Biophysical methods articles within Nature Reviews Genetics

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• Journal Club | 06 February 2023

  Regulatory promoter architectures in the hands of thermodynamic modelling

  Julio Collado-Vides recalls two 2005 publications that provide a conceptual framework based on a statistical thermodynamics approach to quantitatively model the regulatory activity at promoters subject to regulation by multiple transcription factors.

  • Julio Collado-Vides

• Review Article | 12 January 2023

  High-throughput biochemistry in RNA sequence space: predicting structure and function

  The vast combinatorial sequence space of RNAs has prohibited quantitative mapping from nucleotide sequence to structure and function. New biochemical methods in vitro, which carry out measurements on hundreds of thousands of molecules at the same time, are now beginning to solve this issue.

  • Emil Marklund
  • , Yuxi Ke
  •  & William J. Greenleaf

• Review Article | 22 May 2017

  Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells

  A full understanding of chromatin in diverse cellular processes requires the consideration of its dynamics, but most standard chromatin assays provide only a static snapshot. This Review describes various emerging methods for probing chromatin dynamics across a wide range of temporal and spatial scales, and discusses the resulting biological insights.

  • Olivier Cuvier
  •  & Beat Fierz

• Review Article | 20 February 2017

  Detecting RNA modifications in the epitranscriptome: predict and validate

  Although it has been known for decades that RNA is subjected to numerous covalent modifications, there has been a recent surge in interest driven by sequencing-based transcriptome-wide detection methods and the realization that RNA modifications have important roles in diverse biological processes. This Review describes the range of detection strategies for RNA modifications, their particular strengths and limitations, and how responsible and complementary application of these techniques will be required to ensure the quality and interpretability of the rapidly accumulating data sets.

  • Mark Helm
  •  & Yuri Motorin

• Review Article | 13 May 2014

  Insights into RNA structure and function from genome-wide studies

  Recent technological advances have enabled the probing of RNA structure across the transcriptomes of various speciesin vitro and in vivo. This Review discusses our latest understanding of how RNA structure influences various steps of gene expression, including translation, mRNA localization and microRNA-mediated gene regulation.

  • Stefanie A. Mortimer
  • , Mary Anne Kidwell
  •  & Jennifer A. Doudna