Volume 19 Issue 1, January 2012

Is there upregulation of the single active X chromosome in mammals or not? Recent studies take different points of view.

Oncogene-induced replication stress and DNA damage are among the hallmarks of cancer. A recent study explores how different levels of replication stress affect animal development and tumorigenesis, and how targeting of the replication stress–signaling pathway of ATR and Chk1 kinases can be exploited for selective killing of cancer cells.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

Recent work has indicated that the Escherichia coli replisome contains three DNA polymerases that are used to replicate two parental strands. A single-molecule approach is now used to compare replisomes reconstituted with two or three polymerases, revealing that the presence of a third polymerase ensures higher processivity overall and more efficient replication of the lagging strand.

The combination of an F-box domain with a single-domain antibody that recognizes green fluorescent protein (GFP) now allows controlled depletion of GFP fusions in mammalian cells and in flies. This system, called deGradFP, should be widely useful, as GFP fusions are available for many proteins in model organisms.

NTPases use a metal ion, typically Mg²⁺, coordinated by a conserved serine or threonine residue, to enable phosphate binding and catalysis. Now cysteine substitutions at the switch 1 motif of different kinesins render them able to use Mn²⁺ instead of Mg²⁺, allowing their enzymatic and motor activities to be modulated by the ratio of Mg²⁺ to Mn²⁺.