Nature Biotechnology

Precise modulation of gene expression through cis-regulatory editing holds promise for nontransgenic crop improvement. However, the sequence-to-function relationships that govern plant promoter activity remain poorly understood. Here we develop a massively parallel reporter assay in Sorghum bicolor to systematically measure the effects of >30,000 mutations spanning deletions, substitutions and mo…

Antibody-drug conjugates enable highly specific delivery of potent cytotoxics to biomarker-expressing cells. In parallel, advances in DNA circuitry and DNA-protein conjugates have allowed programmable integration of molecular inputs and signal amplification via hybridization chain reactions (HCRs). Here we present a system using affibody-DNA and aptamer-DNA conjugates to execute a Boolean logic o…

Tissue engineering of the esophagus has been limited by stent dependance and poor muscle regeneration. Here we report an integrated strategy to engineer a 2.5-cm esophageal segment by microinjecting autologous pericyte-like myogenic precursors and fibroblasts in a decellularized porcine scaffold to repair circumferential defects in 10-kg minipigs (n = 8), modeling pediatric use. Bioreactor matura…

The initial development of adenine base editors (ABEs), which facilitate A•T to G•C base pair changes in the genome, used directed evolution to install 14 mutations into the wild-type deaminase TadA, producing the first-of-its-kind editor ABE7.10. Here we study the installed mutations' impacts on TadA fitness using comprehensive reversion analysis and apply our results to engineer more efficient,…

TnpB is a diverse family of RNA-guided endonucleases associated with prokaryotic transposons. Because of their small size and putative evolutionary relationship to CRISPR-Cas12, TnpB enzymes hold great potential for genome editing. However, most TnpBs lack robust gene-editing activity. Here, we mapped comprehensive sequence-function landscapes of a TnpB ribonucleoprotein using deep mutational sca…