Lighting the shadows: methods that expose nuclear and cytoplasmic gene regulatory control

•Nucleus-targeted techniques reveal complex chromatin interactions and RNA biology.•Targeting RNA binding proteins and ribosomes exposes intermediary regulatory steps.•Bioorthogonal amino acid tagging yields a de novo synthesized proteome in plants.•Nucleus and protein capture methods enable profiling of gene regulatory processes.

Within cells, myriad interconnected processes orchestrate the progression of gene expression from chromatin, to mRNA, and to protein. Assessment of DNA methylation, histone modification, transcript isoform abundance, and the proteome are frequently performed to examine this progression, but do not resolve many intermediary steps in the coordinated regulation of gene expression. Here, we consider single and multiplexed technologies that yield genome-wide assessment of gene and mRNA activity, from transcription factor access to DNA to de novo synthesis of protein. An emphasis is placed on methods that can resolve gene regulatory processes in cells of defined identity within multicellular organs at spatial and temporal scales, leading to more effective design of gene regulatory cassettes for biotechnology.

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