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Studies of gene-expression levels in embryos of Caenorhabditis elegans and of other phyla reveal the timing and location of expression of all genes and support a model in which the endoderm program dates back to the origin of multicellularity while the ectoderm originated as a secondary germ layer freed from ancestral feeding functions. A germ-layer chronology The germ-layer theory — which holds that all the cells and tissues of the body can be grouped into three fundamental layers — goes back to the roots of developmental biology as a discipline 150 years ago. The skin and many external organs are formed of ectoderm; the guts of endoderm, and organs in the middle, such as muscles and bones, form the mesoderm. The mesoderm seems to have been the last of the three layers to have evolved, as Itai Yanai and colleagues confirm with studies on the expression of genes in the embryo of the roundworm Caenorhabditis elegans . But which came first, the ectoderm or the endoderm? Further studies on a range of animals, including the sponge Amphimedon queenslandica , which lacks clear germ layers, show that the endoderm expresses evolutionarily older genes than the ectoderm. The authors speculate that the most primitive animals consisted of what would later become endoderm, with the ectoderm differentiating as cells were freed from the primary function of feeding. The concept of germ layers has been one of the foremost organizing principles in developmental biology, classification, systematics and evolution for 150 years (refs 1 , 2 , 3 ). Of the three germ layers, the mesoderm is found in bilaterian animals but is absent in species in the phyla Cnidaria and Ctenophora, which has been taken as evidence that the mesoderm was the final germ layer to evolve 1 , 4 , 5 . The origin of the ectoderm and endoderm germ layers, however, remains unclear, with models supporting the antecedence of each as well as a simultaneous origin 4 , 6 , 7 , 8 , 9 . Here we determine the temporal and spatial components of gene expression spanning embryonic development for all Caenorhabditis elegans genes and use it to determine the evolutionary ages of the germ layers. The gene expression program of the mesoderm is induced after those of the ectoderm and endoderm, thus making it the last germ layer both to evolve and to develop. Strikingly, the C. elegans endoderm and ectoderm expression programs do not co-induce; rather the endoderm activates earlier, and this is also observed in the expression of endoderm orthologues during the embryology of the frog Xenopus tropicalis , the sea anemone Nematostella vectensis and the sponge Amphimedon queenslandica . Querying the phylogenetic ages of specifically expressed genes reveals that the endoderm comprises older genes. Taken together, we propose that the endoderm program dates back to the origin of multicellularity, whereas the ectoderm originated as a secondary germ layer freed from ancestral feeding functions.

Background The process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrometry. While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise. Results Combining in-depth transcriptome sequencing and high resolution mass spectrometry, we here use proteotranscriptomics to improve gene annotation of protein-coding genes in the Bombyx mori cell line BmN4 which is an increasingly used tool for the analysis of piRNA biogenesis and function . Using this approach we provide the exact coding sequence and evidence for more than 6200 genes on the protein level. Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins. We show that our approach outperforms current Bombyx mori annotation attempts in terms of accuracy and coverage. Conclusions We show that proteotranscriptomics is an efficient, cost-effective and accurate approach to improve previous annotations or generate new gene models. As this technique is based on de-novo transcriptome assembly, it provides the possibility to study any species also in the absence of genome sequence information for which proteogenomics would be impossible.

Embryos in a particular phylum of the animal kingdom tend to most resemble one another at a stage in the middle of embryogenesis known as the phylotypic period; a transcriptional analysis of embryogenesis from single embryos of ten different phyla reveals that the transcripts expressed at the phylotypic stage (or mid-developmental transition) differ greatly between phyla, and a ‘phylum’ may be defined as a set of species sharing the same signals and transcription factor networks during the mid-developmental transition. Stage set for defining a phylum Embryos in a particular phylum tend to resemble one another closely at some point in the middle of embryogeny. This is known as the phylotypic stage, and it has been established that embryos at this stage tend to express a conserved set of genes that are evolutionarily older than the genes expressed before and after. This, however, only applies within a phylum, as Yanai and colleagues demonstrate in an analysis of transcriptomes from individual embryos of ten disparate phyla. Considered across the whole animal kingdom, the transcripts expressed at the phylotypic stage differ greatly between phyla and could be said to define the characters of a particular phylum. This work also provides an operational definition for a phylum as a set of species — with a common ancestor — that share the same molecular mechanisms at the phylotypic stage. Animals are grouped into ~35 ‘phyla’ based upon the notion of distinct body plans 1 , 2 , 3 , 4 . Morphological and molecular analyses have revealed that a stage in the middle of development—known as the phylotypic period—is conserved among species within some phyla 5 , 6 , 7 , 8 , 9 . Although these analyses provide evidence for their existence, phyla have also been criticized as lacking an objective definition, and consequently based on arbitrary groupings of animals 10 . Here we compare the developmental transcriptomes of ten species, each annotated to a different phylum, with a wide range of life histories and embryonic forms. We find that in all ten species, development comprises the coupling of early and late phases of conserved gene expression. These phases are linked by a divergent ‘mid-developmental transition’ that uses species-specific suites of signalling pathways and transcription factors. This mid-developmental transition overlaps with the phylotypic period that has been defined previously for three of the ten phyla, suggesting that transcriptional circuits and signalling mechanisms active during this transition are crucial for defining the phyletic body plan and that the mid-developmental transition may be used to define phylotypic periods in other phyla. Placing these observations alongside the reported conservation of mid-development within phyla, we propose that a phylum may be defined as a collection of species whose gene expression at the mid-developmental transition is both highly conserved among them, yet divergent relative to other species.

