Chen 2014, 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.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: n/a

From C. elegans (May 2008 WS190/ce6).

ChIP-seq data:

	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

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• 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. doi: 10.1101/gr.161992.113. Epub 2014 Mar 20. 24653213
• GEO series GSE49870: HOT regions are CpG dense promoters in C. elegans and humans