Reviews & Analysis

In this Review, Wiedenheft and colleagues retrace events that led from early endeavours to understand the role of Cas9 in CRISPR-mediated adaptive immunity to current efforts aimed at developing this enzyme for programmable genetic editing.

Shah and Kuriyan highlight how the analysis of sequence variation synergizes with protein structure information, to provide new insights into specificity and allosteric regulation of signaling proteins.

The intertwined structure of the Taf5–Taf6–Taf9 subcomplex is dependent on the chaperonin CCT for its assembly and subsequent integration into the general transcription factor TFIID.

Zhou, Gaullier and Luger review insights derived from cutting-edge biophysical and structural approaches applied to the study of nucleosome dynamics and nucleosome-binding factors, with a focus on the experimental advances driving the research.

Recent advances in the ability to detect mRNA base modifications have led to a renewed appreciation for the diversity of the epitranscriptome and its ability to influence gene expression. Now, a study in Cell adds acetylated cytidine (ac⁴C) to the list, identifying it as a widespread mark in cellular mRNAs that influences both mRNA stability and translation.

This Review discusses mechanistic insights into 5´–3´ RNA decay, such as translation–decay coupling, coordination between complexes that process 5´ & 3´ RNA termini, conformational control of enzymatic activity, phase separation, & RNA modifications.

Diederichs and colleagues review RNA motifs, focusing on four recent studies identifying nuclear-retention motifs, and discuss the limited specificity of short RNA motifs and the resulting challenge for effective functional prediction.

Cells rely on the synthesis, translocation, folding and turnover of proteins. Owing to complexity, spatiotemporal regulation and surveillance of these processes are vital. Advances in the field were discussed at the international symposium ‘Proteins: From the Cradle to the Grave’ that took place in the wonderful setting of a Buddhist temple located close to Kyoto, Japan. The emerging theme was the interdependence among cellular processes and organelle compartments.

Attempts to develop a method for 3D genome reconstruction of single cells have been frustrated by the inability to distinguish between chromosome homologs. A novel Hi-C workflow uses haplotype imputation to map the nuclear organization of single diploid cells.

Cross-linking mass spectrometry has developed into a robust and flexible tool that provides medium-resolution structural information. This review highlights notable successes of this technique and discusses common pipelines.

In this Review, Haoxing Xu and colleagues summarize current knowledge of TRP channels and their roles in the response to environmental and cellular signals, focusing in particular on the least known class, the organellar TRPs.

The σ₁ receptor, an endoplasmic reticulum–resident transmembrane protein, modulates many physiological and pathological processes and binds multiple drugs, but is nonetheless poorly understood. In a recent issue, Kruse and colleagues illustrate structural differences between agonist- and antagonist-bound receptor and propose that agonist binding may impair oligomerization, making a major step in understanding σ₁ function. They also use a combination of kinetic and molecular dynamic modeling to explain how ligands access the binding pocket.

Nichols and Corces summarize the current knowledge of SMC structure and function and propose a new mechanism for SMC motor activity, which is central to the DNA loop extrusion model of genome organization.

RNA uridylation offers a basis for diverse post-transcriptional regulation. Two recent studies reveal new roles of uridylation in immune defense against viruses and retrotransposons.

Cramer and colleagues review and discuss how the structural elucidation of transcription factors and functional complexes of human mitochondrial RNA polymerase have informed emerging understanding of the mechanism of mitochondrial gene transcription.

A symposium in June 2018 sponsored by the Center on Membrane Protein Production and Analysis, a unit of the New York Structural Biology Center, focused on the structures of proteins residing in biological membranes. Explicit emphasis was placed on currently developing technologies aimed at determining such structures and at understanding their dynamics, mechanisms and complex interactions.

The mechanism underlying CCG-repeat expansions in patients with fragile X premutation is not well understood. Using a new experimental system in mammalian cells, a study in this issue reports that break-induced replication has a role in CGG-repeat instability.

A series of new cryo-EM structures reveals a surprising twist in how the RAG complex initiates V(D)J recombination. The initial complex with substrate DNA adopts two conformations: in one, the DNA is relatively undistorted but the scissile phosphate is far from the active site, and in the other the DNA is partially melted and unwound by half a turn, which allows the scissile phosphate to dock into the active site. Similar pre-catalysis DNA melting may occur with other DDE recombinases, for which equivalent complexes with uncleaved substrate DNA are not yet available.

The effects of RNA secondary structure on translation have been well recognized; however, the global interplay between both in a dynamic cellular system is poorly understood. Beaudoin, Giraldez and colleagues have analyzed RNA structure dynamics during zebrafish embryonic development and have found that the ribosome unzips mRNA secondary structure during translation, thus leading to a global decrease of structure in highly translated transcripts. Furthermore, the authors establish RNA structure in the 3′ untranslated regions of mRNAs as a major regulator of transcript stability in this context.