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A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Seung-Tae Lee

PROVIDER: E-GEOD-45461 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network.

Lee Seung-Tae ST Xiao Yuanyuan Y Muench Marcus O MO Xiao Jianqiao J Fomin Marina E ME Wiencke John K JK Zheng Shichun S Dou Xiaoqin X de Smith Adam A Chokkalingam Anand A Buffler Patricia P Ma Xiaomei X Wiemels Joseph L JL

Nucleic acids research 20121016 22

The epigenetic changes during B-cell development relevant to both normal function and hematologic malignancy are incompletely understood. We examined DNA methylation and RNA expression status during early B-cell development by sorting multiple replicates of four separate stages of pre-B cells derived from normal human fetal bone marrow and applied high-dimension DNA methylation scanning and expression arrays. Features of promoter and gene body DNA methylation were strongly correlated with RNA ex ...[more]

PMID: 23074194

Similar Datasets

DNA Methylation data from early human B-cell development

Project description:A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Res. 2012 Dec;40(22):11339-51. We examined DNA methylation and RNA expression status during early B-cell development by sorting multiple replicates of four separate stages of pre-B cells derived from normal human fetal bone marrow and applied high-dimension DNA methylation scanning and expression arrays. We identified a distinct development-dependent demethylation signature which has gene expression regulatory properties for pre-B cells, and provide a catalog reference for the epigenetic changes that occur in pre-B-cell leukemia and other B-cell-related diseases. Human fetal bone marrow was obtained, and using flow cytometry antibodies, four populations of B-cell developmental stages including stage 1 (S1; predominantly multipotent progenitors before lineage commitment and common lymphoid progenitors), stage II (S2; pre-B-I cells), stage 3 (S3; pre-B-II cells) and stage 4 cells (S4; immature B cells). For 8 indibiduals, DNAs and RNAs were isolated and the methylation and expression changes during early B-cell development were identified using the Illumina HumanMethylation450 Beadchip (Illumina) and GeneChip Human Gene 1.0 ST Array (Affymetrix).

2013-03-26 | E-GEOD-45459 | biostudies-arrayexpress

DNA methylation changes are a late event in Acute Promyelocytic Leukemia and coincide with loss of transcription factor binding (Illumina Methylation)

Project description:The origin of aberrant DNA methylation in cancer remains largely unknown. In this study, we elucidated the DNA methylome in primary Acute Promyelocytic Leukemia (APL) and the role of PML-RARa in establishing these patterns. APL patients showed increased genome-wide DNA methylation with higher variability than healthy CD34+ cells, promyelocytes and remission bone marrow. A core set of differentially methylated regions in APL was identified. Age at diagnosis, Sanz score and Flt3-mutation status characterized methylation subtypes. Transcription factor binding sites, e.g. c-myc binding sites were associated with low methylation. SUZ12 and REST binding sites identified in embryonic stem cells were, however, preferentially DNA hypermethylated in APL. Unexpectedly, PML-RARa binding sites were also protected from aberrant DNA methylation in APL. In line, myeloid cells from pre-leukemic PML-RARa knock-in mice did not show altered DNA methylation and expression of PML-RARa in hematopoietic progenitor cells prevented differentiation without affecting DNA methylation. ATRA treatment of APL blasts did also not result in DNA methylation changes. These results suggest that aberrant DNA methylation is associated with leukemia phenotype but not required for PML-RARa-mediated initiation of leukemogenesis. Bisulphite converted DNA from the 10 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2012-11-08 | E-GEOD-42118 | biostudies-arrayexpress

Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates

Project description:Genome wide DNA methylation profiling of individuals across a large age range. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450k CpGs from human whole blood. Bisulphite converted DNA from the 656 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2012-11-21 | E-GEOD-40279 | biostudies-arrayexpress

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2012-08-09 | E-GEOD-40005 | biostudies-arrayexpress

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2013-01-10 | E-GEOD-42882 | biostudies-arrayexpress

Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans (Methylation BeadChip)

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2012-08-27 | E-GEOD-37966 | biostudies-arrayexpress

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Project description:Genome wide DNA methylation profiling of Rett syndrome monozygotic twins. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles in primary skin fibroblast cells from Rett syndrome monozygotic twins. Bisulphite converted DNA from the 2 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2012-12-27 | E-GEOD-43141 | biostudies-arrayexpress

DNA methylation profiling in breast cancer discordant identical twins

Project description:We obtained a comprehensive DNA methylation profile of 15 breast cancer discordant twins, using the high resolution Infinium HumanMethylation450 BeadChip platform (450K, Illumina), previously established to reliably detect methylation changes of more than 450,000 CpG sites. To provide insight into the temporal and causal relationships and predictive potential, samples from breast cancer patients before (7) and after diagnosis (8) were also analyzed. Using whole blood from 15 twin pairs discordant for breast cancer and high-resolution (450k) DNA methylation analysis we identified 403 differentially methylated CpG sites including known and novel potential breast cancer genes. 30 Samples

2012-10-17 | E-GEOD-37965 | biostudies-arrayexpress

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2012-06-12 | E-GEOD-30870 | biostudies-arrayexpress

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2012-10-19 | E-GEOD-41169 | biostudies-arrayexpress

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