Biology subjects

Shou, J.

Publications and source records attributed to Shou, J..

3 recordsLinked to original sources

bioRxiv2026

Double-strand break end configuration and 3D genome architecture are crucial for chromosomal translocation

Chromosomal translocations originate from erroneous rejoining of DNA double-strand break (DSB) ends and mechanisms of their formation remain largely unknown. Here we reveal DSB end configuration and three-dimensional (3D) genome architecture cooperatively shape both translocation frequency and junctional indel pattern. By integrating multiplex CRISPR/Cas9 editing with an optimized translocation assay, we find that translocation frequency correlates with spatial proximity. In addition, templated insertions emerge as a defining structural feature of translocation junctions induced by Cas9-mediated staggered cleavage and confirmed by DISCOVER-seq. Interestingly, translocation frequency is correlated with cleavage geometry. Finally, engineered Cas9 variants with altered DSB end configurations enable programmable modulation of junctional indel patterns. These findings shed significant insights into mechanisms of recurrent chromosomal rearrangements in human diseases and have interesting implications in safe applications of genome editing.

cell biology↗

bioRxiv2022

Super-resolution vibrational imaging based on photoswitchable Raman probe

Super-resolution vibrational microscopy is a promising tool to increase the degree of multiplexing of nanometer-scale biological imaging, because the spectral linewidth of molecular vibration is about 50 times narrower than that of fluorescence. However, current techniques of super-resolution vibrational microscopy still suffer from various limitations including the need for cell fixation, high power loading or complicated frequency-modulated detection schemes. Herein we utilize photoswitchable stimulated Raman scattering (SRS) to develop a method that we call reversible saturable optical Raman transitions (RESORT) microscopy, which overcomes these limitations. We first describe a new kind of photoswitchable Raman probe designated DAE620 and then we employ a standard SRS detection scheme to validate its signal activation and depletion characteristics when exposed to low-power (microwatt level) continuous-wave laser light. By harnessing the SRS signal depletion of DAE620 through a donut-shaped beam, we demonstrate super-resolution vibrational imaging of mammalian cells with excellent chemical specificity and spatial resolution beyond the optical diffraction limit. Our results indicate RESORT microscopy to be an effective tool with high potential for multiplexed super-resolution imaging of live cells.

bioengineering↗

bioRxiv2017

Precise And Predictable DNA Fragment Editing Reveals Principles Of Cas9-Mediated Nucleotide Insertion

DNA fragment editing (DFE) or chromosomal engineering including inversions, deletions, and duplications by Cas9 with paired sgRNAs are important to investigate structural genome variations and developmental gene regulation, but little is known about the underlying mechanisms. Here we report that debilitating CtIP, which is thought to function in NHEJ, enhances precise DNA fragment deletion. By analyzing the inserted nucleotides at the junctions of DNA fragment inversions, deletions, and duplications, we find that Cas9 cleaves the noncomplementary strand with a flexible profile upstream of the PAM site and rationally-designed Cas9 nucleases have distinct cleavage profiles. Finally, Cas9-mediated nucleotide insertions of DFE are nonrandom and are equal to the combined sequences upstream of both PAM sites with predicted frequencies. Thus, precise and predictable DFEs could be achieved by perturbing DNA repair genes and using appropriate PAM configurations. These findings have important applications regarding 3D chromatin folding and enhancer insulation during gene regulation.

genetics↗