Articles in 2012

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

Procollagen, the precursor of collagen, contains a large C-terminal domain called COLFI that initiates homotrimerization and harbors mutations associated with different diseases. Now the crystal structure of the COLFI domain from human procollagen III is presented, revealing the mechanisms for specificity of trimer formation and the position of disease-related mutations.

Most membrane proteins are co-translationally inserted into the membrane with the aid of Sec-type translocons. Using so-called translation-arrest peptides derived from bacterial and mammalian proteins as natural force sensors, a new study now demonstrates how force is exerted on a nascent chain at two distinct points in a transmembrane helix during its transit through the translocon channel into the membrane.

APOBEC3 (A3) proteins are cytidine deaminases that can restrict retroviral replication by causing hypermutation of the viral genome. The HIV-1 protein Vif counteracts the action of A3s by promoting their degradation. Now the crystal structure of A3C and homology models for A3F and A3DE, together with mutagenesis analyses, allow the identification of their interaction interface with Vif, which is different from a previously implicated region in A3G.

The mechanisms that initiate heterochromatin formation and maintain its distinction from euchromatin have remained elusive. However, a new study reveals a pathway in which transcriptional repression of pericentric repeats by sequence-specific transcription factors is essential for the integrity of heterochromatin, thereby considerably expanding the role of transcription factors beyond euchromatic gene regulation.

The function of nuclear Argonaute proteins in somatic mammalian cells has remained elusive. A new study shows that chromatin-bound Argonaute-1 and Argonaute-2 associate with splicing factors and affect the deposition of histone marks, thereby facilitating spliceosome recruitment and modulating the RNA polymerase II elongation rate. This in turn favors inclusion of variant exons in the mature mRNA.

Rail1 is a component of the mRNA 5′-end quality-control mechanism in yeast. Structural, biochemical and functional studies of its homolog in Kluyveromyces lactis now reveal that the enzyme, dubbed Dxo1, has not only decapping but also 5′-3′ exonuclease activity, enabling it to single-handedly decap and degrade mRNAs from the 5′ end.

The exon junction complex (EJC) links splicing to downstream events including mRNA localization, translation and stability. A combination of in vitro and in vivo approaches were used to identify the splicing factor CWC22 as a direct partner of EJC component eIF4AIII in flies and humans and to demonstrate its functions in preventing eIF4AIII binding to RNA and in escorting eIF4AIII to active spliceosomes before EJC assembly.

Synaptotagmin promotes SNARE-mediated membrane fusion in a Ca²⁺-dependent manner, but the mechanism by which it acts is still unclear. In vitro studies have shown that synaptotagmin can make interactions with its own vesicle membrane, inhibiting its ability to stimulate fusion with target membranes. New data now suggest that ATP and other polybasic anions may have a role in directing synaptotagmin to its target membrane in vivo.