which form large blocks that expand significantly in the fibroblasts relative to ES cells. Additionally, we identified numerous small and punctuated regions outside of promoters that are associated with many active chromatin modification marks, and show that chromatin dynamics at these potential regulatory sequences are associated with change in DNA methylation between the ES cells and fibroblasts. Our results provide new insights into epigenetic regulatory mechanisms underlying properties of pluripotency and cell fate commitment. ChIP-Seq Analysis of OCT4, KLF4, MYC, TAFII and P300 in hESC H1 cells. 36 cycles of sequencing was done on the Illumina Genome Analyzer or Analyzer II platforms.

Dataset Information

Beta cell 5’-shifted isomiRs are candidate regulatory hubs in type 2 diabetes

Publications

Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes.

Similar Datasets

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