Allele-specific genome editing of imprinting genes by preferentially targeting non-methylated loci using Staphylococcus aureus Cas9 (SaCas9)

Liu, Yajing; Li, Jianan; Zhou, Chunmei; Meng, Bin; Wu, Yu; Yang, Guang; Lu, Zongyang; Shen, Qingmei; Yang, Hui; Qiao, Yong

doi:10.1016/j.scib.2019.08.023

Cited by 10 publications

(13 citation statements)

References 29 publications

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“…Besides, it has been reported that BEs-induced RNA off-target editing acts in an sgRNA-independent manner 6 , 9 , thus we do not consider the sgRNA-dependent effects in the current study. While these findings remind us to reconsider the off-targeting activities of our and others’ reported dCas9-fused epigenome editing tools 24 , 25 . In addition, replacement of the deaminases or Cas9n of base editors, such as APOBEC3B, APOBEC3G, or YE1 variants, is a feasible strategy to reduce their sgRNA-independent DNA or RNA off-targeting activities 26 – 28 .…”

Section: Discussionmentioning

confidence: 53%

Structure-guided engineering of adenine base editor with minimized RNA off-targeting activity

Huang

et al. 2021

Nat Commun

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Both adenine base editors (ABEs) and cytosine base editors (CBEs) have been recently revealed to induce transcriptome-wide RNA off-target editing in a guide RNA-independent manner. Here we construct a reporter system containing E.coli Hokb gene with a tRNA-like motif for robust detection of RNA editing activities as the optimized ABE, ABEmax, induces highly efficient A-to-I (inosine) editing within an E.coli tRNA-like structure. Then, we design mutations to disrupt the potential interaction between TadA and tRNAs in structure-guided principles and find that Arginine 153 (R153) within TadA is essential for deaminating RNAs with core tRNA-like structures. Two ABEmax or mini ABEmax variants (TadA* fused with Cas9n) with deletion of R153 within TadA and/or TadA* (named as del153/del153* and mini del153) are successfully engineered, showing minimized RNA off-targeting, but comparable DNA on-targeting activities. Moreover, R153 deletion in recently reported ABE8e or ABE8s can also largely reduce their RNA off-targeting activities. Taken together, we develop a strategy to generate engineered ABEs (eABEs) with minimized RNA off-targeting activities.

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Section: Discussionmentioning

confidence: 53%

Structure-guided engineering of adenine base editor with minimized RNA off-targeting activity

Huang

et al. 2021

Nat Commun

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“…Besides, it has been reported that BEs-induced RNA off-target editing acts in a sgRNA-independent manner [6,9], and we do not consider the sgRNA-dependent effects in the current study. While these ndings remind us to reconsider the off-targeting activities of our and others' reported dCas9-fused epigenome editing tools [21,22].…”

Section: Discussionmentioning

confidence: 64%

Upgraded adenine base editor (uABE) with minimized RNA off-targeting activity

Huang

et al. 2020

Preprint

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Both adenine base editors (ABEs) and cytosine base editors (CBEs) have been recently revealed to induce transcriptome-wide RNA off-target editing in a guide RNA-independent manner. As the optimized ABE, ABEmax, induces highly efficient A-to-I (inosine) editing within an E.coli tRNA-like structure, we construct a reporter system containing E.coli Hokb gene with a tRNA-like motif for robust detection of RNA editing activities. Then, we design mutations to disrupt the interaction between TadA and tRNAs in structure-guided principles, and find that Arginine 153 (R153) within TadA is essential for recognizing core tRNA-like structures. Two ABEmax or mini ABEmax variants (TadA* fused with Cas9 (D10A)) with deletion of R153 within TadA and/or TadA* (named as del153/del153* and mini del153) are successfully engineered, showing minimized RNA editing, but comparable DNA on-targeting activities. Moreover, del153 in recently reported ABE8e or ABE8s can also largely reduce their RNA off-targeting activities. Taken together, we develop a strategy to generate upgraded ABEs (uABEs) with minimized RNA off-target activities.

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“…ChIP-seq was performed as previously described 62 , 63 . Fresh tissues obtained during surgery were collected and digested into single cells or small cell aggregates, and ~1 × 10 5 cells were fixed with 1% formaldehyde for 10 min in PBS at room temperature.…”

Section: Methodsmentioning

confidence: 99%

Oncogenic enhancers drive esophageal squamous cell carcinogenesis and metastasis

Fan

Xiong

et al. 2021

Nat Commun

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The role of cis-elements and their aberrations remains unclear in esophageal squamous cell carcinoma (ESCC, further abbreviated EC). Here we survey 28 H3K27ac-marked active enhancer profiles and 50 transcriptomes in primary EC, metastatic lymph node cancer (LNC), and adjacent normal (Nor) esophageal tissues. Thousands of gained or lost enhancers and hundreds of altered putative super-enhancers are identified in EC and LNC samples respectively relative to Nor, with a large number of common gained or lost enhancers. Moreover, these differential enhancers contribute to the transcriptomic aberrations in ECs and LNCs. We also reveal putative driver onco-transcription factors, depletion of which diminishes cell proliferation and migration. The administration of chemical inhibitors to suppress the predicted targets of gained super-enhances reveals HSP90AA1 and PDE4B as potential therapeutic targets for ESCC. Thus, our epigenomic profiling reveals a compendium of reprogrammed cis-regulatory elements during ESCC carcinogenesis and metastasis for uncovering promising targets for cancer treatment.

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Allele-specific genome editing of imprinting genes by preferentially targeting non-methylated loci using Staphylococcus aureus Cas9 (SaCas9)

Cited by 10 publications

References 29 publications

Structure-guided engineering of adenine base editor with minimized RNA off-targeting activity

Structure-guided engineering of adenine base editor with minimized RNA off-targeting activity

Upgraded adenine base editor (uABE) with minimized RNA off-targeting activity

Oncogenic enhancers drive esophageal squamous cell carcinogenesis and metastasis

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