Reviews & Analysis

RAF family kinases, which were first described over 30 years ago, primarily act as signalling relays downstream of RAS. Key mechanistic and structural studies are shaping our view of how RAF proteins and RAF-related pseudokinases are regulated; they also highlight the mechanisms underlying pathological RAF signalling and the unforeseen limitations of RAF inhibitors.

Somatic stem cells are responsible for tissue maintenance and repair throughout life. Studies on blood, skin and intestinal epithelium have revealed that multiple types of stem cells with distinct roles perform such regenerative functions. Moreover, stem cells have greater developmental flexibility than had previously been appreciated under stress conditions such as acute injury.

Advances in mass spectrometry-based proteomics are enabling the multidimensional analysis of protein properties such as abundance, localization, post-translational modifications and interactions for thousands of proteins. Complemented by new tools for data analysis and integration, these advances are transforming our understanding of various biological processes.

How endocytic pits are formed in clathrin- and caveolin-independent endocytosis remains poorly understood. However, recent insight suggests that different forms of clathrin-independent endocytosis might involve the actin-driven focusing of membrane constituents, the lectin–glycosphingolipid-dependent construction of endocytic nanoenvironments and the use of Bin–Amphiphysin–Rvs (BAR) domain proteins as scaffolding modules.

Recent technical advances have shown that scaffold proteins can hold members of a signal transduction cascade in place, focus enzyme activity at a particular site of action and/or provide a structural platform for the recruitment of signal transduction and signal termination enzymes.

Genome-wide mapping of chromatin contacts reveals the structural and organizational changes that the metazoan genome undergoes during cell differentiation. These changes involve entire chromosomes, which are influenced by contacts with nuclear structures such as the lamina, and local interactions mediated by transcription factors and chromatin looping.

Recent studies of mRNA distribution and translation show that, in addition to serving as the site of protein translocation into the endoplasmic reticulum (ER), ER-bound ribosomes translate a large fraction of mRNAs that encode cytosolic proteins. This, along with the discovery of many mechanisms for recruiting translation to the ER, suggests an expansive role for the ER in post-transcriptional gene expression.

Replication perturbation causes replication fork reversal (remodelling). Recent studies have visualized replication forks in metazoan cells and identified fork remodelling factors, showing fork reversal to be a global and regulated process with potential effects on replication termination, genome stability and the DNA damage response.

Transcription of eukaryotic protein-coding genes requires the assembly of a conserved initiation complex at promoter DNA. Structural information on this complex, which comprises RNA polymerase II and the general transcription factors, is beginning to reveal the mechanisms underlying the initial steps of transcription, such as the recognition and opening of promoter DNA.

RNA polymerase II (Pol II) is globally regulated by Mediator, a large, conformationally flexible protein complex with a variable subunit composition. These biochemical characteristics are fundamental for the ability of Mediator to control processes involved in transcription, including the organization of chromatin architecture and the regulation of Pol II pre-initiation, initiation, re-initiation, pausing and elongation.

Pausing of RNA polymerase II (Pol II) in promoter-proximal regions and its release to initiate productive elongation are key steps in the regulation of transcription, and involve many factors. Evidence is now emerging that transcriptional elongation is highly dynamic. Elongation rates vary between genes and across the length of a gene, affecting splicing, termination and genome stability.

Access of RNA polymerase II to DNA is regulated by the ordered disassembly of nucleosomes and by histone exchange. Chromatin modifications, chromatin remodellers, histone chaperones and histone variants control nucleosomal dynamics, and dysregulation of these components results in aberrant transcription.

Transcription termination has a central role in regulating gene expression, maintaining the stability of the transcriptome and controlling pervasive transcription. New insights have recently been gained into the molecular basis of termination and the timely and efficient dismantling of elongation complexes at mRNA-coding and non-coding RNA loci.

Many gene expression patterns are dictated by enhancers. Mammalian genomes contain millions of potential enhancers, but only a small subset of them is active in any cell type. Emerging data uncover how cell type-specific enhancer function is established, including the involvement of higher-order genomic organization in the process.

Considerable progress has been made in the past few years in our ability to visualize the structure of G protein-coupled receptors (GPCRs) and their signalling complexes. This is due to a series of technical improvements in areas such as protein engineering, lipidic cubic phase-based crystallization and microfocus synchrotron beamlines.

The anaphase-promoting complex (also known as the cyclosome) is an E3 ubiquitin ligase that has a crucial function in the regulation of mitosis, particularly during anaphase and mitotic exit. Its activity is tightly controlled by several factors to ensure the timely degradation of key mitotic regulators and thus the proper progression of mitotic events.

Retinoic acid regulates transcription by interacting with nuclear retinoic acid receptors, which bind to retinoic acid response elements near target genes. Recent studies have refined our knowledge of retinoic acid function in the limb, which serves as a paradigm for understanding how it regulates other developmental processes, such as somitogenesis, neuronal differentiation and organogenesis.