GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE24178 Query DataSets for GSE24178
Status Public on Oct 05, 2010
Title Genome wide localization of Activation induced cytidine deaminase (AID), Spt5, and RNA Polymerase II (PolII) in mouse
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Activation induced cytidine deaminase (AID) initiates antibody gene diversification by creating U:G mismatches. However, AID is not specific for antibody genes. Off-target lesions can activate oncogenes or cause chromosome translocations. Despite its importance in these key transactions little is known about how AID finds its target sites. To examine AID regulation we performed an shRNA screen. We found that Spt5, a factor associated with paused RNA polymerase II (Pol II) and single stranded DNA (ssDNA), is required for class switch recombination (CSR). Spt5 interacts with AID, it is required for the association of AID and Pol II, and for AID recruitment to switch regions. ChIP-seq experiments reveal that Spt5 co-localizes with AID and stalled Pol II. Further, Spt5 accumulation at sites of Pol II pausing is predictive of AID-induced mutation. Our data suggest that Spt5 acts as an adaptor, which brings AID to Pol II on target DNA.
Overall design PolII, AID, and Spt5 were immunoprecipitated from in vitro activated B cells. For Spt5 and AID, two different antibodies were used in separate, biological replicates.

Notes: Peaks of enrichment relative to a random background model were identified with SICER 1.03 (Zhang et al., 2009). For AID, the parameters used were window size = 100, gap size = 100, e = 0.000001, redundancy = 1, fragment size = 127 (AID+/+, ab1), 115 (AID-/-, ab1), and 125 (AID+/+, ab2). Fragment size estimates were calculated from the data based on a shifting algorithm that attempts to minimize a Shannon entropy measure. Read counts were adjusted for library size and are given as reads per million non-redundant aligned reads (RPM). Densities were then filtered to only display windows falling onto enriched regions as identified by SICER. AID-/- densities were additionally scaled by a factor of 0.592 to correct for an overestimation of background levels at 104 genes that displayed higher read densities in AID-/- cells than AID+/+ cells. Corrected values were used to calculate RPKM values in Table S1 of Yamane et al. (PMID 21113164) and for display in browser tracks. Please note a typo in Fig. 1a of Yamane et al. (PMID 21113164) where the Y axes of AID+/+ and AID-/- samples should read 0.15-1.2, instead of 0-1.2.
Contributor(s) Gazumyan A, Yamane A, San-Martin BR, Ansarah-Sobrinho C, Root D, Robbiani DF, Sun H, Klein I, Nussenzweig MC, Di Virgilio M, Jankovic M, Kuo N, Casellas R, Pavri R, Neiland T, Barreto V, Resch W, Li Z
Citation(s) 20887897, 21113164, 23706737
Submission date Sep 16, 2010
Last update date May 15, 2019
Contact name Seolkyoung Jung
Organization name NIH
Department NIAMS
Lab biodata mining and discovery section
Street address 10 Center Dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (7)
GSM594827 ActivatedBCell_Spt5_rep1
GSM594828 ActivatedBCell_Spt5_rep2
GSM594829 ActivatedBCell_AID
SRA SRP003605
BioProject PRJNA130101

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE24178_RAW.tar 6.4 Gb (http)(custom) TAR (of BAM, BEDGRAPH)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap