GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE129895 Query DataSets for GSE129895
Status Public on Apr 17, 2019
Title Phosphorylation at the S2056 1 cluster of DNA-PKcs is dispensable for lymphocyte development and class switch recombination in mice.
Organism Mus musculus
Experiment type Other
Summary The classical non-homologous end-joining (cNHEJ) pathway is a major DNA double-strand break repair pathway in mammalian cells and is required for lymphocyte development and maturation. The DNA-dependent protein kinase (DNA-PK) is a cNHEJ factor that encompasses the Ku70-Ku80 (KU) heterodimer and the large catalytic subunit (DNA-PKcs). In mouse models, loss of DNA-PKcs (DNA-PKcs-/-) abrogates end-processing (e.g., hairpin-opening), but not end-ligation, while expression of the kinase-dead DNA-PKcs protein (DNA-PKcsKD/KD) abrogates end-ligation, suggesting a kinases-dependent structural function of DNA-PKcs during cNHEJ. Lymphocyte development is abolished in DNA-PKcs-/- and DNA-PKcsKD/KD mice due to the requirement for both hairpin-opening and end-ligation during V(D)J recombination. DNA-PKcs itself is the best-characterized substrate of DNA-PK. The S2056-cluster is the best characterized auto-phosphorylation site on human DNA-PKcs. Here we show that radiation can induce phosphorylation of murine DNA-PKcs at the corresponding S2053 and generated knockin mouse models with alanine- (DNA-PKcsPQR) or phospho-mimetic aspartate (DNA-PKcsSD) substitutions at the S2053 cluster. Despite moderate radiation sensitivity in the DNA-PKcsPQR/PQR fibroblasts and lymphocytes, both DNA-PKcsPQR/PQR and DNA-PKcsSD/SD mice retain normal kinase activity, and undergo efficient V(D)J recombination and class switch recombination, indicating that phosphorylation at the S2053-cluster of mouse DNA-PKcs (corresponding to S2056 of human DNA-PKcs), although important for radiation resistance, is dispensable for the end-ligation and hairpin-opening function of DNA-PK essential for lymphocyte development.
Overall design HTGTS analyzes thousands of CSR junctions between the 5’ of Sμ and its joining partner genome wide, including both internal deletion (Sμ-Sμ) and potentially productive switching (Sμ-Sγ1). We also used HTGTS to uncover a prominent shift to MH, extensive erosion within switch region, and relative increase of inversion in DNA-PKcs-/- B cells with only moderate CSR defects. So we performed HTGTS analyses of CSR junctions from DNA-PKcsPQR/PQR B cells along with control DNA-PKcs-/- B cells. While the results confirmed S region erosion and increased MH usage in DNA-PKcs-/- B cells, no alteration in MH usage and Sµ junction distribution is noted in DNA-PKcsPQR/PQR B cells.
Contributor(s) Wang XS, Crowe JL, Shao Z, Lee BJ, Zha S
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 16, 2019
Last update date Apr 20, 2019
Contact name Zhengping Shao
Phone 212-851-4785
Organization name Columbia University Medical Center
Department ICG
Lab Shan Zha Lab
Street address 1130 St. Nicholas Ave
City New Yprk
State/province New York
ZIP/Postal code 10033
Country USA
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (3)
GSM3724623 DNA-PKcs -/- -5
GSM3724624 DNA-PKcs PQR/PQR -1
GSM3724625 DNA-PKcs PQR/PQR -2
BioProject PRJNA533107
SRA SRP192737

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
GSE129895_DNA_PKcs_KO_pool_results.xlsx 4.2 Mb (ftp)(http) XLSX
GSE129895_DNA_PKcs_PQR_pool_results.xlsx 1.5 Mb (ftp)(http) XLSX
GSE129895_RAW.tar 1.3 Mb (http)(custom) TAR (of XLSX)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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