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Holly A. Rees
Broad Institute
Molecular biologygenomic DNABase pairDNABiology
18Publications
10H-index
1,205Citations
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Publications 20
Newest
#1Yi YuH-Index: 1
#2Thomas LeeteH-Index: 1
Last. Nicole M. GaudelliH-Index: 6
view all 9 authors...
Cytosine base editors (CBEs) enable efficient, programmable reversion of T*A to C*G point mutations in the human genome. Recently, cytosine base editors with rAPOBEC1 were reported to induce unguided cytosine deamination in genomic DNA and cellular RNA. Here we report eight next-generation CBEs (BE4 with either RrA3F [wt, F130L], AmAPOBEC1, SsAPOBEC3B [wt, R54Q], or PpAPOBEC1 [wt, H122A, R33A]) that display comparable DNA on-target editing frequencies, whilst eliciting a 12- to 69-fold reduction...
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#1Nicole M. GaudelliH-Index: 6
#2Dieter K. LamH-Index: 1
Last. Alexander J. LiquoriH-Index: 1
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The foundational adenine base editors (e.g. ABE7.10) enable programmable C:G to T:A point mutations but editing efficiencies can be low at challenging loci in primary human cells. Here we further evolve ABE7.10 using a library of adenosine deaminase variants to create ABE8s. At NGG PAM sites, ABE8s result in ~1.5x higher editing at protospacer positions A5-A7 and ~3.2x higher editing at positions A3-A4 and A8-A10 compared with ABE7.10. Non-NGG PAM variants have a ~4.2-fold overall higher on-targ...
1 CitationsSource
#1Yi YuH-Index: 1
#2Thomas LeeteH-Index: 1
Last. Nicole M. GaudelliH-Index: 6
view all 9 authors...
Cytosine base editors (CBEs) are molecular machines which enable efficient and programmable reversion of T.A to C.G point mutations in the human genome without induction of DNA double strand breaks. Recently, the foundational cytosine base editor (CBE) "BE3", containing rAPOBEC1, was reported to induce unguided, genomic DNA and cellular RNA5 cytosine deamination when expressed in living cells. To mitigate spurious off-target events, we developed a sensitive, high-throughput cellular assay to sel...
2 CitationsSource
#1Shannon M. Miller (Broad Institute)H-Index: 3
#2Tina Wang (Broad Institute)H-Index: 7
Last. David R. Liu (Broad Institute)H-Index: 73
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The targeting scope of Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants is largely restricted to protospacer-adjacent motif (PAM) sequences containing G bases. Here we report the evolution of three new SpCas9 variants that collectively recognize NRNH PAMs (where R is A or G and H is A, C or T) using phage-assisted non-continuous evolution, three new phage-assisted continuous evolution strategies for DNA binding and a secondary selection for DNA cleavage. The targeting capabilitie...
8 CitationsSource
#1Holly A. Rees (Broad Institute)H-Index: 10
#2Wei-Hsi YehH-Index: 3
Last. David R. Liu (Broad Institute)H-Index: 73
view all 3 authors...
In mammalian cells, double-stranded DNA breaks (DSBs) are preferentially repaired through end-joining processes that generally lead to mixtures of insertions and deletions (indels) or other rearrangements at the cleavage site. In the presence of homologous DNA, homology-directed repair (HDR) can generate specific mutations, albeit typically with modest efficiency and a low ratio of HDR products:indels. Here, we develop hRad51 mutants fused to Cas9(D10A) nickase (RDN) that mediate HDR while minim...
Source
#1Holly A. Rees (Broad Institute)H-Index: 10
#2Christopher Wilson (Broad Institute)H-Index: 3
Last. David R. Liu (Broad Institute)H-Index: 73
view all 4 authors...
Adenine base editors (ABEs) enable precise and efficient conversion of target A∙T base pairs to G·C base pairs in genomic DNA with a minimum of by-products. While ABEs have been reported to exhibit minimal off-target DNA editing, off-target editing of cellular RNA by ABEs has not been examined in depth. Here, we demonstrate that a current ABE generates low but detectable levels of widespread adenosine-to-inosine editing in cellular RNAs. Using structure-guided principles to design mutations in b...
10 CitationsSource
#1Kendell Clement (Broad Institute)H-Index: 16
#2Holly A. Rees (Broad Institute)H-Index: 10
Last. Luca Pinello (Broad Institute)H-Index: 22
view all 11 authors...
18 CitationsSource
#1Yamini Krishnan (MIT: Massachusetts Institute of Technology)H-Index: 3
#2Holly A. Rees (Broad Institute)H-Index: 10
Last. Alan J. Grodzinsky (MIT: Massachusetts Institute of Technology)H-Index: 78
view all 10 authors...
Abstract Osteoarthritis (OA), the most common form of arthritis, is a multi-factorial disease that primarily affects cartilage as well as other joint tissues such as subchondral bone. The lack of effective drug delivery, due to the avascular nature of cartilage and the rapid clearance of intra-articularly delivered drugs via the synovium, remains a major challenge in the development of disease modifying drugs for OA. Cationic delivery carriers can significantly enhance the uptake, penetration an...
5 CitationsSource
#1Holly A. Rees (Broad Institute)H-Index: 10
#2David R. Liu (Broad Institute)H-Index: 73
The originally published article contained errors in reference numbering throughout table 1 (DNA base editors and their approximate editing windows) due to the unintended propagation of reference numbering from an earlier version of the table. The article has now been corrected online. The editors apologize for this error.
3 CitationsSource
#1Holly A. Rees (Broad Institute)H-Index: 10
#2David R. Liu (Broad Institute)H-Index: 73
RNA-guided programmable nucleases from CRISPR systems generate precise breaks in DNA or RNA at specified positions. In cells, this activity can lead to changes in DNA sequence or RNA transcript abundance. Base editing is a newer genome-editing approach that uses components from CRISPR systems together with other enzymes to directly install point mutations into cellular DNA or RNA without making double-stranded DNA breaks. DNA base editors comprise a catalytically disabled nuclease fused to a nuc...
75 CitationsSource
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