Transcriptomics

Dataset Information

5

Transcription profiling by array of primary human CD4+T-cells overexpressing TET1 polarized towards Th1


ABSTRACT: Differentiation of CD4+T-cells into effector subsets is a critical component of the adaptive immune system and an incorrect response can lead to autoimmunity or immune deficiency. Cellular differentiation including T-cell differentiation is accompanied by large-scale epigenetic remodeling, including changes in DNA methylation at key regulators of T-cell differentiation. The TET family of enzymes were recently shown to be able to catalyse methylated cytosine (5mC) into 5-hydroxymethylcytosine (5hmC) enabling a pathway of active removal of DNA methylation. Here, we characterize 5hmC, 5mC and transcriptional dynamics during human CD4+T-cell polarisation in a time series approach and relate these changes to profiles in ex-vivo CD4+memory subsets. We observed large-scale remodelling during early CD4+T-cell differentiation which was predictive of subsequent changes during late time points, these changes were also related to disease associated regions which we show can act as functional regulatory elements. This dataset was designed to assess how TET1 affects gene expression during human CD4+T-cell differentiation. We observed that TET1 was highly expressed in primary lymphocytes compared to other human tissues and loss of TET1 gene expression was seen within 6 hours of naïve CD4+T-cell activation. Primary human naïve T-cells were transfected with different TET1 containing plasmids and polarized towards Th1 for 24h. When comparing cells transfected with full length TET1 to catalytically inactive TET1, we observed mis-expression of several cytokine/chemokine genes related to T-cell differentiation. This was not observed for cells expressing the catalytic domain of TET1. Note that the expression array only targets the DNA binding domain of the TET1 gene, therefore we validated ectopic expression of TET1 by qPCR targeting the catalytic domain. This submission contains data from Transcription profiling by array of primary human CD4+T-cells overexpressing TET1 polarized towards Th1. See related experiments: E-MTAB-4686, E-MTAB-4687, E-MTAB-4688, E-MTAB-4689.

INSTRUMENT(S): Agilent Surescan High Resolution DNA Microarray Scanner

ORGANISM(S): Homo sapiens  

SUBMITTER: Antonio Lentini  

PROVIDER: E-MTAB-4685 | ArrayExpress | 2016-07-11

REPOSITORIES: ArrayExpress

Dataset's files

Source:
Action DRS
E-MTAB-4685.idf.txt Idf
E-MTAB-4685.idf.txt_original Idf
E-MTAB-4685.processed.1.zip Processed
E-MTAB-4685.raw.1.zip Raw
E-MTAB-4685.sdrf.txt Txt
Items per page:
1 - 5 of 5
altmetric image

Publications


5-methylcytosine (5mC) is converted to 5-hydroxymethylcytosine (5hmC) by the TET family of enzymes as part of a recently discovered active DNA de-methylation pathway. 5hmC plays important roles in regulation of gene expression and differentiation and has been implicated in T cell malignancies and autoimmunity. Here, we report early and widespread 5mC/5hmC remodeling during human CD4(+) T cell differentiation ex vivo at genes and cell-specific enhancers with known T cell function. We observe simi  ...[more]

Similar Datasets

2011-01-01 | S-EPMC3099128 | BioStudies
2016-07-11 | E-MTAB-4688 | ArrayExpress
2016-07-11 | E-MTAB-4687 | ArrayExpress
2016-11-10 | E-MTAB-4687 | ExpressionAtlas
2016-07-11 | E-MTAB-4686 | ArrayExpress
1000-01-01 | S-EPMC5600463 | BioStudies
2014-01-01 | S-EPMC4120082 | BioStudies
2015-01-01 | S-EPMC4731232 | BioStudies
2020-01-01 | S-EPMC7316867 | BioStudies
2016-07-11 | E-MTAB-4689 | ArrayExpress