the binding of elongation factors but impairs the binding of ter- mination factors. Phosphorylation of Tyr1 decreases before the polyadenylation site, which then facilitates binding of the termi- nation factors.12 Histone Modification and Cryptic Transcription Jerry Workman, from the Stowers Institute for Medical Research, presented his latest contributions to understanding Set2-mediated H3K36 methylation and its role in regulating histone exchange at transcribed genes. Set2 interacts with elongating RNAP II and methylates H3K36 co-transcriptionally. This not only prevents histone exchange over the coding regions, but also recruits the histone deacetylase Rpd3S, leading to suppression of cryptic transcripts. This suggested that co-transcriptional acetylation is a consequence of histone exchange. Probing for a mechanism to explain histone exchange suppression, Dr Workman’s group found that the Isw1 and Chd1 chromatin remodelers associ- ate with H3K36me3, to which the Isw1b complex is recruited. Catalytic mutants or depletion of ISW1 and CHD1 caused wide- spread cryptic transcription and caused increased exchange of histones at transcribed genes. Depletion of ISW1 predominantly affected infrequently transcribed genes, whereas CHD1 had a stronger effect on genes transcribed over ten times per hour. Depletion of both remodeling enzymes increased histone acetyla- tion. Together, these data reveal an exciting new role for ISW1, CHD1 and chromatin structure in suppressing cryptic transcrip- tion in yeast.13,14 Stephen Buratowski (Harvard Medical School) presented a model for the role of co-transcriptional histone modifications and non-coding RNA (ncRNA) in gene expression. In collaboration with Lars Steinmetz (EMBL, Germany), Dr Buratowski found that Set3 suppresses the initiation of cryptic ncRNA transcrip- tion in regions where H3K4me2 is highest. Cryptic 3' end anti- sense ncRNAs overlap with the gene body and slow the kinetics of gene induction. Antisense transcripts likely function by recruit- ing H3K4me2 to the gene promoter. As H3K4me2 recruits Set3 and, thus, deacetylation,15 cryptic transcription may function by delaying the gene regulatory circuit. This would ensure that gene expression is only upregulated by persistent signals. Frank Holstege, from the University Medical Center Utrecht (Netherlands), presented his advances in the development of a method to analyze the effect that deletion of each regulator has on gene expression in yeast. This approach allowed the identi- fication of linear signaling pathways and smaller protein (sub) complexes, as well as the topology of chromatin interaction path- ways. Dr Holstege found that loss of H3K4 methylation by Set1 knockout caused derepression and delays in repression kinetics. Genes affected by Set1 showed H3K4me3 signatures at the 3' end, as well as 3' end antisense transcripts that are involved in gene repression. Set1 knockout decreased 3' end antisense tran- scription, thereby promoting sense transcription.18 In yeast, H3K4me1–3 and Set1 are thus involved in repression through 3' end antisense transcription. Expression Fine-Tuning Transcription of genes in metazoans is often regulated during early elongation, when RNAP II pauses during initial RNA syn- thesis. Karen Adelman (NIEHS/NIH) reported that genes with paused RNAP II are particularly enriched in developmental or stimulus responsive pathways. The negative elongation factor (NELF) induces pausing to keep RNAP II near these promot- ers. Interestingly, Dr Adelman showed that NELF knockdown did not release RNAP II downstream, but decreased the level of RNAP II at the promoter and within the gene body, down- regulating gene expression. This resulted from an increase in pro- moter nucleosome occupancy, suggesting that paused RNAP II and chromatin compete for promoter binding. Paused RNAP II was significantly enriched at genes encoding immune signaling components. In addition, NELF depletion globally dampened the immune response.16,17 Pausing thus seems to target key factors in signal transduction and plays an important role in fine-tuning gene expression. Chromatin Dynamics and Transcription Shannon Lauberth, from Robert Roeder’s lab at the Rockefeller University, presented a novel mechanism for DNA motif inde- pendent recruitment of the basal transcription machinery. Trimethylation of H3K4 selectively enhances p53-dependent transcription by stimulating the rate of pre-initiation complex (PIC) formation at the promoter. H3K4me3, but not H3K4, was sufficient to recruit the transcriptional machinery and initiate active transcription to an otherwise inactive promoter in vitro. Dr Lauberth found that the Taf3 subunit of TFIID was essen- tial for PIC recruitment to H3K4m3. Genome-wide binding of Taf3 overlaps with H3K4me3, suggesting that H3K4me3 may contribute to global TFIID recruitment, potentially in a core pro- moter motif independent manner. Modifications of histone tails are well known and were shown to play an important role in gene regulation. The role of modifi- cations on the lateral surface of histones, however, is less known. Robert Schneider (Max Planck Institute of Immunobiology and Epigenetics, Germany, now at IGBMC in Strasbourg, France) presented a mechanism for a previously unidentified acetylation residue to function as a transcription stimulating, lateral surface chromatin mark. This residue is located close to the pseudo-dyad of the nucleosome and its modifications have the potential to impact chromatin dynamics and structure. Dr Schneider showed that acetylation of this residue correlates with gene expression, active chromatin marks and histone variants H3.3 and H2A.Z. It also co-localizes with H3K4me and marks active and tissue- specific enhancers. Transcriptional activity of chromatin tem- plates was enhanced by acetylation of this single residue in vitro, which was rapidly acetylated by p300 upon gene induction in vivo. Mechanistic studies showed that acetylation on this core residue decreased nucleosome stability and increased the rate of DNA dissociation, likely stimulating transcription via histone www.landesbioscience.com Epigenetics 1213