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Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short-read RNA-Seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is crucial, however, when it comes to understanding the interplay between the various steps of plastid gene expression. Here, we describe a protocol to study the plastid transcriptome using nanopore sequencing. In the leaf of Arabidopsis thaliana, with about 1.5 million strand-specific reads mapped to the chloroplast genome, we could recapitulate most of the complexity of the plastid transcriptome (polygenic transcripts, multiple isoforms associated with post-transcriptional processing) using virtual Northern blots. Even if the transcripts longer than about 2500 nucleotides were missing, the study of the co-occurrence of editing and splicing events identified 42 pairs of events that were not occurring independently. This study also highlighted a preferential chronology of maturation events with splicing happening after most sites were edited.

The present report examines a possible co-maturation pattern between different frequency ranges on the spontaneous electroencephalogram (EEG) during development in childhood, adolescence and young adulthood. One hundred and sixty-seven subjects, between 6 and 26 years old were recorded during 3 min of spontaneous EEG. The power spectral density (PSD) logarithm was computed. There was a decrease in all frequency band ranges between 1 and 46 Hz. Correlation matrices for these frequencies were computed. A general trend of PSD correlation with neighboring frequencies was obtained. Furthermore, there was a high correlation during development between theta and beta ranges, and between high-beta and gamma frequency ranges. The correlation of theta versus beta was particularly high between the anterior and posterior electrode sites. Principal component analysis allowed the extraction of six components explaining the variance associated with the delta, theta, alpha, low-beta, high-beta and gamma ranges. Interestingly, the component explaining the theta rhythm also explained a fraction of the low-beta rhythm during development. The results suggest a pattern of co-maturation in the PSD of spontaneous EEG between theta and low-beta, and between high-beta and gamma, which would be due to the maturation of neural tissue underlying the sources of different frequencies. The possible functional role of theta-beta co-maturation in fronto-parietal electrode sites is suggested. [ABSTRACT FROM AUTHOR]

Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short-read RNA-Seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is crucial, however, when it comes to understanding the interplay between the various steps of plastid gene expression. Here, we describe a protocol to study the plastid transcriptome using nanopore sequencing. In the leaf of Arabidopsis thaliana, with about 1.5 million strand-specific reads mapped to the chloroplast genome, we could recapitulate most of the complexity of the plastid transcriptome (polygenic transcripts, multiple isoforms associated with post-transcriptional processing) using virtual Northern blots. Even if the transcripts longer than about 2500 nucleotides were missing, the study of the co-occurrence of editing and splicing events identified 42 pairs of events that were not occurring independently. This study also highlighted a preferential chronology of maturation events with splicing happening after most sites were edited. [ABSTRACT FROM AUTHOR]