More Like this

1. Two organelle RNA recognition motif proteins affect distinct sets of RNA editing sites in the Arabidopsis thaliana plastid

   https://doi.org/10.1002/pld3.213  

   Searing, Audrey M. ; Satyanarayan, Manasa B. ; O′Donnell, James P. ; Lu, Yan ( April 2020 , Plant Direct)
2. Identification of rfk-1 , a Meiotic Driver Undergoing RNA Editing in Neurospora

   https://doi.org/10.1534/genetics.119.302122  

   Rhoades, Nicholas A. ; Harvey, Austin M. ; Samarajeewa, Dilini A. ; Svedberg, Jesper ; Yusifov, Aykhan ; Abusharekh, Anna ; Manitchotpisit, Pennapa ; Brown, Daren W. ; Sharp, Kevin J. ; Rehard, David G. ; et al ( May 2019 , Genetics)
3. Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain

   https://doi.org/10.1073/pnas.1811768116  

   Sapiro, Anne L. ; Shmueli, Anat ; Henry, Gilbert Lee ; Li, Qin ; Shalit, Tali ; Yaron, Orly ; Paas, Yoav ; Billy Li, Jin ; Shohat-Ophir, Galit ( February 2019 , Proceedings of the National Academy of Sciences)

   Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a ubiquitous mechanism that generates transcriptomic diversity. This process is particularly important for proper neuronal function; however, little is known about how RNA editing is dynamically regulated between the many functionally distinct neuronal populations of the brain. Here, we present a spatial RNA editing map in theDrosophilabrain and show that different neuronal populations possess distinct RNA editing signatures. After purifying and sequencing RNA from genetically marked groups of neuronal nuclei, we identified a large number of editing sites and compared editing levels in hundreds of transcripts across nine functionally different neuronal populations. We found distinct editing repertoires for each population, including sites in repeat regions of the transcriptome and differential editing in highly conserved and likely functional regions of transcripts that encode essential neuronal genes. These changes are site-specific and not driven by changes inAdarexpression, suggesting a complex, targeted regulation of editing levels in key transcripts. This fine-tuning of the transcriptome between different neurons by RNA editing may account for functional differences between distinct populations in the brain.
4. Uncovering Cis -Regulatory Elements Important for A-to-I RNA Editing in Fusarium graminearum

   https://doi.org/10.1128/mbio.01872-22  

   Feng, Chanjing ; Cao, Xinyu ; Du, Yanfei ; Chen, Yitong ; Xin, Kaiyun ; Zou, Jingwen ; Jin, Qiaojun ; Xu, Jin-Rong ; Liu, Huiquan ( October 2022 , mBio)

   Lin, Xiaorong (Ed.)

   ABSTRACT Adenosine-to-inosine (A-to-I) RNA editing independent of adenosine deaminase acting on RNA (ADAR) enzymes was discovered in fungi recently, and shown to be crucial for sexual reproduction. However, the underlying mechanism for editing is unknown. Here, we combine genome-wide comparisons, proof-of-concept experiments, and machine learning to decipher cis -regulatory elements of A-to-I editing in Fusarium graminearum . We identified plenty of RNA primary sequences and secondary structural features that affect editing specificity and efficiency. Although hairpin loop structures contribute importantly to editing, unlike in animals, the primary sequences have more profound influences on editing than secondary structures. Nucleotide preferences at adjacent positions of editing sites are the most important features, especially preferences at the −1 position. Unexpectedly, besides the number of positions with preferred nucleotides, the combination of preferred nucleotides with depleted ones at different positions are also important for editing. Some cis -sequence features have distinct importance for editing specificity and efficiency. Machine learning models built from diverse sequence and secondary structural features can accurately predict genome-wide editing sites but not editing levels, indicating that the cis -regulatory principle of editing efficiency is more complex than that of editing specificity. Nevertheless, our model interpretation provides insights into the quantitativemore »contribution of each feature to the prediction of both editing sites and levels. We found that efficient editing of FG3G34330 transcripts depended on the full-length RNA molecule, suggesting that additional RNA structural elements may also contribute to editing efficiency. Our work uncovers multidimensional cis -regulatory elements important for A-to-I RNA editing in F. graminearum , helping to elucidate the fungal editing mechanism. IMPORTANCE A-to-I RNA editing is a new epigenetic phenomenon that is crucial for sexual reproduction in fungi. Deciphering cis -regulatory elements of A-to-I RNA editing can help us elucidate the editing mechanism and develop a model that accurately predicts RNA editing. In this study, we discovered multiple RNA sequence and secondary structure features important for A-to-I editing in Fusarium graminearum . We also identified the cis -sequence features with distinct importance for editing specificity and efficiency. The potential importance of full-length RNA molecules for editing efficiency is also revealed. This study represents the first comprehensive investigation of the cis -regulatory principles of A-to-I RNA editing in fungi.« less
5. Guide RNA Engineering Enables Dual Purpose CRISPR-Cpf1 for Simultaneous Gene Editing and Gene Regulation in Yarrowia lipolytica

   https://doi.org/10.1021/acssynbio.9b00498  

   Ramesh, Adithya ; Ong, Thomas ; Garcia, Jaime A. ; Adams, Jessica ; Wheeldon, Ian ( April 2020 , ACS Synthetic Biology)