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Xuebing Wu
Massachusetts Institute of Technology
31Publications
20H-index
13kCitations
Publications 32
Newest
#1Josh Tycko (Stanford University)H-Index: 4
#2Luis A. BarreraH-Index: 17
Last.Patrick Hsu (Salk Institute for Biological Studies)H-Index: 17
view all 10 authors...
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...
1 CitationsSource
#1Josh Tycko (Stanford University)H-Index: 4
#2Luis A. BarreraH-Index: 17
Last.Patrick Hsu (Salk Institute for Biological Studies)H-Index: 17
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 ...
8 CitationsSource
#1Cheng Zhang (Salk Institute for Biological Studies)H-Index: 2
#2Silvana Konermann (Salk Institute for Biological Studies)H-Index: 13
Last.Dmitry Lyumkis (Salk Institute for Biological Studies)H-Index: 18
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...
19 CitationsSource
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#1Anthony C. Chiu (MIT: Massachusetts Institute of Technology)H-Index: 2
#2Hiroshi I. Suzuki (MIT: Massachusetts Institute of Technology)H-Index: 19
Last.Phillip A. Sharp (MIT: Massachusetts Institute of Technology)H-Index: 139
view all 6 authors...
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 ...
27 CitationsSource
#1X. Shawn Liu (MIT: Massachusetts Institute of Technology)H-Index: 2
#2Hao Wu (MIT: Massachusetts Institute of Technology)H-Index: 12
Last.Rudolf Jaenisch (MIT: Massachusetts Institute of Technology)H-Index: 175
view all 15 authors...
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 ...
83 CitationsSource
#1Xuebing Wu (MIT: Massachusetts Institute of Technology)H-Index: 20
#2David P. Bartel (MIT: Massachusetts Institute of Technology)H-Index: 99
23 CitationsSource
#1Xuebing Wu (MIT: Massachusetts Institute of Technology)H-Index: 20
#2David P. Bartel (MIT: Massachusetts Institute of Technology)H-Index: 99
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...
38 CitationsSource
#1Xuebing WuH-Index: 20
#2David P. BartelH-Index: 99
Last.David BartelH-Index: 1
view all 3 authors...
19 Citations
#1X. Shawn Liu (MIT: Massachusetts Institute of Technology)H-Index: 2
#2Hao Wu (MIT: Massachusetts Institute of Technology)H-Index: 12
Last.Rudolf Jaenisch (MIT: Massachusetts Institute of Technology)H-Index: 175
view all 10 authors...
Mammalian DNA methylation is a critical epigenetic mechanism orchestrating gene expression networks in many biological processes. However, investigation of the functions of specific methylation events remains challenging. Here, we demonstrate that fusion of Tet1 or Dnmt3a with a catalytically inactive Cas9 (dCas9) enables targeted DNA methylation editing. Targeting of the dCas9-Tet1 or -Dnmt3a fusion protein to methylated or unmethylated promoter sequences caused activation or silencing, respect...
380 CitationsSource
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