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Series GSE70267 Query DataSets for GSE70267
Status Public on Nov 08, 2016
Title COSMIC-seq of bioactive N-methylpyrrole/N-methylimidazole polyamides
Organism Homo sapiens
Experiment type Other
Summary Targeting the genome with sequence-specific DNA-binding molecules is a major goal at the interface of chemistry, biology, and precision medicine. Polyamides, composed of N-methylpyrrole and N-methylimidazole monomers, are a class of synthetic molecules that can be rationally designed to “read” specific DNA sequences. However, the impact of different chromatin states on polyamide binding to its cognate sites across the genome is a crucial parameter that remains unresolved. We applied COSMIC-seq (crosslinking of small molecules to isolate chromatin) to directly map, for the first time, the genome-wide binding profiles of two bioactive and structurally distinct polyamides in cells.
Overall design To directly map polyamide binding sites across the genome in living cells, we developed COSMIC-seq. COSMIC consists of treating live cells with trifunctional derivatives of polyamides. These molecules were comprised of a DNA-binding polyamide, an affinity handle, and a photocrosslinker. The polyamide confers sequence specificity, while the affinity handle, biotin, is used to purify polyamide–DNA adducts with streptavidin-coated magnetic beads. The photocrosslinker, psoralen, enables the temporally-controlled formation of a covalent bond between the polyamide and DNA. Cells were first treated with the polyamide derivative, crosslinked with 365 nm UV light, lysed, sonicated to shear DNA, and streptavidin-coated magnetic beads were used to capture polyamide-DNA adducts. Because psoralen crosslinks are reversible, the captured genomic DNA can be separated from the polyamide, purified, and identified by massively parallel, next-generation sequencing (NGS). Sequencing reads are mapped to their location across the genome, and loci bound by polyamides show enrichment of sequencing reads relative to a reference input sample.
Contributor(s) Erwin GS, Ansari AZ
Citation(s) 27830652
Submission date May 10, 2016
Last update date May 15, 2019
Contact name Aseem Ansari
Organization name University of Wisconsin-Madison
Department Biochemistry and The Genome Center
Lab Ansari
Street address 440 Henry Mall
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (13)
GSM2149181 20nM_2_Rep1
GSM2149182 20nM_2_Rep2
GSM2149183 20nM_4_Rep1
BioProject PRJNA321205
SRA SRP059875

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Supplementary file Size Download File type/resource
GSE70267_2.peaks.bed.gz 7.6 Kb (ftp)(http) BED
GSE70267_4.peaks.bed.gz 46.1 Kb (ftp)(http) BED
GSE70267_400nM.2.peaks.bed.gz 14.0 Kb (ftp)(http) BED
GSE70267_400nM.4.peaks.bed.gz 24.1 Kb (ftp)(http) BED
GSE70267_RAW.tar 710.0 Mb (http)(custom) TAR (of BEDGRAPH)
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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