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
- Input file format: SRA
- Download date: n/a
From C. elegans (May 2008 WS190/ce6).
FASTQ files were extracted from SRA files using fastq-dump
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
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.
HOT regions are CpG dense promoters in C. elegans and humans