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ItemDiscovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.Grapotte, M ; Saraswat, M ; Bessière, C ; Menichelli, C ; Ramilowski, JA ; Severin, J ; Hayashizaki, Y ; Itoh, M ; Tagami, M ; Murata, M ; Kojima-Ishiyama, M ; Noma, S ; Noguchi, S ; Kasukawa, T ; Hasegawa, A ; Suzuki, H ; Nishiyori-Sueki, H ; Frith, MC ; FANTOM consortium, ; Chatelain, C ; Carninci, P ; de Hoon, MJL ; Wasserman, WW ; Bréhélin, L ; Lecellier, C-H (Springer Science and Business Media LLC, 2021-06-02)Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
ItemIdentification of a Sacral, Visceral Sensory Transcriptome in Embryonic and Adult MiceSmith-Anttila, CJA ; Mason, EA ; Wells, CA ; Aronow, BJ ; Osborne, PB ; Keast, JR (SOC NEUROSCIENCE, 2020-01-01)Visceral sensory neurons encode distinct sensations from healthy organs and initiate pain states that are resistant to common analgesics. Transcriptome analysis is transforming our understanding of sensory neuron subtypes but has generally focused on somatic sensory neurons or the total population of neurons in which visceral neurons form the minority. Our aim was to define transcripts specifically expressed by sacral visceral sensory neurons, as a step towards understanding the unique biology of these neurons and potentially leading to identification of new analgesic targets for pelvic visceral pain. Our strategy was to identify genes differentially expressed between sacral dorsal root ganglia (DRG) that include somatic neurons and sacral visceral neurons, and adjacent lumbar DRG that comprise exclusively of somatic sensory neurons. This was performed in adult and E18.5 male and female mice. By developing a method to restrict analyses to nociceptive Trpv1 neurons, a larger group of genes were detected as differentially expressed between spinal levels. We identified many novel genes that had not previously been associated with pelvic visceral sensation or nociception. Limited sex differences were detected across the transcriptome of sensory ganglia, but more were revealed in sacral levels and especially in Trpv1 nociceptive neurons. These data will facilitate development of new tools to modify mature and developing sensory neurons and nociceptive pathways.
ItemUnique properties of a subset of human pluripotent stem cells with high capacity for self-renewalLau, KX ; Mason, EA ; Kie, J ; De Souza, DP ; Kloehn, J ; Tull, D ; McConville, MJ ; Keniry, A ; Beck, T ; Blewitt, ME ; Ritchie, ME ; Naik, SH ; Zalcenstein, D ; Korn, O ; Su, S ; Romero, IG ; Spruce, C ; Baker, CL ; McGarr, TC ; Wells, CA ; Pera, MF (Nature Research, 2020-05-15)Archetypal human pluripotent stem cells (hPSC) are widely considered to be equivalent in developmental status to mouse epiblast stem cells, which correspond to pluripotent cells at a late post-implantation stage of embryogenesis. Heterogeneity within hPSC cultures complicates this interspecies comparison. Here we show that a subpopulation of archetypal hPSC enriched for high self-renewal capacity (ESR) has distinct properties relative to the bulk of the population, including a cell cycle with a very low G1 fraction and a metabolomic profile that reflects a combination of oxidative phosphorylation and glycolysis. ESR cells are pluripotent and capable of differentiation into primordial germ cell-like cells. Global DNA methylation levels in the ESR subpopulation are lower than those in mouse epiblast stem cells. Chromatin accessibility analysis revealed a unique set of open chromatin sites in ESR cells. RNA-seq at the subpopulation and single cell levels shows that, unlike mouse epiblast stem cells, the ESR subset of hPSC displays no lineage priming, and that it can be clearly distinguished from gastrulating and extraembryonic cell populations in the primate embryo. ESR hPSC correspond to an earlier stage of post-implantation development than mouse epiblast stem cells.