In a paper published online in advance in Cell this week, a team led by investigators at Cornell University reports on "the immediate effects of estrogen signaling on the transcriptome of breast cancer cells using global run-on and sequencing — GRO-seq." Notably, the team found that estrogen signaling "directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner." In particular, the team shows that estrogen signaling regulates all three RNA polymerases and a variety of non-coding RNAs.
In another Cell advance online publication, researchers at the University of California, San Francisco, and their colleagues at the Broad Institute and elsewhere describe "an epigenetic signature for monoallelic olfactory receptor expression." Magklara et al. report data suggesting that olfactory receptor gene silencing occurs before OR gene expression, thus "indicating that it is not the product of an OR-elicited feedback signal," a finding that contrasts the current view of the "process of OR choice."
An international team led by investigators at The Hebrew University in Jerusalem reports its investigation of the replication dynamics of newly transformed cells, in which it found that the "increased transcription of nucleotide biosynthesis genes, mediated by expressing the transcription factor c-myc, increased the nucleotide pool and also rescued … replication-induced DNA damage." The researchers suggest "a model for early oncogenesis in which uncoordinated activation of factors regulating cell proliferation leads to insufficient nucleotides that fail to support normal replication and genome stability."
And in a Cell resource appearing in the current issue, researchers at the University of California, San Diego, and their colleagues report profiling 554 key C. elegans genes "by imaging gonad architecture and scoring 94 phenotypic features." With the resulting data, the team manually partitioned the genes into 102 phenotypic classes and predicted functions — across diverse processes — for all uncharacterized genes. "Using this classification as a benchmark, we developed a robust computational method for constructing gene networks from high-content profiles based on a network context-dependent measure that ranks the significance of links between genes," the authors write, adding that "multi-parametric profiling in a complex tissue yields functional maps with a resolution similar to genetic interaction-based profiling in unicellular eukaryotes."