Chromatin Structure & Function 2013

Abcam

Highlights

Fresh off the beaches of Grand Cayman Island, check out the coverage of Abcam’s Chromatin Strucuture and Function 2013 meeting from Johns Hopkins University’s Allison Chambliss

Meeting Summary

Since 2004, Abcam has teamed with Tony Kouzarides, deputy director of the Gurdon Institute at the University of Cambridge, to host its ‘Chromatin Structure and Function’ conferences. The meetings are held in the warmest and most tropical locations during the month of November (11-14th, 2013), just as those of us in Northern Hemisphere are getting used to the wrath of the cold autumn wind. I was lucky enough to jet off to Grand Cayman Island with over 150 of the world’s leading chromatin researchers for the seventh meeting in the series.

The conference venue was a gorgeous resort on the water’s edge of Seven Mile Beach, a tropical paradise on the west side of the island. “You can do science and have fun at the same time!” Tony urged at the meeting’s opening session, and he made sure that the conference participants took his advice. On the last evening of the conference, Tony moved the lectures outside to the pool!  We sat with feet dangling in the water as Kristian Helin kicked off the session with a poolside projector system. Here are summaries from just a few of the many exciting talks.

Chromatin Changes in Eukaryotic Senescence and Cancer

Shelley Berger, University of Pennsylvania

Shelley Berger nicely related our new surroundings, the picturesque Cayman tropical landscape, to the epigenetic “landscape” in cellular senescence. Senescence is the arrest of cell division that is believed to promote tissue aging and tumor suppression. Berger’s group recently compared histone modifications among proliferating and senescent human cells and found dramatic differences in landscape of the respective genomes. In senescent cells, the team identified areas that were enriched with H3K4me3 and H3K27me3 (“mesas”) and areas that were depleted in H3K27me3 (“canyons”) when compared to proliferative cells. Interestingly, the mesas were found to form at lamin B1-associated chromatin domains. Nuclear lamins line the inside of the nuclear membrane and aid in nuclear shaping and DNA replication.

Using shRNA to knockdown lamin B1 in the proliferating cells, the group demonstrated that lamin B1 depletion caused senescence, and the same H3K4me3 mesas, H3K27me3 mesas, and H3K37me3 canyons that were present in senescent control cells were present in these lamin B1-depleted cells. A cell model of Hutchinson-Gilford progeria syndrome, an accelerated aging disorder caused by a lamin A mutation, also showed the enriched mesas. These conclusions have led Berger and her group to become increasingly interested in how lamin B1 down-regulation in senescence and its associated chromatin changes can be implicated in aging and cancer.

Remodeling the Remodeler: Oncogenic BAF Complexes

Cigall Kadoch, Stanford University School of Medicine

Cigall Kadoch and her post-doctoral adviser, Gerald Crabtree, both gave exciting talks on the mSWI/SNF (BAF) complex, which is essentially a group of proteins that functions to remodel how chromatin is packaged. The complex has major implications in cancer, as Kadoch has found that about 20% of all human cancers exhibit mutations in at least one BAF subunit. She recently discovered that the SS18-SSX1 fusion protein, generated by a translocation that is a hallmark of human synovial sarcoma, is bound to BAF complexes and alters their composition.

Additionally, when compared to control cell lines, synovial sarcoma cells exhibit lower expression of the tumor suppressor subunit BAF47. After further investigating the mechanism behind the cancer-causing mutations, Kadoch found that these alterations in the BAF complex composition led to removal of H3K27me3 repression and activation of pluripotency factor Sox2, which drives cell proliferation. Interestingly, the phenomenon could be reversed by reducing SS18-SSX levels or by increasing wild-type SS18 levels. These fascinating findings point towards a novel potential cancer therapeutic target.

Histone H2B Methylation – A Guardian of Transposable Elements

Robert Schneider, IGBMC, France

Robert Schneider pointed out that while immense studies have characterized modifications of histones H3 and H4, modifications of H2A and H2B are much less studied. Thus, the goal of his research is to identify new histone modifications and determine their role in disease processes. Specifically, his group has recently identified a novel histone H2B methylation. After developing and characterizing custom antibodies to detect the mono and di-methylation of H2B, they screened for the methylating enzyme and identified PMT2, a new class of methyltransferases. A γ-H2AX assay to mark DNA damage revealed that PMT2-depletion increased genomic instability. Additionally, mono- and d-methylation of H2B was shown to be decreased in colon cancer. Overall, the work establishes H2B methylation as a key regulator of genomic integrity and opens possibilities for potential new cancer therapies.

Cis Gene Regulation at the Single Cell, Chromosome, Molecule, and Base Level

Arjun Raj, University of Pennsylvania

Arjun Raj opened with the most simplistic description of his lab group’s work: “We make tools to visualize gene expression in cells.” He then proceeded to dazzle us with beautiful, vibrant images of single-molecule RNA visualization in cell nuclei. A 2008 Nature Methods publication from the Raj group introduced a novel in situ hybridization method, termed “single molecule RNA FISH,” which enables the fluorescent visualization of individual mRNA molecules in fixed cells. Most recently, the group has investigated how organization of genes into chromosomes affects gene expression.

They developed a new spin on their original method, this time called “intron chromosomal expression FISH” (iceFISH), that fluorescently labels introns using oligonucleotides in order to simultaneously measure and relate gene expression with chromosome structure. They used the method to identify 20 genes along chromosome 19 in human foreskin fibroblasts and then examined whether transcriptional status of one gene was at all affected by transcriptional status of another gene on the same chromosome. While most expression relationships among these 20 genes showed low likelihood of any correlation, one pair of genes, RPS19 and ZNF444, showed a fair anticorrelation. They found that the particular anticorrelation was absent in the other chromosome 19, indicating that the interaction between the genes was a cis effect confined to a single chromosome. The same interaction pattern was observed in HeLa cells as well. Raj’s single-cell and single-molecule methods will undoubtedly become increasingly powerful tools to study the inherent variability of gene expression.

Takeaways

Clearly, hot topics at this conference included the important roles of chromatin structure and function in aging and cancer. Newly-discovered and lesser-studied epigenetic modifications were explored, such as H2B methylation by Robert Schneider and H3 threonine 118 phosphorylation by Jessica Tyler (MD Anderson Cancer Center). Non-coding RNAs were also commonly discussed by conference regulars such as John Rinn and Robert Kingston (both from Harvard University). The past few years have brought great strides in chromatin research, and there is hope that these many exciting findings will continue to guide us to new insight into disease cause and treatment possibilities.

 ***EpiGenie would like to give thanks and a big shout out to Allison Chambliss for taking on the “dirty job” of providing this conference coverage. Allison is a  PhD candidate in Denis Wirtz’s lab in the Department of Chemical & Biomolecular Engineering and Institute for NanoBioTechnology at Johns Hopkins University.