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Series GSE58989 Query DataSets for GSE58989
Status Public on Sep 15, 2015
Title DNMT1-associated long non-coding RNA regulate global gene expression and DNA methylation in colon cancer
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary The investigation of the association of long non-coding RNAs (lncRNAs) with DNMT1 by RIP-seq reveals that DNMT1 interacts with DACOR1. We identified the genomic occupancy sites of DACOR1 through ChIRP-seq, which we found to significantly overlap with known differentially methylated regions (DMRs) in colon tumors. Induction of DACOR1 in colon cancer cell lines significantly reduced their ability to form colonies in vitro, suggesting a growth suppressor function. Consistent with the observed phenotype, induction of DACOR1 led to the activation of tumor-suppressor pathways and attenuation of cancer-associated metabolic pathways. Notably, DACOR1 induction resulted in down-regulation of Cystathionine β-synthase (CBS), which is known to lead to increased levels of S-adenosyl methionine (SAM) – the key methyl donor for DNA methylation.
Overall design The DNA methyltransferase DNMT1 was immunoprecipitated and all associated RNAs were identified by RNA-seq and subsequent bioinformatic analyses. Samples were prepared for DNA sequencing through the ChIRP-seq protocol which uses antisense DNA oligos to bind to DACOR1 and pull down associated DNA in complex. We sequenced one sample with DACOR1 specific probes and non-specific DNA probes as control. Three samples were collected for each control lentivirus transduced V852 colon cancer line and DACOR1 lentivirus transduced V852. Samples were processed for RNA-sequencing and analyzed through differential expression analysis.
Contributor(s) Khalil AM
Citation(s) 26307088
Submission date Jul 01, 2014
Last update date May 15, 2019
Contact name Ahmad M Khalil
Organization name Case Western Reserve University
Department Genetics and Genome Sciences
Lab BRB719
Street address 2109 Adelbert Rd
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
Platforms (2)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM1423494 Input
GSM1423495 Gp2
GSM1423496 Gp4
BioProject PRJNA254057
SRA SRP043961

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE58989_DACOR1_v_Control_MACS2_peaks.txt.gz 909.2 Kb (ftp)(http) TXT
GSE58989_RAW.tar 3.7 Mb (http)(custom) TAR (of TXT)
GSE58989_V852_DACOR1_fpkm.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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