DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID

UID: 10700

Author(s): Teater, Matt, Elemento, Olivier

Description: Summary from the GEO: "Changes in DNA methylation are required for the formation of germinal centers (GC), but the mechanisms of such changes are poorly understood. Activation-induced cytidine deaminase (AID) has been recently implicated recently in DNA demethylation through its deaminase activity coupled with DNA repair. We investigated the epigenetic function of AID in vivo in germinal center B cells (GCB) isolated from wild type (WT) and AID-deficient (Aicda-/-) mice. We determined that the transit of B cells through the GC is associated with marked locus-specific loss of methylation and increased methylation diversity, both of which are lost in Aicda-/- animals. Differentially methylated cytosines (DMCs) between GCB and naïve B cells (NB) are enriched in genes that are targeted for somatic hypermutation (SHM) by AID and these genes form networks required for B cell development and proliferation. Finally, we observed significant conservation of AID-dependent epigenetic reprogramming between mouse and human B cells."

Overall design from the GEO: "ERRBS and RNA-seq of wild type and Aicda knockout murine naive and germinal center B cells. ERRBS of human naive and germinal center B cells

Subject of Study

Subject(s)

Access via GEO
Plain Text files of expression and methylation profiling by high throughput sequencing
Accession #: GSE71702

Access via SRA
Bisulfite and RNA Sequencing of 50 samples
Accession #: SRP062639

Access via BioProject
Additional information about the overall inititative.
Accession #: PRJNA293379
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files.
Associated Publications: Dominguez P, Teater M, Chambwe N, et al. DNA methylation dynamics of germinal center B cells are mediated by AID. Cell Reports. 2015; 12(12):2086-2098.
Data Type: Genomic
Equipment Used: Illumina HiSeq 2000
High throughput gene sequencing system
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): Plain Text, SRA, TAR
Data Tool(s): RNA Seq

Bisulfite-Seq
Dataset Size: 772.1 MB (TAR of TXT), 222.3 GB (SRA)

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