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Series GSE117730 Query DataSets for GSE117730
Status Public on Jul 26, 2021
Title A novel role for the conserved, orphan deaminase APOBEC2 [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The AID (activation induced deaminase)/APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) family of proteins are zinc-dependent cytidine deaminases active on polynucleotides and involved in RNA editing, DNA demethylation or DNA editing. The enzymatic activity, substrate or physiological target(s) of APOBEC2, a member of the AID/APOBEC, remain elusive. Here, we combined next generation sequencing (NGS) techniques with state-of-the-art molecular biology to comprehensively examine the physiological effects of APOBEC2 on the transcriptome and methylome using C2C12 myoblasts differentiating in culture. We also examined APOBEC2’s genome wide-binding specificity. Using RNA sequencing (RNA-seq) by polyA capture, we detected no evidence that APOBEC2 is an RNA editor. In the same system, enhanced reduced representation bisulfite sequencing (eRRBS) data did not support the proposed role of APOBEC2 as a 5-methyl-C (5mC) deaminase. However, chromatin immunoprecipitation sequencing (ChIP-Seq) did reveal specific locations of genomic occupancy of APOBEC2 with a specific motif preference. Combining biochemical, ChIP-Seq and RNA-Seq gene expression analyses we demonstrate that APOBEC2 acts as a negative regulator of gene expression in muscle cells. Our data support a model of APOBEC2 acting as a chromatin-binding factor that leads to inhibition of transcription of genes involved in cell cycle regulation during C2C12 differentiation.
 
Overall design Here we have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. We use a cell culture muscle differentiation system (C2C12), a system where APOBEC2 protein expression progressively increases. Control (GFP shRNA) and APOBEC2 deficient (A2shRNA, where Apobec2 is knocked down) C2C12 cells were evaluated at different time points following induction of differentiation. We profiled these cells for: gene expression changes and RNA editing changes between control and APOBEC2 deficient groups (n=3) using RNA sequencing (RNA-Seq) by polyA capture; 5-methylCytosine changes between control and APOBEC2 deficient group (n=5) in DNA using enhanced Reduced Representation Bisulfite Sequencing (eRRBS). Lastly, we identify specific APOBEC2 binding regions in the DNA using Chromatin Immunoprecipitation Sequencing (ChIP-Seq) (n=3).
 
Contributor(s) Molla L, Papavasiliou FN, Harjanto D, Carroll ST
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Submission date Jul 26, 2018
Last update date Jul 27, 2021
Contact name Nina Papavasiliou
E-mail(s) n.papavasiliou@dkfz-heidelberg.de
Organization name German Cancer Research Center (DKFZ)
Department Division of Immune Diversity (D150) Deutsches Krebsforschungszentrum
Lab Prof. Dr. Nina Papavasiliou
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (18)
GSM3307829 RNA-seq_GFP knockdown control day0 #1
GSM3307830 RNA-seq_GFP knockdown control day0 #2
GSM3307831 RNA-seq_GFP knockdown control day0 #3
This SubSeries is part of SuperSeries:
GSE117732 A novel role for the conserved, orphan deaminase APOBEC2
Relations
BioProject PRJNA483032
SRA SRP155395

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
GSE117730_Group_A2_d0_minus_G_d0DEG.txt.gz 1.0 Mb (ftp)(http) TXT
GSE117730_Group_A2_d1_minus_A2_d0DEG.txt.gz 1.0 Mb (ftp)(http) TXT
GSE117730_Group_A2_d1_minus_G_d1DEG.txt.gz 1.0 Mb (ftp)(http) TXT
GSE117730_Group_A2_d2_minus_A2_d0DEG.txt.gz 1.1 Mb (ftp)(http) TXT
GSE117730_Group_A2_d2_minus_A2_d1DEG.txt.gz 1.0 Mb (ftp)(http) TXT
GSE117730_Group_A2_d2_minus_G_d2DEG.txt.gz 1.0 Mb (ftp)(http) TXT
GSE117730_Group_G_d1_minus_G_d0DEG.txt.gz 1.0 Mb (ftp)(http) TXT
GSE117730_Group_G_d2_minus_G_d0DEG.txt.gz 1.1 Mb (ftp)(http) TXT
GSE117730_Group_G_d2_minus_G_d1DEG.txt.gz 1.0 Mb (ftp)(http) TXT
GSE117730_RAW.tar 1.8 Gb (http)(custom) TAR (of BW, TXT)
GSE117730_TPM_rnaseq_tximportAndSalmon.csv.gz 1.4 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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