Chen14, CFP-1 and H3K4me3 occupancy profiles


Most vertebrate promoters lie in unmethylated CpG-dense islands, whereas methylation of the more sparsely distributed CpGs in the remainder of the genome is thought to contribute to transcriptional repression. Nonmethylated CG dinucleotides are recognized by CXXC finger protein (also known as CFP1). Genomic regions enriched for CpGs are thought to be either absent or irrelevant in invertebrates that lack DNA methylation, such as C. elegans; however, a CXXC1 ortholog (CFP-1) is present. In this experiment they demonstrate that C. elegans CFP-1 targets promoters with high CpG density, and these promoters are marked by high levels of H3K4me3. Furthermore, as for mammalian promoters, high CpG content is associated with nucleosome depletion irrespective of transcriptional activity. It is also shown that highly occupied target (HOT) regions identified by the binding of a large number of transcription factors are CpG-rich promoters in C. elegans and human genomes, suggesting that the unusually high factor association at HOT regions may be a consequence of CpG-linked chromatin accessibility.


Data can be downloaded from: GEO dataset GSE49870


From C. elegans genome WC190 (ce6).

Filename Description Feature GEO-ID
1 GSM1208362.sga whole embryo|H3K4me3|rep 1 H3K4me3 GSM1208362
2 GSM1208361.sga whole embryo|H3K4me3|rep 2 H3K4me3 GSM1208361
3 GSM1208360.sga whole embryo|CFP-1::GFP|rep 1 CFP-1::GFP GSM1208360
4 GSM1208359.sga whole embryo|CFP-1::GFP|rep 2 CFP-1::GFP GSM1208359

Technical Notes

SRA files were downloaded from GEO GSE49870 and converted in FASTQ using fastq-dump program from sratoolkit. Mapping was done using Bowtie and sam files were converted in sga files using samtools and chipseq.


  1. Chen RA, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J.
    Extreme HOT regions are CpG-dense promoters in C. elegans and humans. Genome Res. 2014 Jul;24(7):1138-46. PMID: 24653213

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