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  • CRISPR–Cas9-based genome editing tools have been developed recently to study non-coding transcriptional regulatory elements, enabling the characterization of enhancers in their endogenous context. The applications, current limitations and future development of such CRISPR–Cas9 tools are discussed, with emphasis on identifying and characterizing enhancer elements in a high-throughput manner.

    • Rui Lopes
    • Gozde Korkmaz
    • Reuven Agami
  • Metabolomics has been utilized extensively for the identification of single metabolites and their use as biomarkers. Owing to recent technical advances, it is now possible to use metabolomics to better understand whole metabolic pathways and to more precisely pinpoint the involvement of metabolites in physiology and pathology.

    • Caroline H. Johnson
    • Julijana Ivanisevic
    • Gary Siuzdak
  • Lipids tailor membrane identities and function as molecular hubs in all cellular processes. The development of pioneering technologies, including affinity-purification lipidomics and the liposome microarray-based assay (LiMA), will enable researchers to decipher protein–lipid interactions and enhance our understanding of how lipids modulate protein function and structure.

    • Antoine-Emmanuel Saliba
    • Ivana Vonkova
    • Anne-Claude Gavin
  • DNA assembly methods are essential to the field of synthetic biology. Casiniet al. discuss the powerful DNA assembly methods and standards developed in the past decade that facilitate the streamlined assembly of genetic networks and even of whole chromosomes and cells.

    • Arturo Casini
    • Marko Storch
    • Tom Ellis
  • The optogenetic toolkit has rapidly expanded to include various proteins and cellular functions, such as cell signalling, that can be controlled by light. The practical considerations in using and deciding between optogenetic systems, such as systems that use light-oxygen-voltage (LOV) domains, phytochrome proteins, CRYPTOCHROME 2 (CRY2) and the fluorescent protein Dronpa, are now well defined.

    • Doug Tischer
    • Orion D. Weiner
  • Transcription activator-like effector nucleases (TALENs) comprise a nonspecific nuclease fused to a sequence-specific DNA-binding domain. This domain can be engineered so that TALENs can target virtually any sequence. TALENs are an efficient tool to modify genes in a wide range of cell types and organisms.

    • J. Keith Joung
    • Jeffry D. Sander
  • Cryo-electron tomography has provided a means of characterizing the architecture of macromolecular complexes in their native environment, and facilitated a better understanding of cellular processes. By combining this method with fluorescence and super-resolution microscopy, the full potential of this approach can be realized.

    • Karen Fridman
    • Asaf Mader
    • Ohad Medalia
  • Advances in biosensor technology have made it possible to simultaneously study the activation of multiple signalling network components in the same cell. This approach has been enhanced by novel computational approaches (referred to as computational multiplexing) that can reveal relationships between network nodes imaged in separate cells.

    • Christopher M. Welch
    • Hunter Elliott
    • Klaus M. Hahn
  • Plant metabolomics — the high-throughput analysis of plant compounds — is an invaluable tool for understanding plant metabolism. Recent innovations in mass-spectrometry-based analyses are shedding light on the structure and regulation of biosynthetic pathways and the temporal and spatial dynamics of the plant metabolome.

    • Robert L. Last
    • A. Daniel Jones
    • Yair Shachar-Hill
  • Stable-isotope labelling by amino acids in cell culture (SILAC) has emerged as a simple and powerful format for quantitative proteomics. What are the current applications for SILAC? And, how will this technology be used in the future?

    • Matthias Mann
  • Several new optical microscopy techniques have recently emerged that each use different combinations of photon properties. These combinatorial microscopy techniques allow the visualization of location, orientation, motion and environment of proteins and organelles well below the classic resolution limit.

    • Daniel Axelrod
    • Geneva M. Omann
  • Recently, a method was developed to encode unnatural amino acids genetically in bacteria, yeast and mammalian cells. This provides a powerful tool for exploring protein structure and functionin vitro and in vivo, and for generating proteins with new or enhanced properties.

    • Jianming Xie
    • Peter G. Schultz
  • Fluorescence microscopy is a powerful tool to assay biological processes in intact living cells. Now, fluorescence microscopy is becoming a quantitative and high-throughput technology that can be applied to functional genomics experiments and can provide data for systems-biology approaches.

    • Rainer Pepperkok
    • Jan Ellenberg
  • Protein-chip technology is a powerful tool for high-throughput assays of protein profiling, protein–DNA interactions and enzyme activity. Improvements in the technology, such as the construction of whole-proteome arrays in yeast, could lead to the description of comprehensive interaction maps in many organisms.

    • Li A. Kung
    • Michael Snyder
  • The visualization of protein complexes in living cells enables the investigation of molecular interactions in their native environment. Bimolecular fluorescence complementation analysis has been used to visualize protein interactions and modifications in different cell types and species.

    • Tom K. Kerppola
  • Cryo-electron tomography is an emerging imaging technique that will allow us to map molecular landscapes inside cells. This 'visual proteomics' will complement and extend mass-spectrometry-based inventories, and will provide a quantitative description of the macromolecular interactions that underlie cellular functions.

    • Stephan Nickell
    • Christine Kofler
    • Wolfgang Baumeister