Articles in 2011

Cis-encoded antisense RNAs (asRNAs) are transcribed from the DNA strand opposite another gene and function by pairing with RNAs expressed from the complementary strand. A new study provides evidence that a bacterial cis-asRNA acts in trans, using a domain outside of its target complementarity sequence, suggesting the need for a mechanistic re-evaluation of asRNA-based gene regulation.

The type III ribonuclease DCR-1 is essential for ERI endogenous RNAi and exogenous RNAi in Caenorhabditis elegans. A new study shows that DCR-1 forms exclusive complexes in each pathway, and characterization of the ERI complex implicates a tudor domain protein in tethering an RNA-dependent RNA polymerase to DCR-1 to potentiate endo-RNAi.

The Msn2 transcription factor is translocated to the nucleus to activate transcription of hundreds of genes in response to various environmental stimuli. Experimental and computational single-molecule analyses reveal how different stimuli elicit different dynamical patterns of Msn2 translocation, which are interpreted by promoters with distinct properties to produce specific patterns of target gene expression.

Eukaryotic MutSβ is a heterodimer composed of Msh2 and Msh3 that recognizes insertion-deletion loops (IDLs) and 3′ overhangs during mismatch repair. Now crystal structures of MutSβ in complex with DNA, containing IDLs of varying lengths, reveal that this complex interacts with its substrate differently than MutSα and bacterial MutS do.

Genome-wide association studies have established a link between the extracellular chaperone clusterin and susceptibility to Alzheimer's disease. A fluorescence approach is now used to reveal that clusterin sequesters Aβ_1–40 oligomers and prevents them from undergoing further aggregation.

The OTU domain deubiquitinase TRABID specifically hydrolyzes atypical Lys29- and Lys33-linked diubiquitin chains. Structural analysis of TRABID reveals an unpredicted ankyrin-repeat domain that binds ubiquitin and is crucial for TRABID efficiency and linkage specificity in vitro and in vivo.

Rab small G proteins regulate membrane trafficking events by recruiting effectors that mediate vesicle tethering. In vitro studies now suggest that Vps21 and other endosomal Rabs in budding yeast can undergo GTP-regulated Rab-Rab interactions that drive tethering in the absence of effectors, implying that they have an intrinsic tethering activity that may function in concert with conventional effectors.

Lin28 prevents the processing of pre-let-7 RNAs, but it is not clear where the Lin28 RNA binding domains interact with the RNA. The NMR structure of the Lin28 zinc knuckles with a short RNA motif reveals that each knuckle interacts with an AG dinucleotide, allowing the determination of a consensus motif for pre-let-7 recognition.

The histone variant H2A.Bbd inhibits folding of nucleosomal arrays and reverses chromatin-mediated transcriptional repression in vitro. New studies have uncovered the related mouse H2A variant H2A.Lap1 as a novel component of the transcription start site of active genes during specific stages of spermatogenesis, which enables transcriptional activation by unfolding the chromatin locally.

A system to reconstitute a collapsed replication fork using Xenopus laevis egg extracts is developed. The study shows that upon fork collapse, DNA Pol epsilon and the GINS complex are uncoupled from the replisome, and their reloading onto DNA requires repair proteins Rad51 and Mre11.

In addition to balancing X-chromosome dosage between males and females via X inactivation, mammals also balance dosage of X chromosomes and autosomes. Allele-specific chromatin immunoprecipitation with deep sequencing (ChIP-seq) analyses now show that the active X chromosome is upregulated at the level of both transcription initiation and elongation.

Ribonucleoside monophosphates (rNMPs) are often incorporated into genomic DNA. Misincorporated rNMPs are now shown to be repaired by mismatch repair and RNases H. If not repaired, they can serve as a template for DNA synthesis and can cause mutagenesis in Escherichia coli and yeast.

Kinetochores assemble on centromeric DNA and link centromeres to spindle microtubules, thus allowing proper segregation during mitosis. The kinetochore subunit Ndc10 makes contacts with centromeric DNA elements, which are now directly observed in a crystal structure. Along with biochemical analyses, the work indicates that Ndc10 functions as a central organizing hub to assemble the inner kinetochore.

Oncogenic activation can generate replicative stress, leading to activation of ATR and Chk1. The hypothesis that these events could be exploited to selectively kill cancer cells is now demonstrated in vivo, using mouse models for cancer development. Myc-driven tumors are shown to be sensitive to ATR deficiency or inhibition of Chk1.

The E3 ubiquitin ligases RNF8 and RNF168 are required for recruitment of tumor surpressor 53BP1 to sites of DNA double-strand breaks. The reasons for this have been unclear, as 53BP1 recognizes histone mark H4K20me2. Now the AAA-ATPase VCP and cofactors are shown to be recruited in a ubiquitination-dependent manner to double-strand break sites, where they remove polycomb protein L3MBTL1 from chromatin.

Dimethylated arginine (DMA) marks are recognized by Tudor domain–containing proteins and play a role in the assembly of ribonucleoprotein complexes. Structural analysis of prototypic Tudor domains from SMN and SPF30 in complex with DMA reveals the recognition mode of DMA, enabling the design of an optimized binding pocket.

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.