Mapping messenger RNA methylations at single base resolution

2021 ◽  
Vol 63 ◽  
pp. 28-37
Author(s):  
Jie Cao ◽  
Xiao Shu ◽  
Xin-Hua Feng ◽  
Jianzhao Liu
Science ◽  
2021 ◽  
pp. eabe7106
Author(s):  
Chunlei Jiao ◽  
Sahil Sharma ◽  
Gaurav Dugar ◽  
Natalia L. Peeck ◽  
Thorsten Bischler ◽  
...  

CRISPR-Cas systems recognize foreign genetic material using CRISPR RNAs (crRNAs). In Type II systems, a trans-activating crRNA (tracrRNA) hybridizes to crRNAs to drive their processing and utilization by Cas9. While analyzing Cas9-RNA complexes from Campylobacter jejuni, we discovered tracrRNA hybridizing to cellular RNAs, leading to formation of “noncanonical” crRNAs capable of guiding DNA targeting by Cas9. Our discovery inspired the engineering of reprogrammed tracrRNAs that link the presence of any RNA-of-interest to DNA targeting with different Cas9 orthologs. This capability became the basis for a multiplexable diagnostic platform termed LEOPARD (Leveraging Engineered tracrRNAs and On-target DNAs for PArallel RNA Detection). LEOPARD allowed simultaneous detection of RNAs from different viruses in one test and distinguished SARS-CoV-2 and its D614G variant with single-base resolution in patient samples.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yubang Gao ◽  
Xuqing Liu ◽  
Bizhi Wu ◽  
Huihui Wang ◽  
Feihu Xi ◽  
...  

AbstractThere are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the estimation of m6A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m6A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m6A-sensitive RNA-endoribonuclease–facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m6A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m6A.


2012 ◽  
Vol 9 (3) ◽  
pp. 685-693 ◽  
Author(s):  
Yossi Kam ◽  
Abraham Rubinstein ◽  
Aviram Nissan ◽  
David Halle ◽  
Eylon Yavin

2009 ◽  
Vol 20 (1) ◽  
pp. 133-141 ◽  
Author(s):  
O. Wurtzel ◽  
R. Sapra ◽  
F. Chen ◽  
Y. Zhu ◽  
B. A. Simmons ◽  
...  

2018 ◽  
Vol 9 (15) ◽  
pp. 3723-3728 ◽  
Author(s):  
Yafen Wang ◽  
Chaoxing Liu ◽  
Xiong Zhang ◽  
Wei Yang ◽  
Fan Wu ◽  
...  

5-Formylcytosine (5fC) is known as one of the key players in the process of active DNA demethylation and displays essential epigenetic functions in mammals.


2011 ◽  
Vol 12 (Suppl 14) ◽  
pp. S7 ◽  
Author(s):  
Shin Suzuki ◽  
Tomohiro Yasuda ◽  
Yuichi Shiraishi ◽  
Satoru Miyano ◽  
Masao Nagasaki

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