There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genomewide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3 and 5 UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3' UTRs more than 5' UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation.tiling array ͉ transcriptone survey ͉ gene architecture ͉ segmentation ͉ antisense regulation P roteins constitute most structural and functional components of cells. The assumption has been that protein-encoding genes are also the main controllers of cellular processes. Recent evidence challenges this assumption, suggesting a wide-spread involvement of noncoding RNA in regulation, including through the activity of untranslated regions of mRNAs (1), antisense transcripts (2, 3), and isolated noncoding RNAs such as microRNA that control transcript levels or their translation (4).High-resolution transcriptome analysis in higher eukaryotes using tiling arrays has improved ORF annotations and exonintron predictions and discovered many new transcripts of currently unknown function (5-7). However, these studies have encountered challenges, due to noise, limited resolution, lack of strand-specific signal, and drawbacks in the analysis methods (8). Sequencing of cloned cDNAs has also revealed a high level of transcriptional complexity, including the presence of many new transcripts, alternative promoter usage, splicing, and polyadenylation, as well as the presence of many sense-antisense transcript pairs (3, 9). However, because of the cost and labor of large-scale sequencing, this approach has been limited. Therefore, there is a need to develop high-throughput, precise, and high-re...

G.H. contributed to the study design and collection and interpretation of the data. R.P.K. performed the analysis of Circle-seq and whole-genome sequencing. E.R.F. performed the data analysis of the whole-genome sequencing data. I.

Exosomes are small membranous vesicles of endocytic origin that are released by almost every cell type. They exert versatile functions in intercellular communication important for many physiological and pathological processes. Recently, exosomes attracted interest with regard to their role in cell-cell communication in the nervous system. We have shown that exosomes released from oligodendrocytes upon stimulation with the neurotransmitter glutamate are internalized by neurons and enhance the neuronal stress tolerance. Here, we demonstrate that oligodendroglial exosomes also promote neuronal survival during oxygen-glucose deprivation, a model of cerebral ischaemia. We show the transfer from oligodendrocytes to neurons of superoxide dismutase and catalase, enzymes which are known to help cells to resist oxidative stress. Additionally, we identify various effects of oligodendroglial exosomes on neuronal physiology. Electrophysiological analysis using in vitro multi-electrode arrays revealed an increased firing rate of neurons exposed to oligodendroglial exosomes. Moreover, gene expression analysis and phosphorylation arrays uncovered differentially expressed genes and altered signal transduction pathways in neurons after exosome treatment. Our study thus provides new insight into the broad spectrum of action of oligodendroglial exosomes and their effects on neuronal physiology. The exchange of extracellular vesicles between neural cells may exhibit remarkable potential to impact brain performance.

R package tilingArray at http://www.bioconductor.org.

MYCN amplification drives one in six cases of neuroblastoma. The supernumerary gene copies are commonly found on highly rearranged, extrachromosomal circular DNA (ecDNA). The exact amplicon structure has not been described thus far and the functional relevance of its rearrangements is unknown. Here, we analyze the MYCN amplicon structure using short-read and Nanopore sequencing and its chromatin landscape using ChIP-seq, ATAC-seq and Hi-C. This reveals two distinct classes of amplicons which explain the regulatory requirements for MYCN overexpression. The first class always co-amplifies a proximal enhancer driven by the noradrenergic core regulatory circuit (CRC). The second class of MYCN amplicons is characterized by high structural complexity, lacks key local enhancers, and instead contains distal chromosomal fragments harboring CRC-driven enhancers. Thus, ectopic enhancer hijacking can compensate for the loss of local gene regulatory elements and explains a large component of the structural diversity observed in MYCN amplification.