Volume 19 Issue 11, November 2012

TET and JBP proteins catalyze the oxidation of methylated C bases in the mammalian genome and of the methyl group of T bases in kinetoplastid genomes, respectively. A recent study in Nature Structural & Molecular Biology suggests a new function of 5-methylcytosine oxidation in regulating RNA polymerase II elongation rate that is reminiscent of that of base J in transcription termination in Leishmania.

According to the 'classical' view, histone modifications are established in an identical fashion on both copies of each of the four core histones, resulting in 'symmetrically' modified nucleosomes. Now, a new study challenges this notion by demonstrating that asymmetric histone modifications exist on individual mononucleosomes in native chromatin and that symmetric and asymmetric modifications signal different biological outcomes, suggesting a radically expanded histone code.

The number and types of known functional noncoding RNAs (ncRNAs) has increased considerably over the past few years, and both cis- and trans-acting ncRNAs have been reported. This Review focuses on long- and short-sized ncRNAs that act in cis; that is, where both the regulatory RNA and the target gene are transcribed from the same locus.

Histone H2A.Z-containing nucleosomes flank the transcription start sites (TSSs) of active mammalian genes. A new study reveals that histone H2A.Z at the TSS is reduced during S phase, which coincides with its gain at centromeric and subtelomeric regions during M phase and mirrors an expansion of the nucleosome-depleted region, which, surprisingly, is unrelated to transcriptional activity.

The AAA ATPase p97 (VCP) is thought to remove specific proteins from chromatin at sites of DNA damage, to allow proper repair or processing, but how p97 targets those sites was unclear. The protein DVC1 is now shown to localize to sites of replication stress and UV-light damage, and to be required for p97 recruitment. DVC1's localization to DNA damage sites requires its UBZ domain and PCNA-interacting motif but not PCNA ubiquitination. DVC1 deficiency caused retention of error-prone translesion polymerase η at foci after UV-light damage and increased mutagenesis levels.

The AAA ATPase p97 (VCP) is thought to remove specific proteins from chromatin at sites of DNA damage, to allow proper repair or processing, but how p97 targets those sites was unclear. The protein DVC1 is now shown to localize to sites of replication stress and UV-light damage, and to be required for p97 recruitment. DVC1's localization to DNA damage sites requires its UBZ domain and PCNA-interacting motif but not PCNA ubiquitination. DVC1 deficiency caused retention of error-prone translesion polymerase η at foci after UV-light damage and increased mutagenesis levels.

The kinase CDC7 is essential for replication initiation in eukaryote organisms. To exert its function, CDC7 requires its activator, DBF4. Now the crystal structures of a minimal CDC7–DBF4 complex, with bound nucleotide or inhibitor, along with functional analyses reveal that DBF4 wraps around CDC7, stabilizing the αC helix in the N lobe and tethering the C lobe of the kinase.

RNA polymerase II (pol II) frequently pauses in the promoter-proximal region to ensure gene-specific regulation and RNA quality control. New research demonstrates that the cyclin-dependent kinase Cdk7 can act to establish the promoter-proximal pause, through its control of the TFIIE-DSIF switch, and to release Pol II from the pause, through its ability to activate Cdk9.

Activation of the anaphase-promoting complex/cyclosome (APC/C) depends on disassembly of the mitotic checkpoint complex (MCC), which has been proposed to require CDC20 autoubiquitylation. A new study involving reconstituted recombinant human APC/C supports the view that the APC15 subunit of APC/C localizes near the MCC binding site and mediates CDC20 autoubiquitylation, thereby promoting MCC disassembly.

The exon junction complex (EJC) has a crucial role in various post-transcriptional control mechanisms. CLIP-Seq analysis of the human EJC component eIF4AIII has revealed peaks in canonical EJC-binding regions, including ~24 nucleotides upstream of exon junctions. Surprisingly, EJCs are also present elsewhere in the transcriptome, uncovering an unexpected heterogeneity of EJC association with mRNAs.

In Gram-negative bacterial outer membranes, lipid A serves as the anchor for lipopolysaccharide. Structural and biochemical data reveal that LpxI, an enzyme involved in lipid A synthesis, uses a hinge-like mechanism to deposit its product into the membrane through the binding of fresh substrate.

Both epigenetic and splicing regulation contribute to tumor progression, but how these contributions are linked is not well understood. A new study reveals a cascade of altered gene-expression events that underlie tumor progression, wherein splicing factors Ddx5 and Ddx17 control the alternative splicing of an epigenetic factor, macroH2A1, leading to transcriptional alterations that switch tumor cells to an invasive phenotype.

Type IIA topoisomerases (topos) control supercoiling and disentangle chromosomes by an ATP-dependent strand-passage mechanism. The structure of a full-length budding-yeast topo II in complex with DNA and an ATP analog now provides a picture of its architecture, revealing a structural basis for unidirectional strand passage and a DNA-induced control mechanism for ATP hydrolysis and topo activity.

The E3 ubiquitin ligase UHRF1 has been genetically linked to the establishment and maintenance of DNA methylation in mammals. A new study now provides mechanistic insight by demonstrating that binding of UHRF1 to methylated histone H3 lysine 9 during mitosis is needed for stability of DNA methyltransferase 1 and the faithful propagation of DNA methylation.

Microtubules bind to the kinetochore at the Ndc80 complex, and this interaction is regulated by phosphorylation events at the N-terminal tail of Ndc80, mediated by the Aurora B kinase. The distinct functions of Ndc80 N-terminal tail are now dissected, revealing a region that binds tubulin and another that contacts the globular head of Ndc80. Both contacts are disrupted by phosphorylation, and the results lead to a mechanistic model for how phosphorylation of Ndc80 controls its interactions with microtubules.

The biological importance of large numbers of retrotransposon-derived Alu repeats present in the human genome has been mysterious. New research reveals that many Alu repeats are bound and induced by retinoic acid receptor to generate RNA polymerase III–dependent transcripts, which are processed in a Dicer-dependent manner. The resulting short, so-called riRNAs post-transcriptionally downregulate target mRNAs, thereby modulating stem-cell proliferation.

Adenovirus infection can suppress antigen presentation by MHC I, by the action of transmembrane protein E3-19K, whose N-terminal domain localizes to the ER lumen and binds MHC I luminal domain. Now the crystal structure of E3-19K in complex with MHC I molecule HLA-A2 is presented, providing atomic-level insight into this interaction.

Adenosylcobalamin is a form of vitamin B₁₂ that serves as a coenzyme in different reactions and as a ligand for riboswitches to control bacterial gene expression. The crystal structure of a B₁₂ riboswitch from Symbiobacterium thermophilum bound to its ligand adenosylcobalamin is now presented, revealing the determinants for ligand recognition and gene expression control.

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.

Previous studies have shown the potential for convergent transcription as a way to induce gene silencing. This Technical Report now demonstrates that introducing convergent transcription plasmids into either fission yeast or mammalian cells can be used to mediate long-term transcriptional gene silencing of endogenous genes, with major advantages over other gene silencing strategies.