Research articles

In fission yeast, the DNA damage kinases Tel1 (ATM) and Rad3 (ATR) are required to recruit telomerase to telomere. The relevant target for these kinases is now identified: shelterin subunit Ccq1 is phosphorylated at Thr93 in a Tel1/Rad3-dependent manner, and this modification is essential for Ccq1 to interact with telomerase subunit Est1.

The EGFR receptor tyrosine kinase is frequently mutated in lung cancer, but the mechanism by which mutations activate kinase activity are not clear. Using purified, nearly full-length EGFR, it is now seen that mutations drive activation and resistance to inhibitors through the formation of the asymmetric kinase domain dimer.

Rnf8 is an E3 ligase involved in the DNA damage response, adding ubiquitin moieties to histones H2A and H2AX at sites of DNA damage. Now Rnf8 is found to modify shelterin subunit Tpp1, and this is important for its stability and retention at telomeres. Cells lacking Rnf8 show telomere shortening and chromosome fusions.

Telomerase uses its associated RNA as a template for processive addition of telomeric DNA repeats. Biochemistry and smFRET analysis are now used to investigate how the RNA template moves along the active site, revealing an accordion mechanism whereby the regions flanking the template alternate between extended and compacted forms.

The Fanconi anemia (FA) DNA-repair pathway is important in processing of DNA interstrand cross-links and in resistance to exogenously added aldehyde. Genetic analyses now reveal the synthetic lethality of deficiencies in the FA pathway and formaldehyde catabolism, indicting that this pathway repairs lesions caused by endogenous formaldehyde.

The FET family proteins FUS, EWSR1 and TAF15 are RNA-binding proteins with diverse nuclear functions. PAR-CLIP analyses now reveal the genome-wide RNA targets of all three human FET proteins and of two FUS mutants that cause amyotrophic lateral sclerosis. Although the RNA-binding properties of the mutants remain unchanged, the spectrum of RNA targets is altered because of the changed subcellular localization of the mutants.

The RITS complex links the RNAi pathway with centromeric heterochromatin formation in fission yeast and comprises the chromodomain protein Chp1, the GW protein Tas3 and the argonaute protein Ago1. X-ray analysis of the structured core of the Chp1–Tas3 subcomplex reveals the presence of a C-terminal PIN domain in Chp1, which contributes to post-transcriptional gene silencing of subtelomeric transcripts independently of RNAi.

Histone acetyltransferase Tip60 is required to activate several target genes of ERα. Now Tip60 is shown to interact directly with ERα and to recognize the enhancer marker H3K4me1, leading to transcriptional activation in response to estrogen.

NSP and Cas family proteins form multidomain signaling platforms that integrate signals to mediate cell migration and invasion. Structural analyses show that the C-terminal domain of human NSP protein BCAR3 adopts the Cdc25-homology fold of Ras GTPase exchange factors, but in a closed conformation incompatible with enzymatic activity. Instead, this closed conformation is instrumental for interactions with Cas proteins.

What happens to histones during transcription is not well understood. Atomic force microscopy snapshots of RNA polymerase II (Pol II)-nucleosome complexes before, during and after transcription show the presence of looped transcriptional intermediates. In addition, a fraction of transcribed histones are remodeled to hexasomes, and the size of this fraction depends on the elongation rate of Pol II.

Common fragile sites (CFSs) can drive genomic instability. The basis for their fragile nature is not clear, but lymphocyte CFSs have been mapped to regions with low replication initiation events and late replication completion. These features are now used to rapidly identify CFSs in different fibroblast cells.

The enzyme Rubisco has a central role in atmospheric CO₂ fixation. Rubisco can be inactivated if its sugar substrate is bound prior to carbamylation of a residue in the active site. The structure of tobacco Rca, the enzyme that removes the bound sugar substrate and activates Rubisco, is now presented, offering insight into this process.

The mechanism by which the noncanonical E1-like enzyme Atg7 activates ubiquitin-like Atg8 to trigger autophagy has not been well understood. The crystal structures of the N-terminal domain of Atg7 alone and C-terminal domain of Atg7 in complex with Atg8 show that this probably proceeds without the need for dramatic conformational rearrangements by Atg7, distinct from other E1 enzymes.

Restoration of p53 activity is a promising chemotherapeutic approach, and because of the high binding affinity between HAUSP, MDM2 and p53, blocking HAUSP activity should have the net effect of robust p53 stabilization. HAUSP is inhibited by belt-like binding of vIRF4 from Kaposi's sarcoma–associated herpesvirus. Two peptides derived from vIRF4 can additively inhibit HAUSP, leading to p53-dependent cell cycle arrest and xenograft tumor regression.

SRP-type GTPases deviate from other GTPases in that they are not activated by GTPase-activating proteins (GAPs). New studies show that the MinD-type protein YlxH activates the SRP-GTPase FlhF, which is involved in flagellar biosynthesis. The crystal structure of the Bacillus subtilis FlhF–effector complex reveals the mechanism of activation, the general concept of which may also apply to RNA-mediated activation of the SRP-GTPases Ffh and FtsY.

Co-transcriptional splicing has been seen in lower eukaryotes as well as for a few mammalian genes, but the extent to which it affects mammalian gene regulation has been unclear. RNA sequencing now shows that co-transcriptional splicing is widespread in human cells and particularly abundant in the human brain.

The eukaryotic proteasome is composed of a regulatory particle and a core particle. Now protein cross-linking is used to map the contacts between regulatory particle and core particle subunits, revealing that some Rpt subunits engage with the core particle in a dynamic fashion that is regulated by nucleotide binding and hydrolysis.

The mitochondrial transcription factor Tfam has a role in organizing the mitochondrial genome, in addition to its transcriptional function. Structural studies of human Tfam in complex with a mitochondrial DNA promoter show that Tfam imposes a U-turn on the DNA similarly to the unrelated HU family of proteins, which play analogous architectural roles in organizing bacterial nucleoids.

The human mitochondrial transcription factor TFAM is essential for DNA packaging as well as transcription. X-ray analysis of TFAM in complex with a mitochondrial promoter reveals that TFAM induces a 180-degree bend in the DNA, which creates an optimal DNA arrangement for transcription initiation, while facilitating DNA compaction of the mitochondrial genome elsewhere.

During protein synthesis, mRNA and tRNAs are iteratively translocated by the ribosome, but which molecular event is rate limiting for translocation has been unknown. Kinetics analyses now reveal that disruption of the interactions between the A-site codon and the ribosome accelerates translocation, suggesting that mRNA release from the decoding center of the ribosome is the rate-limiting step.