The EMBO Meeting

The EMBO Meeting 2012





Monday, 18 Nov 2013

Chromatin & chromosomes – The dynamic genome


Saturday, 22 September 18:30-20:00, Apollon Auditorium

HHMI & Fred Hutchinson Cancer Research Centre

Mapping genome-wide nucleosome dynamics

Eukaryotic gene expression occurs in the context of chromatin, and maintaining a region accessible to DNA-binding proteins for transcriptional regulation requires active processes that mobilize nucleosomes. Our approach to studying these processes has been to map nucleosome dynamics genome-wide, and we have introduced several different strategies to achieve this goal: (1) To measure relative levels of histone replacement across the genome, we have followed incorporation of the replication-independent histone variant, H3.3, which replaces replication-coupled H3 over the course of the cell cycle. (2) To map histone turnover kinetics directly we have developed a novel method based on metabolic labeling of proteins followed by affinity purification of newly synthesized histone core particles. (3) To map classical 'active' chromatin genome-wide we have applied salt fractionation to intact micrococcal nuclease-treated nuclei. (4) To effectively profile chromatin landscapes at single base-pair resolution, we have developed a simple sequencing library preparation protocol and data display method that we have applied to mapping transcription factors, nucleosome remodelers, nucleosomes and kinetochores from a single dataset. (5) To extend genome-wide chromatin profiling to tissues, we have introduced an affinity-based method for purification of nuclei expressing a nuclear envelope protein under control of a cell-type-specific promoter. Application of these methods to model organism genomes suggests that nucleosome turnover is crucial for epigenetic inheritance of gene activity and for maintaining a single centromere on a chromosome.


Steven Henikoff received a BS degree in Chemistry from the University of Chicago and a Ph.D. degree in Biochemistry and Molecular Biology from Harvard University, and carried out postdoctoral research at the University of Washington. He joined the Fred Hutchinson Cancer Research Center in Seattle in 1981, where he is a Member of the Basic Sciences Division and an Affiliate Professor of Genome Science at the University of Washington. He has been an Investigator of the Howard Hughes Medical Institute since 1990 and a Member of the US National Academy of Sciences since 2005. He is co-Editor-in-Chief of Epigenetics & Chromatin and a member of the Editorial Boards of Trends in Genetics, Current Opinion in Genetics and Development and Genome Biology. His laboratory studies chromatin processes, epigenetic inheritance, centromere structure, function and evolution, and develops tools for epigenomics.

German Cancer Research Centre

Non-coding RNA controls epigenetic processes

Constitutive heterochromatin exerts a crucial function in maintaining genomic stability. I will talk about the molecular mechanisms that direct epigenetic silencing of rRNA genes, focussing on the role of the chromatin remodeling complex NoRC in targeting chromatin modifying enzymes to the rDNA promoter. Data will be presented showing that NoRC-associated RNA in sense orientation to the rDNA promoter forms a DNA:RNA triplex with a transcription factor binding site, and this triplex structure is specifically recognized by the DNA methyltransferase DNMT3b. The results reveal a compelling RNA-based strategy for epigenetic programming, implying that noncoding RNAs may guide DNA methyltransferase to specific genomic sites to methylate DNA and silence transcription.
In addition, rDNA is also transcribed in antisense orientation, yielding a heterogeneous population of long RNA polymerase II-directed transcripts that cover the pre-rRNA coding region and the rDNA promoter. These antisense transcripts  alter the epigenetic signature of rRNA genes in response to growth factor availability. RNA transcribed in antisense orientation to the rDNA promoter specifically interacts with the histone methyltransferase Suv4-20h2, mediating trimethylation of H4K20 (H4K20me3) and compaction of chromatin in growth-arrested cells. A genome-wide increase in H4K20me3 was observed in quiescent cells, suggesting a general RNA-based targeting mechanism that directs Suv4-20h2 to regulatory sequences, creating a chromatin environment that impairs transcription. The results link growth-dependent transcriptional regulation to transcription of antisense RNA and trimethylation of H4K20, suggesting a compelling mechanism of gene regulation that links changes in chromatin structure to cell growth and proliferation.


Ingrid Grummt received her PhD in 1970 at the Humboldt-University in Berlin, worked as a Postdoc at the German Academy of Sciences in Berlin-Buch and the Max-Planck-Institute of Biochemistry in Munich, and has led a research group since 1977. She has been Head of a Research Division at the German Cancer Research Center in Heidelberg since 1990 where she addresses the mechanisms that link transcription to cell proliferation and chromatin structure, focusing on the role of ncRNA in chromatin structure and epigenetic regulation. Her work has uncovered a novel RNA-based strategy for epigenetic programming, demonstrating that DNA:RNA triplexes serve as binding platforms for chromatin modifying enzymes.

She is an elected member of several academic councils and scientific advisory boards and has received numerous awards for her work, ranging from the Gottfried Wilhelm Leibniz Prize for German Scientists in 1990 to the FEBS/EMBO Women in Science Award in 2010.

Wellcome Trust Centre for Cell Biology, University of Edinburgh

The Dinucleotide CG as a Genomic Signalling Module

The DNA sequence 5'CG (CpG) is unusual in several respects. It is self-complementary and can exist in three chemical forms depending on the modification status of its cytosine moiety. To understand the functional significance of the CpG dinucleotide, we study proteins that bind either its methylated or unmethylated form. These proteins are likely mediators of CpG signalling that influence chromatin modification and thereby genome activity. The local density of CpG varies dramatically within genomic DNA. In the bulk genome CpG is rare and highly methylated, but in so-called "CpG islands" (CGIs) it is dense and usually non-methylated. A signature histone mark at non-methylated CGIs and also at transcriptionally active genes is trimethylation of histone H3 lysine 4. We are exploring the mechanisms by which DNA sequence features that are shared by all CGIs influence this and other epigenetic marks. Proteins binding to CpG appear to be key players in setting up "promoter-friendly" chromatin at CGIs. In contrast, proteins that interact with methyl-CpG promote gene silencing by recruiting transcriptional corepressors. In particular mutations in the gene for the methyl-CpG binding protein MeCP2 cause the autism spectrum disorder Rett Syndrome. By studying MeCP2 we are learning about both the biology of DNA methylation and the molecular pathology of this neurological condition.


Adrian Bird, who holds the Buchanan Chair of Genetics at the University of Edinburgh, studies the basic biology and biomedical significance of DNA methylation. His laboratory identified CpG islands as gene markers in the vertebrate genome and discovered proteins that read the DNA methylation signal to influence chromatin structure. Mutations in one of these proteins, MeCP2, cause the autism spectrum disorder Rett Syndrome. Dr Bird's laboratory established a mouse model of Rett Syndrome and showed that the resulting severe neurological phenotype in mice can be cured. Awards include the Louis-Jeantet Prize for Medicine (1999) and the Gairdner International Award (2011).



The EMBO Meeting
facebook twitter youtube
Sign up to: