MOST SIGNIFICANT DISCOVERIES
We decipher how FACT is recruited to active genes, a long-standing question in the field. Our work shows that FACT is recruited to the first nucleosome encountered by the RNA polymerase II after initiation. FACT recognizes the nucleosome as its DNA is being peeled off from the histone octamer by the engaging polymerase. Hence, FACT is targeted to transcribed regions without the need of a recruiting factor. Once bound to the first nucleosome, FACT is transferred to the next nucleosome with the help the chromatin remodeler Chd1. This process requires the chromatin remodeling activity of Chd1, but does not require the previously described interaction between Chd1 and FACT.
We showed that the histone chaperones FACT and Spt6 are required for the maintenance of histone modification patterns along genes during transcription. In the absence of FACT or Spt6, transcription leads to histone eviction. The evicted histones are reincorporated by other chromatin assembly pathways, leading to mislocalization of the histone marks they carry. This work highlights the importance of FACT and Spt6 in epigenetics maintenance.
We showed that the tyrosines in the RNA pol II CTD mediate pausing events early after initiation. This pausing contributes to the termination of non-coding RNA transcription by the Nrd1-Nab3-Sen1 pathway. This represents a first hint as to how pausing is regulated in Saccharomyces cerevisiae.
We described a dynamic model for how the different Mediator modules interact with genes. The Kinase module is recruited to upstream activating sequences (UAS) with the whole Mediator, where it negatively regulates Mediator-UAS interactions via its kinase activity. The Kinase module is then released from the complex upon integration of Mediator into the pre-initiation complex (PIC). Surprisingly, we found that the Tail module, which is required for the recruitment of Mediator to UAS, is dispensable for Mediator to interact with the PIC. The essential (core) function of Mediator is therefore carried out by the Head and Middle modules at the PIC and is regulated by the Kinase and Tail modules, respectively impairing and increasing Mediator occupancy at the neighboring UAS.
H2A.Z is incorporated in promoter nucleosomes via the targeted recruitment of SWR-C, but whether additional mechanisms contribute to H2A.Z distribution is unclear. In a paper published in Molecular Cell, we showed that the histone chaperones FACT and Spt6 prevent accumulation of H2A.Z in gene bodies. This work also showed that H2A.Z mislocalization contributes to cryptic transcription.
We performed a thorough analysis of the genomic localization of Mediator in budding yeast. Our work revealed that Mediator remains associated with upstream activating sequences until it becomes transiently associated with core promoters during initiation. Phosphorylation of the CTD of Rpb1 at Ser5 by Kin28 releases Mediator prior to elongation.
We deciphered how the RNAPII CTD phosphorylation cycle is established. We showed that the cycle is similar at virtually all genes and that a complex interplay between kinases, phosphatases and a prolyl isomerase are involved in its establishment.
We showed that the Rpd3S complex, previously thought to be recruited to genes via the recognition of some histone modifications, is actually recruited in two steps. Prior to be anchored on methylated nucleosomes, Rpd3S has to be recruited to the elongating RNAPII in a manner that require the phosphorylation of the CTD and which is regulated by the elongation factor DSIF.
We published a genome-wide map of gammaH2AX, therefore defining fragile sites in the yeast genome. We made the surprising discovery that transcriptionally repressed loci are among the most fragile sites. This has important implications in our understanding of genomic instabilities.
We showed that human H2A.Z in not only found in promoters and regulatory elements but is also part of facultative heterochromatin. We also made the surprising finding that transcription plays a role in establishing proper H2A.Z patterns.
We have measured histone dynamics at the genomic level and found that nucleosomes in promoters are the most labile of the genome. We also showed that the chaperone Asf1 is involved in this process. This finding has important implications in the regulation of transcription.
We have made a series of computational predictions for regulatory modules across the human genome. These allowed us to discover general characteristics of regulatory elements and the transcription factors that associate with them.
We determine the genome-wide location of the variant histone H2A.Z and discovered that it associates with specific nucleosomes in most promoters. We also showed that the incorporation of H2A.Z within a nucleosome can influence its positioning. These discoveries had a great impact on our understanding of the function of this histone variant.