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Most of the current alternative splicing (AS) analysis tools are powerless to analyse complex splicing. To address this, we developed SUVA (Splice sites Usage Variation Analysis) that decomposes complex splicing events into five types of splice junction pairs. By analysing real and simulated data, SUVA showed higher sensitivity and accuracy in detecting AS events than the compared methods. Notably, SUVA detected extensive complex AS events and screened out 69 highly conserved and dominant AS events associated with cancer. The cancer-associated complex AS events in FN1 and the co-regulated RNA-binding proteins were significantly correlated with patient survival. [ABSTRACT FROM AUTHOR]

N6-methyladenosine (m6A) is considered as a reversible RNA modification occurring more frequently on the GAC than AAC context in vivo, which regulates post-transcriptional gene expression in mammalian cells. m6A 'writers' METTL3 and METTL14 demonstrate a strong preference for binding AC-containing motifs in living cells. However, this evidence is currently lacking for m6A erasers, leaving the dynamics of the internal m6A modification under debate recently. We analysed three recently published FTO CLIP-seq data sets and two generated in this study, one of the two known m6A 'erasers'. FTO binding peaks from all cell lines contain RRACH motifs. Only those from K562, 3T3-L1and HeLa cells were enriched in AC-containing motifs, while those from HEK293 were not. The exogenously overexpressed FTO effectively binds to m6A motif-containing RNA sites. FTO overexpression specifically removed m6A modification from GGACU and RRACU motifs in a concentration-dependent manner. These findings underline the dynamics of FTO in target selection, which is predicted to contribute to both the m6A dynamics and the FTO plasticity in biological functions and diseases. [ABSTRACT FROM AUTHOR]

Background The halophyte Suaeda aralocaspica performs complete C4 photosynthesis within individual cells (SCC4), which is distinct from typical C4 plants, which require the collaboration of 2 types of photosynthetic cells. However, despite SCC4 plants having features that are valuable in engineering higher photosynthetic efficiencies in agriculturally important C3 species such as rice, there are no reported sequenced SCC4 plant genomes, limiting our understanding of the mechanisms involved in, and evolution of, SCC4 photosynthesis. Findings Using Illumina and Pacific Biosciences sequencing platforms, we generated ∼202 Gb of clean genomic DNA sequences having a 433-fold coverage based on the 467 Mb estimated genome size of S. aralocaspica. The final genome assembly was 452 Mb, consisting of 4,033 scaffolds, with a scaffold N50 length of 1.83 Mb. We annotated 29,604 protein-coding genes using Evidence Modeler based on the gene information from ab initio predictions, homology levels with known genes, and RNA sequencing–based transcriptome evidence. We also annotated noncoding genes, including 1,651 long noncoding RNAs, 21 microRNAs, 382 transfer RNAs, 88 small nuclear RNAs, and 325 ribosomal RNAs. A complete (circular with no gaps) chloroplast genome of S. aralocaspica 146,654 bp in length was also assembled. Conclusions We have presented the genome sequence of the SCC4 plant S. aralocaspica. Knowledge of the genome of S. aralocaspica should increase our understanding of the evolution of SCC4 photosynthesis and contribute to the engineering of C4 photosynthesis into economically important C3 crops. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) play roles in various biological processes, but their functions in the rice ( Oryza sativa ) response to Magnaporthe oryzae remain elusive. Here, we demonstrate that circRNAs are involved in the rice- M. oryzae interaction using comparative circRNA-sequencing and transgenic approaches. We identified 2932 high-confidence circRNAs from young leaves of the blast-resistant accession International Rice Blast Line Pyricularia-Kanto51-m-Tsuyuake (IR25) and the blast-susceptible accession Lijiangxin Tuan Heigu (LTH) under M oryzae -infected or uninfected conditions; 636 were detected specifically upon M oryzae infection. The circRNAs in IR25 were significantly more diverse than those in LTH, especially under M. oryzae infection. Particularly, the number of circRNAs generated per parent gene was much higher in IR25 than in LTH and increased in IR25 but decreased in LTH upon M. oryzae infection. The higher diversity of circRNAs in IR25 was further associated with more frequent 3' and 5' alternative back-splicing and usage of complex splice sites. Moreover, a subset of circRNAs was differentially responsive to M oryzae in IR25 and LTH. We further confirmed that circR5g05160 promotes rice immunity against M oryzae Therefore, our data indicate that circRNA diversity is associated with different responses to M oryzae infection in rice and provide a starting point to investigate a new layer of regulation in the rice- M oryzae interaction., (© 2020 American Society of Plant Biologists. All Rights Reserved.)

N 6 -methyladenosine (m 6 A) is considered as a reversible RNA modification occurring more frequently on the GAC than AAC context in vivo , which regulates post-transcriptional gene expression in mammalian cells. m 6 A 'writers' METTL3 and METTL14 demonstrate a strong preference for binding AC-containing motifs in living cells. However, this evidence is currently lacking for m 6 A erasers, leaving the dynamics of the internal m 6 A modification under debate recently. We analysed three recently published FTO CLIP-seq data sets and two generated in this study, one of the two known m 6 A 'erasers'. FTO binding peaks from all cell lines contain RRACH motifs. Only those from K562, 3T3-L1and HeLa cells were enriched in AC-containing motifs, while those from HEK293 were not. The exogenously overexpressed FTO effectively binds to m 6 A motif-containing RNA sites. FTO overexpression specifically removed m 6 A modification from GGACU and RRACU motifs in a concentration-dependent manner. These findings underline the dynamics of FTO in target selection, which is predicted to contribute to both the m 6 A dynamics and the FTO plasticity in biological functions and diseases.