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mRNA-binding proteins have crucial regulatory functions in gene expression. A global analysis in budding yeast now uncovers 120 proteins that cross-link to mRNA, including 66 new mRNA-binding proteins. CLIP analyses of P-body components further identify sites of interaction on specific mRNAs, revealing principles by which these proteins assemble into P-body mRNPs.
Tissue- and disease-specific features of nucleosome positioning have recently been reported. A new study set out to identify features of nucleosome positioning at functional genomic elements during lineage commitment from mouse embryonic stem cells to neural progenitors and embryonic fibroblasts. The results reveal regulatory mechanisms of cell differentiation that involve nucleosome positioning.
A systematic, unbiased screen for general intronic splicing enhancers (ISEs) identified >100 ISEs that promote intron splicing but inhibit splicing in exons. Putative trans-factors for clusters of ISEs were identified, validated and were found to control ISE activity in a context-dependent manner. Altogether, the data provide a comprehensive picture of how ISEs function depending on their location and cognate trans-factors.
The 5-hydroxymethylcytosine (5-hmC) nucleoside is abundant in the brain for unknown reasons. Genome-wide analysis of the distribution of 5-hmC versus 5-methylcytosine (5-mC) in human and mouse tissues now shows that 5-hmC is enriched in genes with synaptic functions. The differential distribution of 5-hmC versus 5-mC at exon-intron boundaries in both human and mouse tissues further suggests a possible role for 5-hmC in pre-mRNA splicing.
RNA 3′-end formation is thought to be crucial in controlling gene expression. Direct RNA sequencing was used to analyze the 3′ ends of Arabidopsis thaliana RNA in unprecedented detail, revealing extreme heterogeneity of RNA 3′ ends, patterns of cleavage and polyadenylation, and previously unrecognized noncoding RNAs.
How metazoans determine where to initiate DNA replication remains mysterious. Now deep sequencing of short nascent strands in different human cell types provides an extensive map of replication origins, identifying cell type–specific signatures and a putative consensus motif with the potential to form G-quadruplex structures.
