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Developmental biology — Packing DNA|
What makes DNA go 'loopy'?
Scientists discover another key to how DNA forms loops to wrap itself inside the cell nucleus - a precise method of "packing" DNA that may affect gene expression.
The journal Science published the research by biologists at Emory University, showing that a process known as hemi-methylation plays a role in looping DNA in a very specific way. They also demonstrated that hemi-methylation is done deliberately, not by random mistakes as previously thought, and is passed down through generations.
"In order for the protein CTCF to make loops in DNA, we discovered it needs to have hemi-methylated DNA close by. Nobody had previously seen that hemi-methylated DNA had a function."
Chromatin is made up of CTCF and other proteins, along with DNA and RNA. CTCF's primary role in chromatin is regulating chromatin's 3D structure. It forms chromatin loops, it binds DNA to cell structures, whilw folding and packaging it into more compact shapes. Growing evidence suggests this folding process is'nt just fitting DNA into a cell nucleus - but plays a role in whether genes operate normally or not at all.
The Corces lab specializes in epigenetics, which is the study of changes to gene function that may be inherited, but don't involve changing the DNA sequence. This includes chromatin folding.
DNA methylation, for example, can modify the activity of DNA by adding methyl groups to both strands of the double helix at the site of particular base pairs. The process can be reversed through demethylation. When cells divide they make a copy of their DNA. To do this, they must untangle each cell's two strands of DNA and split them apart. This split allows each parental DNA strand to replicate a daughter strand as a new cell to buiid tissue and organs for the body.
"When cells divide, it's important that methylation is the same for both strands," Corces explains, altered patterns of methylation are associated with cancer and diseases.
Chenhuan Xu, post-doctoral fellow in the Corces lab, developed on human cells new experimental methods for mapping DNA methylation. His methods allowed the team to observe DNA hemi-methylation in real-time before, during and after cell division. These methods continued to map DNA as cells continued replicating.
Corces: "If parental DNA was hemi-methylated, daughter DNA was also hemi-methylated at the same place in the genome. The process is not random. It's maintained from one cell generation to the next over weeks." Researchers observed that hemi-methlyation only happens near CTCF binding sites - the main protein involved in organizing DNA into loops. "If we got rid of hemi-methlyation, CTCF did not make loops," Corces explains. It was also observed that when CTCF makes a loop, it does so by binding ahead, going forward in the DNA sequence.
"Research suggests that some disorders are associated with where CTCF binds - either mutations in the protein itself or with the DNA sequence where the protein binds," Corces adds. "It comes back to the story of how important these loops are to the three-dimensional organization of chromatin, and how that organization affects gene expression [function]."
Hemimethylation drives chromatin assembly
Cytosine DNA methylation is a heritable and essential epigenetic mark. During DNA replication, cytosines on mother strands remain methylated, but those on daughter strands are initially unmethylated. These hemimethylated sites are rapidly methylated to maintain faithful methylation patterns. Xu and Corces mapped genome-wide strand-specific DNA methylation sites on nascent chromatin, confirming such maintenance in the vast majority of the DNA methylome (see the Perspective by Sharif and Koseki). However, they also identified a small fraction of sites that were stably hemimethylated and showed their inheritance at CTCF (CCCTC-binding factor)/cohesin binding sites. These inherited hemimethylation sites were required for CTCF and cohesin to establish proper chromatin interactions.
The faithful inheritance of the epigenome is critical for cells to maintain gene expression programs and cellular identity across cell divisions. We mapped strand-specific DNA methylation after replication forks and show maintenance of the vast majority of the DNA methylome within 20 minutes of replication and inheritance of some hemimethylated CpG dinucleotides (hemiCpGs). Mapping the nascent DNA methylome targeted by each of the three DNA methyltransferases (DNMTs) reveals interactions between DNMTs and substrate daughter cytosines en route to maintenance methylation or hemimethylation. Finally, we show the inheritance of hemiCpGs at short regions flanking CCCTC-binding factor (CTCF)/cohesin binding sites in pluripotent cells. Elimination of hemimethylation causes reduced frequency of chromatin interactions emanating from these sites, suggesting a role for hemimethylation as a stable epigenetic mark regulating CTCF-mediated chromatin interactions.
Authors: Chenhuan Xu, Victor G. Corces.
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Nucleus interior shows (YELLOW) chromatin fiber arranged in 3-D loops around (PINK) CTCF protein. DNA is shown as thin BLUE lines on the chromatin. Image Graphic: Victor Corces.