Chromatin: From Structure to Epigenetics
Abcam’s latest conference on chromatin took place in Strassbourg, France and marked the second leg of Lauren Blair’s European, epigenetic road trip from her home at Yale University. See Lauren’s report to get all the chromatin conference details:
Chromatin: From Structure to Epigenetics Meeting Summary
This meeting was set up interestingly in that it began with talks addressing the structure of chromatin and slowly transitioned into epigenetics. This provided a unique environment to look at both the big picture and more detailed aspects of chromatin, how it is regulated and how it regulates gene expression. The setting was the Institute of Genetics and Molecular and Cellular Biology (IGMCB) in Strasbourg, France. Two beautiful, sunny days full of interesting science ended in a discussion of the field and where it is going.
Nuclear Compartments in Epigenetics
Peter Becker, Munich University
Dr. Becker began by introducing the concept of nuclear compartments and by explaining how they may be important in epigenetics. He defines them as having a local microenvironment, being enriched in certain molecules and as having specificity. He proposes the X chromosome in male flies as a nuclear compartment. The MSL complex is responsible for the dosage compensation effect in male flies. One particular component of the complex, MSL2, is only expressed in male flies. The MOF component of the MSL complex acetylates H4K16 which contributes to activation of x-linked genes. In male flies, MOF is concentrated on the X chromosome but in female flies, MOF is distributed throughout the genome. MOF in combination with MSL proteins forms the dosage compensation complex (DCC).
The Becker lab did ChIP-chip previously and has recently done ChIP-seq on various components of the DCC. They found, surprisingly, that their results did not necessarily overlap. After some investigation they concluded that the high shear conditions used for ChIP-seq can dissociate complexes. They suggest that using ChIP-CHIP may be better when studying complexes than using ChIP-seq. In their studies of the MSL complex, they saw that MSL3 was retained in both techniques so they believe that it is the protein that most directly binds chromatin. MSL2 and MLE tend to make contact with high affinity entry sites on DNA while MOF and MSL1 tend to bind promoters independently of DCC machinery. They suggest that MSL2 binds to these high affinity sites and then somehow recruits MSL3. They hypothesize that MLE and the ncRNA ROX have something to do with this recruitment. They noticed that high affinity sites are clustered together in male flies but not in females and they suggest that MSL1 and MSL2 are responsible for this high affinity site clustering.
Nucleosome Disfavoring Sequences Alter Gene Expression
Eran Segal, Weizmann Institute of Science
Dr. Segal’s lab is interested in studying how primary DNA sequence can dictate information on how genes are activated. They work off of the hypothesis that nucleosome disfavoring sequences may allow predictable tuning of gene expression. Dr. Segal addressed polyA/T sequences specifically in this talk. It has been shown that polyA/T sequences can serve as promoter-like elements in yeast. They are correlated with nucleosome depletion. The Segal lab introduced polyA sites upstream of promoters in yeast and saw that longer stretches of polyA led to increased gene expression.
The distance of the polyA site from the transcription start site was also important. The closer the polyA was to the TSS, the higher the gene expression. Some genes in yeast are single copy but they still need to be expressed at similar levels to double copy genes. How they accomplish this is not well understood. The Segal lab wanted to see if polyA placement played a role in this phenomenon so they looked at the nucleosome occupancy of strong promoters. They found that nucleosome depletion existed near the TSS of strong promoters that contained polyA sites. They then mutated these polyA sites and saw significant decreases in gene expression. They determined that yeast use polyA sites and one mechanism to overcome dosage compensation issues.
Danny Reinberg, Howard Hughes Medical Institute
The Reinberg lab studies polycomb complexes PRC1 and PRC2 which bind to chromatin to restrict gene expression. The exact mechanisms by which PRC complexes lay the initial marks, and the mechanism by which they propagate and maintain these marks, are not well understood. Dr. Reinberg spoke about advances in the field made by his lab in these areas. He began by pointing out that the mechanism by which PRC2 is recruited for de novo modification is unclear. His lab has discovered that JARID2 containing PRC2 complexes can bind RNA.
Specifically, JARID2 has a DNA binding domain that interacts with ncRNAs including MEG3 and Rian which are within the Dlk1 locus. Ezh2 and JARID2 both bind to the Dlk1 locus. When the Reinberg lab knocked out JAIRD2 and pulled down Ezh2 or Suz12 they found a decrease in target ncRNAs indicating that JAIRD2 binding is important to ncRNA expression. They showed that the RNA-protein interaction of JARID2 enhances its binding to Ezh2. They proposed a mechanism by which JAIRD2 binds GC rich regions on DNA and interacts with ncRNA which also interacts with Ezh2 and allows it to lay down de novo H3K27me marks. The PRC2 complex that contains Ezh1 instead of Ezh2 is thought to be involved in maintenance of epigenetic marks.
Jane Mellor, University of Oxford
Dr. Mellor discussed antisense transcripts in yeast (asRNA). These RNAs bind promoters and prevent acetylation of histones, therefore inhibiting transcription. Dr. Mellor noted that genes with a high incidence of asRNA tend to have non-canonical distributions of H3K4me3 levels. Her lab determined that these changes were not from histone modifying enzymes but were from histone remodeling Histone turnover is higher at these sites and new histones are more likely to be acetylated that older histones. They determined that these asRNA “reset” the state of the promoter in many cells and high levels of asRNA keep the genes plastic. She introduced asRNA transcription as a major mechanism for histone exchange over gene bodies and promoters.
There was some discussion during the conference over the histone code and whether or not epigenetic mechanisms should really be called “heritable.” In the end, most of the arguments centered on the terminology we use in the field and whether or not we should use terms such as “activating” and “repressive” for epigenetic marks. Also, the meeting participants pointed out the importance in distinguishing between chromatin structure and epigenetics as many people use the two terms interchangeably. One delegate noted that when using the term “environment” we must be careful as epigeneticists when speaking to the general public.
**EpiGenie would like to thank Lauren Blair, a Postdoc Associate in the Yan lab at the Yale School of Medicine, for providing coverage of this conference.