Resources

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.

A large-scale screen for changes in alternative splice forms in cancer now reveals that almost half of the active alternative splicing events are shifted in breast and ovarian cancer tissues. In addition, many of these changes occur near consensus binding sequences for FOX2 binding sites. This correlates with changes in Fox2 expression or splicing in tissues assessed, and FOX2 depletion results in similar shifts in splice isoforms.

A genome-wide analysis of methylated DNA from human embryonic stem cells and adult tissues provides a comprehensive view of unmethylated regions and leads to the identification of sequence motifs that can predict whether a region escapes de novo methylation. This algorithm is used to identify novel, non-CpG unmethylated regions, including intragenic and tissue-specific ones.

A comprehensive library encompassing alanine scanning mutations across yeast histones is presented as a Resource that will facilitate screening of chromatin processes. The utility of the library is indicated by screening in cis and in trans for residues that affect histone H3K4 trimethylation, a modification that is associated with actively transcribed genes and known to be mediated by the Set1-COMPASS complex.

The Schizosaccharomyces pombe SWI/SNF family of ATP-dependent chromatin-remodeling complexes is now comprehensively analyzed, through composition, phenotypic and microarray analyses, thus broadly setting the stage for S. pombe as a new model organism for examining the SWI/SNF family remodelers. The S. pombe complexes are more akin to the metazoan SWI/SNF remodelers and have specific roles in repression of iron-transport genes.