Research articles

A genome-wide mapping approach of DNA supercoiling in cells demonstrates that the genome is organized in supercoiling domains. Domains are formed and remodeled by transcription and topoisomerase activity and are flanked by GC-AT boundaries and CTCF binding sites. DNA supercoiling impacts on higher levels of chromatin organization and 'underwound' domains correlate with transcriptional activity.

The connection between dynamic DNA supercoiling and transcription is not well understood. High-resolution mapping of in vivo DNA supercoiling at transcription start sites (TSSs) now reveals that supercoils spread about 1.5 kb upstream of the TSSs of active genes. Highly expressed genes rely on topoisomerase II to dissipate dynamic supercoiling, whereas moderately expressed genes depend on topoisomerase I.

Naive pluripotent embryonic stem cells (ESCs) and embryonic germ cells (EGCs) have distinct developmental origins. Genome-wide expression and global DNA-methylation analyses now reveal that ESCs and ESGs are highly similar at the transcriptome level and, contrary to previous assumptions, are both characterized by DNA hypomethylation. Also, global methylation levels in both ESCs and EGCs are directly responsive to culture conditions.

Influenza virus hemagglutinin (HA) binds to sialic acid receptors on the host cell, but receptor analogs have failed as viral-entry inhibitors. Now crystal structures of H2 HA in complex with Fab fragments from three neutralizing antibodies reveal a new mode to target HA. All three antibodies use an aromatic residue to plug a conserved cavity in the HA-binding site for sialic acid.

The role of co-chaperone and Hsp90 activator Aha1 is now examined in conjunction with other co-chaperones in vivo and in vitro, to reveal how they regulate the progression of the Hsp90 cycle. Aha1 and Cpr6 interact with and activate Hsp90 in a synergistic manner and displace the inhibitory co-chaperone Sti1. Aha1 is eventually released from Hsp90 by p23.

The cytotoxic effects of topoisomerase I inhibitors such as camptothecin can be modulated by replication fork reversal, in a process that requires Poly(ADP-ribose) polymerase (PARP) activity. Here human RECQ1 helicase is shown to restore such regressed replication forks, whereas PARP1 activity restrains this RECQ1 function.

The regulatory importance of the C-terminal coiled-coil domain of PLCβ has long been known yet remains poorly understood. The crystal structure and cryo-EM reconstruction of full-length PLCβ3 bound to its activator Gα_q reveals that the C terminus makes contact with both the catalytic core and Gα_q to contribute to the complex regulation of the enzyme.

Competitive binding of 53BP1 and BRCA1 determines DNA repair pathway choice at double-strand breaks. New work shows that acetylation of H4K16 by TIP60 tips the balance in favor of BRCA1 by limiting 53BP1 binding, thereby promoting repair through homologous recombination over nonhomologous end joining.

Trim24 and Trim33 are co-repressor complexes that suppress hepatocarcinogenesis. A new study now uncovers a function for Trim24 and Trim33 as repressors of VL30-type endogenous retroviruses in the liver. When derepressed, VL30 long terminal repeats (LTRs) function as promoter and enhancer elements deregulating expression of neighboring genes and generating noncoding enhancer RNAs that are required for LTR enhancer activity in hepatocytes.

Oligomeric Trax–Translin complexes, known as C3PO, are involved in RNA interference and tRNA processing in eukaryotic species including humans. Structural and functional analysis of a Trax-like protein from Archaeoglobus fulgidus that forms an octameric assembly resembling human C3PO provides insight into the mechanism of RNA recognition and cleavage.

Repetitive elements in differentiated cells are usually silenced. Genome-wide analyses in early mouse development show that repetitive-element expression decreases during development accompanied by the loss of active chromatin marks. LINE-1 and IAP retrotransposons become reactivated after fertilization, and LINE-1 transcription is regulated by short LINE-1 RNAs, which suggests that repetitive elements may be regulated through RNA during the earliest developmental stages.

Prokaryotic condensins usually comprise an SMC homodimer, kleisin ScpA and ScpB. Structural and functional analyses of Bacillus subtilis condesin reveal an asymmetric bridge in which the termini of ScpA bind to distinct regions in each of the two SMC monomers. The findings suggest that the basic architecture for the tripartite condensin ring evolved before the emergence of eukaryotes.

GltPh is a homotrimeric Na+-coupled aspartate transporter that belongs to the glutamate transporter family. The conformational changes that occur during GltPh transport are now directly observed using EPR spectroscopy, revealing that the transporting domains sample multiple states, regardless of the presence of substrate or ions.

The ISWI chromatin remodelers interact with extranucleosomal DNA to mediate nucleosome positioning. A new study now shows that the conserved SLIDE domain in the Isw2 subunit, which binds linker DNA, facilitates unidirectional linker DNA movement into nucleosomes. These findings suggest that the SLIDE domain functions in conjunction with the ATPase domain to mobilize nucleosomes.

The sodium and aspartate symporter Glt_Ph mediates transport by alternating between outward-facing and inward-facing states. These conformational changes are now probed using double electron-electron resonance (DEER) spectroscopy. The data show that Glt_Ph samples both states with similar probabilities, and that each protomer in the Glt_Ph homotrimer behaves independently of the others.

Crystal structures of HIV-1 reverse transcriptase (RT) bound to an RNA/DNA hybrid (without any cross-linking) and in the presence of non-nucleotide RT inhibitors (NNRTIs) nevirapine and efavirenz are now reported. The structures show the RNA/DNA hybrid in a previously unseen conformation with ready access to the RNase-H active site of RT.

In budding yeast, EcoI acetylates cohesin to establish sister chromatid cohesion in S phase. EcoI is subsequently modified by the ubiquitin E3 ligase SCF-Cdc4 and rapidly degraded. New work shows how sequential phosphorylation by three independent kinases generates a binding site for SCF-Cdc4 to promote EcoI degradation, thereby coupling EcoI activity, and thus sister chromatid cohesion, to the cell cycle.

The MSL complex acts on chromatin to and is required for X-chromosome dosage compensation. Chromatin-interacting protein MS (ChIP-MS) is now used to identify proteins and histone modifications interacting with the MSL complex, leading to the identification of CG4747. Functional analysis indicates that this protein is involved in targeting MSL to H3K36me3-containing chromatin.

The protein α-catenin has an essential role in stabilizing cell-cell junctions, and it is involved in multiple interactions with other cytoskeleton proteins. The crystal structure of nearly full-length human α-catenin now reveals a handshake-like dimer with the two monomers in distinct conformations. This dimer asymmetry is important for F-actin binding and for interactions with activated vinculin.

Histone deacetylase 3 (HDAC3) has low enzymatic activity in vitro unless associated with the nuclear receptor corepressors NCOR1 and SMRT through the deacetylase activation domain (DAD). Mice lacking functional DADs in both NCOR1 and SMRT are born and reach adulthood but lack HDAC3 activity, whereas mice lacking HDAC3 are embryonic lethal, which suggests an essential deacetylase-independent function of HDAC3.