Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here, we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ∼1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for crosstalk between neighboring genes and estimate that enhancers can influence gene expression on average over ∼20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation.
SummaryThe RNA-guided DNA endonuclease Cas9 is a powerful tool for genome editing. Little is known about the kinetics and fidelity of the double-strand break (DSB) repair process that follows a Cas9 cutting event in living cells. Here, we developed a strategy to measure the kinetics of DSB repair for single loci in human cells. Quantitative modeling of repaired DNA in time series after Cas9 activation reveals variable and often slow repair rates, with half-life times up to ∼10 hr. Furthermore, repair of the DSBs tends to be error prone. Both classical and microhomology-mediated end joining pathways contribute to the erroneous repair. Estimation of their individual rate constants indicates that the balance between these two pathways changes over time and can be altered by additional ionizing radiation. Our approach provides quantitative insights into DSB repair kinetics and fidelity in single loci and indicates that Cas9-induced DSBs are repaired in an unusual manner.
Although ferromagnets have many applications, their large magnetization and the resulting energy cost for switching magnetic moments bring into question their suitability for reliable low-power spintronic devices. Non-collinear antiferromagnetic systems do not suffer from this problem, and often have extra functionalities: non-collinear spin order may break space-inversion symmetry and thus allow electric-field control of magnetism, or may produce emergent spin-orbit effects that enable efficient spin-charge interconversion. To harness these traits for next-generation spintronics, the nanoscale control and imaging capabilities that are now routine for ferromagnets must be developed for antiferromagnetic systems. Here, using a non-invasive, scanning single-spin magnetometer based on a nitrogen-vacancy defect in diamond, we demonstrate real-space visualization of non-collinear antiferromagnetic order in a magnetic thin film at room temperature. We image the spin cycloid of a multiferroic bismuth ferrite (BiFeO) thin film and extract a period of about 70 nanometres, consistent with values determined by macroscopic diffraction. In addition, we take advantage of the magnetoelectric coupling present in BiFeO to manipulate the cycloid propagation direction by an electric field. Besides highlighting the potential of nitrogen-vacancy magnetometry for imaging complex antiferromagnetic orders at the nanoscale, these results demonstrate how BiFeO can be used in the design of reconfigurable nanoscale spin textures.
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