Deep learning models incorporating endogenous factors beyond DNA sequences improve the prediction accuracy of base editing outcomes
文献类型： 外文期刊
作者： Yuan T.;Wu L.;Li S.;Zheng J.;Li N.;Xiao X.;Zhang H.;Fei T.;Xie L.;Zuo Z.;Li D.;Huang P.;Feng H.;Cao Y.;Yan N.;Wei X.;Shi L.;Sun Y.;Wei W.;Sun Y.;Zuo E.
作者机构：
关键词： （1-1-1）
期刊名称： Cell Discovery
ISSN： 2056-5968
年卷期： 2024 年 10 卷 1 期
页码：
收录情况： SCIE（2024版）
摘要： Adenine base editors (ABEs) and cytosine base editors (CBEs) enable the single nucleotide editing of targeted DNA sites avoiding generation of double strand breaks, however, the genomic features that influence the outcomes of base editing in vivo still remain to be characterized. High-throughput datasets from lentiviral integrated libraries were used to investigate the sequence features affecting base editing outcomes, but the effects of endogenous factors beyond the DNA sequences are still largely unknown. Here the base editing outcomes of ABE and CBE were evaluated in mammalian cells for 5012 endogenous genomic sites and 11,868 genome-integrated target sequences, with 4654 genomic sites sharing the same target sequences. The comparative analyses revealed that the editing outcomes of ABE and CBE at endogenous sites were substantially different from those obtained using genome-integrated sequences. We found that the base editing efficiency at endogenous target sites of both ABE and CBE was influenced by endogenous factors, including epigenetic modifications and transcriptional activity. A deep-learning algorithm referred as BE_Endo, was developed based on the endogenous factors and sequence information from our genomic datasets, and it yielded unprecedented accuracy in predicting the base editing outcomes. These findings along with the developed computational algorithms may facilitate future application of BEs for scientific research and clinical gene therapy. © The Author(s) 2023.
分类号：
- 相关文献
作者其他论文 更多>>
-
Both yields of maize and soybean and soil carbon sequestration in typical Mollisols cropland decrease under future climate change: SPACSYS simulation
作者：Liang S.;Sun N.;Longdoz B.;Meersmans J.;Ma X.;Gao H.;Zhang X.;Qiao L.;Colinet G.;Xu M.;Wu L.
关键词：carbon sequestration efficiency;climate change;long-term fertilization;Mollisols;SOC stock;SPACSYS model;yield
-
Exposure to nicotine regulates prostaglandin E2 secretion and autophagy of granulosa cells to retard follicular maturation in mammals
作者：Zhou X.;He Y.;Quan H.;Yang J.;Li S.;Jiang Y.;Li J.;Yuan X.
关键词：（）Apoptosis;Autophagy;COX1;Follicular maturation;Nicotine
-
Long-term nitrogen fertilization enhances crop yield potential in no-tillage systems through enhancing soil fertility
作者：Li S.;Wu X.;Song X.;Liu X.;Gao H.;Liang G.;Zhang M.;Zheng F.;Yang P.
关键词：Conservation agriculture;Productivity;Rainfall;Soil quality;Sustainable development
-
Soil nitrogen availability drives the response of soil microbial biomass to warming
作者：Li S.;Tang S.;Chen H.;Jin K.
关键词：Meta-analysis;Soil microbial biomass;Soil moisture;Soil nitrogen availability;Warming
-
STnc1280, a trans-coding sRNA is involved in virulence modulation via targeting gldA mRNA in Salmonella Typhimurium
作者：Ning C.;Li N.;Wang L.;Guo Y.;Ji C.;Li Z.;Shang Y.;Zhang X.;Sun Y.;Huang X.;Leng Q.;Cai X.;Meng Q.;Qiao J.
关键词：modulation;Salmonella Typhimurium;sRNA;STnc1280;virulence
-
Characterization of key aroma compounds in roasted chicken using SPME, SAFE, GC-O, GC–MS, AEDA, OAV, recombination-omission tests, and sensory evaluation
作者：Nie R.;Zhang C.;Liu H.;Wei X.;Gao R.;Shi H.;Zhang D.;Wang Z.
关键词：ADEA;GC−O-MS;Recombination and omission test;Roasted chicken;SAFE
-
Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution
作者：Fang Y.;Xiao X.;Lin J.;Lin Q.;Wang J.;Liu K.;Li Z.;Xing J.;Liu Z.;Wang B.;Qi Y.;Long X.;Zeng X.;Hu Y.;Qi J.;Qin Y.;Yang J.;Zhang Y.;Zhang S.;Ye D.;Zhang J.;Liu J.;Tang C.
关键词：