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Xuebing Wu
Massachusetts Institute of Technology
Cas9Molecular biologyGeneticsBiologyCRISPR
46Publications
22H-index
16.4kCitations
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Publications 35
Newest
#1Cheng Zhang (Salk Institute for Biological Studies)H-Index: 3
#2Silvana Konermann (Salk Institute for Biological Studies)H-Index: 16
Last. Dmitry Lyumkis (Salk Institute for Biological Studies)H-Index: 20
view all 10 authors...
Summary CRISPR-Cas endonucleases directed against foreign nucleic acids mediate prokaryotic adaptive immunity and have been tailored for broad genetic engineering applications. Type VI-D CRISPR systems contain the smallest known family of single effector Cas enzymes, and their signature Cas13d ribonuclease employs guide RNAs to cleave matching target RNAs. To understand the molecular basis for Cas13d function and explain its compact molecular architecture, we resolved cryoelectron microscopy str...
29 CitationsSource
#1Josh Tycko (Stanford University)H-Index: 5
#2Luis A. BarreraH-Index: 17
Last. Patrick Hsu (Salk Institute for Biological Studies)H-Index: 19
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The original HTML version of this Article incorrectly listed an affiliation of Josh Tycko as ‘Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA’, instead of the correct ‘Present address: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA’. It also incorrectly listed an affiliation of this author as ‘Present address: Arrakis Therapeutics, 35 Gatehouse Dr., Waltham, MA, 02451, USA’.The original HTML version incorrectly list...
2 CitationsSource
#1Josh Tycko (Stanford University)H-Index: 5
#2Luis A. BarreraH-Index: 22
Last. Patrick Hsu (Salk Institute for Biological Studies)H-Index: 19
view all 10 authors...
Therapeutic genome editing with Staphylococcus aureus Cas9 (SaCas9) requires a rigorous understanding of its potential off-target activity in the human genome. Here we report a high-throughput screening approach to measure SaCas9 genome editing variation in human cells across a large repertoire of 88,692 single guide RNAs (sgRNAs) paired with matched or mismatched target sites in a synthetic cassette. We incorporate randomized barcodes that enable whitelisting of correctly synthesized molecules ...
11 CitationsSource
#1Wei JiangH-Index: 79
#1Wei JiangH-Index: 1
Last. Dengke K. Ma (UCSF: University of California, San Francisco)H-Index: 16
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How multicellular organisms respond to and are impacted by severe hypothermic stress is largely unknown. From C. elegans screens for mutants abnormally responding to cold-warming stimuli, we identify a molecular genetic pathway comprising ISY-1, a conserved uncharacterized protein, and ZIP-10, a bZIP-type transcription factor. ISY-1 gatekeeps the ZIP-10 transcriptional program by regulating the microRNA mir-60. Downstream of ISY-1 and mir-60, zip-10 levels rapidly and specifically increase upon ...
4 CitationsSource
#1Wei JiangH-Index: 79
#1Wei JiangH-Index: 1
Last. Dengke K. Ma (UCSF: University of California, San Francisco)H-Index: 16
view all 9 authors...
Source
#1X. Shawn Liu (MIT: Massachusetts Institute of Technology)H-Index: 14
#1X. Shawn Liu (MIT: Massachusetts Institute of Technology)H-Index: 2
Last. Rudolf Jaenisch (MIT: Massachusetts Institute of Technology)H-Index: 145
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Summary Fragile X syndrome (FXS), the most common genetic form of intellectual disability in males, is caused by silencing of the FMR1 gene associated with hypermethylation of the CGG expansion mutation in the 5′ UTR of FMR1 in FXS patients. Here, we applied recently developed DNA methylation editing tools to reverse this hypermethylation event. Targeted demethylation of the CGG expansion by dCas9-Tet1/single guide RNA (sgRNA) switched the heterochromatin status of the upstream FMR1 promoter to ...
128 CitationsSource
#1Anthony C. Chiu (MIT: Massachusetts Institute of Technology)H-Index: 3
#2Hiroshi I. Suzuki (MIT: Massachusetts Institute of Technology)H-Index: 21
Last. Phillip A. Sharp (MIT: Massachusetts Institute of Technology)H-Index: 142
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Summary Regulation of RNA polymerase II (Pol II) elongation is a critical step in gene regulation. Here, we report that U1 snRNP recognition and transcription pausing at stable nucleosomes are linked through premature polyadenylation signal (PAS) termination. By generating RNA exosome conditional deletion mouse embryonic stem cells, we identified a large class of polyadenylated short transcripts in the sense direction destabilized by the RNA exosome. These PAS termination events are enriched at ...
41 CitationsSource
#1Xuebing Wu (MIT: Massachusetts Institute of Technology)H-Index: 22
#2David P. Bartel (MIT: Massachusetts Institute of Technology)H-Index: 100
: Motifs of only 1-4 letters can play important roles when present at key locations within macromolecules. Because existing motif-discovery tools typically miss these position-specific short motifs, we developed kpLogo, a probability-based logo tool for integrated detection and visualization of position-specific ultra-short motifs from a set of aligned sequences. kpLogo also overcomes the limitations of conventional motif-visualization tools in handling positional interdependencies and utilizing...
37 CitationsSource
#1Xuebing Wu (MIT: Massachusetts Institute of Technology)H-Index: 22
#2David P. Bartel (MIT: Massachusetts Institute of Technology)H-Index: 100
Summary The physiological relevance of structures within mammalian mRNAs has been elusive, as these mRNAs are less folded in cells than in vitro and have predicted secondary structures no more stable than those of random sequences. Here, we investigate the possibility that mRNA structures facilitate the 3′-end processing of thousands of human mRNAs by juxtaposing poly(A) signals (PASs) and cleavage sites that are otherwise too far apart. We find that RNA structures are predicted to be more preva...
48 CitationsSource
#1Xuebing WuH-Index: 22
#2David P. BartelH-Index: 100
Last. David BartelH-Index: 1
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2 Citations
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