Biology subjects

Ji, W.

Publications and source records attributed to Ji, W..

3 recordsLinked to original sources

bioRxiv2018

Trio deep-sequencing does not reveal unexpected mutations in Cas9-edited monkeys

CRISPR-Cas9 is a widely-used genome editing tool, but its off-target effect remains a concern, especially in view of future clinical applications. Non-human primates (NHPs) share close genetic and physiological similarities with humans, making them an ideal preclinical model for developing Cas9-based therapies. However, no comprehensive in vivo off-target assessment has been conducted in NHPs. Here we performed whole genome trio sequencing of Cas9-treated monkeys. We found they only carried a small number of de novo mutations that can be explained by expected spontaneous mutations, and no unexpected mutations were detected.

bioengineering↗

bioRxiv2018

Candidate Gene Networks for Acylsugar Metabolism and Plant Defense in Wild Tomato Solanum pennellii

Many plants in the Solanaceae family secrete acylsugars, which are branched-chain and straight-chain fatty acids esterified to glucose or sucrose. These compounds have important roles in plant defense and potential commercial applications. However, several acylsugar metabolic genes remain unidentified, and little is known about regulation of this pathway. We used comparative transcriptomic analysis between low- and high-acylsugar-producing accessions of Solanum pennellii and found that expression levels of most acylsugar metabolic genes, including known acylsucrose biosynthetic genes and novel candidate genes (putatively encoding a ketoacyl-ACP synthase IV/II-like enzyme, peroxisomal acyl-activating enzymes, ABC transporters, and central carbon metabolic enzymes), were positively correlated with acylsugar accumulation, except two acylglucose biosynthetic genes. Genes putatively encoding oxylipin metabolic proteins, subtilisin-like proteases, and other antimicrobial defense proteins were upregulated in low-acylsugar-producing accessions, possibly to compensate for diminished defense activities of acylsugars. Gene co-expression network analysis clustered most differentially expressed genes into two separate modules and identified genetic networks associated with acylsugar production and plant defense. Transcriptome analysis after inhibition of biosynthesis of branched-chain amino acids (precursors to branched-chain fatty acids) further supported the coordinated regulation of most acylsugar candidate genes and identified three putative AP2-family transcription factor genes that form a strong co-expression network with many acylsugar metabolic genes.

plant biology↗

bioRxiv2017

Coordination between discrete Mitotic Arrest Deficient 1 (MAD1) domains is required for efficient mitotic checkpoint signaling

As a sensitive signaling system, the mitotic checkpoint ensures faithful chromosome segregation by delaying anaphase onset when even a single kinetochore is unattached. The key signal amplification reaction for the checkpoint is the conformational conversion of open MAD2 (O-MAD2) into closed MAD2 (C-MAD2). The reaction was suggested to be catalyzed by an unusual catalyst, a MAD1:C-MAD2 tetramer, but how the catalysis is executed and regulated remains elusive. Here we report that in addition to the well-characterized middle region (MIM), both amino- and carboxyl-terminal domains (NTD and CTD) of MAD1 also contribute to the mitotic checkpoint. In contrast to MIM that stably associates with C-MAD2, MAD1-NTD and CTD surprisingly bind to both O-MAD2 and C-MAD2, suggesting their interactions with substrates and products of the O-C conversion. MAD1-NTD also interacts with CTD. MPS1 kinase interacts with and phosphorylates both NTD and CTD. The phosphorylation reduces the NTD:CTD interaction and CTD interaction with MPS1. Mutating CTD phosphorylation sites including Thr716 compromises MAD2 binding and the checkpoint responses. Ser610 and Tyr634 also contribute to the checkpoint. Our results have uncovered previously unknown interactions of MAD1-NTD and CTD with MAD2 conformers and their regulation by MPS1 kinase, providing novel insights into the mitotic checkpoint signaling.

cell biology↗