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In fission yeast, the RNAi pathway has been linked to formation of heterochromatin at centromeres. Fusing Dicer to DNA adenine methyltransferase now revealed that Dcr1 also associates with euchromatic regions of the S. pombe genome to mediate co-transcriptional gene silencing.
Antibodies are a primary tool to assess histone post-translational modifications. However, different antibodies and batches might vary in their ability to recognize those modifications, depending on the kind of assay used. Now a systematic analysis of different antibodies and an open database containing the validation results are presented.
Nucleosomes consist of two copies of each histone. H2A.Z is a variant H2A-related histone known to be enriched around transcription start sites. However, an H2A.Z-containing nucleosome could contain contain two copies of H2A.Z (homotypic) or one of H2A.Z and one of canonical H2A (heterotypic). Homotypic and heterotypic H2A.Z nucleosomes are now mapped and their distributions relative to promoters analyzed.
The C-terminal domain (CTD) of RNA polymerase II (Pol II) contains a number of repeats, phosphorylation of which influences RNA processing factor recruitment. Genome-wide CTD phosphorylation is now assessed and found not to be scaled to gene length. The kinases mediating these modifications are found not to alter Pol II distribution across a given gene uniformly, arguing that CTD phosphorylation is gene specific.
The genome-wide occupancy profiles for yeast RNA polymerase II in different phosphorylated forms, as well as transcription factors, are presented. The resulting analysis captures a 5' transition in which initiation factors are replaced by a general set of elongation factors that form a productive complex, which disassembles in two steps at the 3' end of the gene.
RNA polymerase II is post-translationally modified on its C terminal domain and these modifications have been associated with different states of Pol II transcription. These modifications are now examined at a genome-wide level, and chemical inhibitors are used to argue that promoter-distal Ser7P is specifically placed anew by the Bur1 kinase.
Recently described tiny RNAs (tiRNAs) are derived from sequences immediately downstream of transcriptional start sites. Here a second class of nuclear ∼17–18 nucleotide small RNAs is described and found to map to the splice donor site of internal exons.
Accessibility may play a key regulatory role affecting factors that bind to or target DNA. Using accessibility to DNA methyltransferases, the genome-wide profile of DNA accessibility in Drosophila melanogaster is presented and analyzed, indicating correlations with PcG repression, H4K16 acetylation and replication initiation.
A quantitative genetic interaction map, or E-MAP, of ∼400 genes involved in plasma membrane biology, in combination with triplet genetic motif analysis, has led to the identification of a new component of the eisosome, Eis1, links the poorly characterized EMP70 gene to endocytic and eisosome functions, and uncovers a link between Rom2—a GDP/GTP exchange factor for Rho1 and Rho2—and the regulation of sphingolipid metabolism.
Genome-wide analysis of the chromatin modification patterns at Pol III genes showed a correlation between histone modifications and tissue specific transcription of Pol III genes. Surprisingly, it was also discovered that Pol II and its associated basal factors are recruited to expressed Pol III transcribed genes. One idea is that Pol II could help keep chromatin around Pol III genes in an open state.
Genome wide analysis of human RNA Polymerase III (Pol) reveals both known and new targets of Pol III, with many of the latter binding regions found near SINEs. Active Pol III genes are near active Pol II promoters, whereas inactive Pol III genes are not. ETC loci, which are bound by TFIIIC but not TFIIIB and Pol III, are near active Pol II promoters and CTCF binding sites.
RNA polymerase (Pol) III transcribes small noncoding RNAs important in translation. Using genomics approaches, Pol III genes are now found to be in close proximity to Pol II genes and Pol III is localized to regions of active chromatin and high CpG content. One idea is that active chromatin could provide Pol III with access to the genome.
Nucleosome occupancy can affect the accessibility of DNA to other factors. A genome-wide map of nucleosomes in Schizosaccharomyces pombe is now presented. Comparisons to published Saccharomyces cerevisiae maps reveal species-specific differences arguing for evolutionary plasticity of nucleosome positioning mechanisms.