Diversification at the transcriptome 3′end is an important and evolutionarily conserved layer of gene regulation associated with differentiation and dedifferentiation processes. Here, we identify extensive transcriptome 3′end-alterations in neuroblastoma, a tumour entity with a paucity of recurrent somatic mutations and an unusually high frequency of spontaneous regression. Utilising extensive RNAi-screening we reveal the landscape and drivers of transcriptome 3′end-diversification, discovering PCF11 as critical regulator, directing alternative polyadenylation (APA) of hundreds of transcripts including a differentiation RNA-operon. PCF11 shapes inputs converging on WNT-signalling, and governs cell cycle, proliferation, apoptosis and neurodifferentiation. Postnatal PCF11 down-regulation induces a neurodifferentiation program, and low-level PCF11 in neuroblastoma associates with favourable outcome and spontaneous tumour regression. Our findings document a critical role for APA in tumorigenesis and describe a novel mechanism for cell fate reprogramming in neuroblastoma with potentially important clinical implications. We provide an interactive data repository of transcriptome-wide APA covering > 170 RNAis, and an APA-network map with regulatory hubs. In gene regulation, diversification at the transcriptome 3′end is linked to differentiation and dedifferentiation. Here, the authors discover extensive transcriptome 3′end-alterations in neuroblastoma, regulated by PCF11, and provide an interactive data repository of transcriptome-wide alternative polyadenylation.

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line [RAW_REF_TEXT] Michal Levin 1 , [/RAW_REF_TEXT] [RAW_REF_TEXT] Marion Scheibe1 & [/RAW_REF_TEXT] [RAW_REF_TEXT] Falk Butter 1 [/RAW_REF_TEXT] BMC Genomics volume 21, Article number: 790 (2020) Cite this article [RAW_REF_TEXT] 74 Accesses [/RAW_REF_TEXT] [RAW_REF_TEXT] Metrics details [/RAW_REF_TEXT] [RAW_REF_TEXT] The original article was published in BMC Genomics 2020 21:690 [/RAW_REF_TEXT] Correction to: BMC Genomics 21, 690 (2020) https://doi.org/10.1186/s12864-020-07088-7 Following publication of the original article [1], it was reported that there were errors in Figs. 1 and 2. Fig. 1 figure1 Genome-free transcriptome assembly approach and assessment of annotation quality. a. Overview of the proteotranscriptomics annotation approach. b. Pie-chart of BUSCO analysis based on the BUSCO arthropoda gene set. c. Barplot summarizing the results of a full-length transcript comparison between the genome-free Trinity assembly to currently available annotations from UniProt, NCBI, SilkBase and SilkDB 3.0 Full size image Fig. 2 figure2 High resolution mass spectrometry provides evidence for superior genome-free annotation. a. Violin plots show distribution of identified MS/MS spectra (in percent) for each database used. Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line [RAW_REF_TEXT] Michal Levin 1 , Marion Scheibe1 & Falk Butter 1 [/RAW_REF_TEXT] BMC Genomics volume 21, Article number: 790 (2020) Cite this article [RAW_REF_TEXT] 74 Accesses Metrics details The original article was published in BMC Genomics 2020 21:690

Cochlear implant (CI) users with prelingual deafness (hearing impairment started before language development was completed) show variable speech-in-noise (SIN) understanding. The present study aimed to assess cortical activation patterns to speech-in-quiet (SIQ) and SIN in prelingual CI users and compared to individuals with normal hearing (NH), using functional Near-Infrared Spectroscopy (fNIRS). Participants included 15 NH who listened to natural speech, 15 NH who listened via 8-channel noise-excited vocoder, and 14 prelingual CI users. fNIRS data were collected in a block design that included three conditions: SIQ, SIN in a signal-to-noise ratio of 0 dB, and noise. Speech reception thresholds in noise (SRTn) were also assessed. Results revealed different patterns of activation between the NH and CI participants in channels covering mainly the right and left middle temporal gyrus (MTG), depending on the SRTn of the CI users. Specifically, while the NH group showed large response to SIQ and SIN in the MTG areas, prelingual CI users with poor SRTn showed significantly smaller response to SIQ, and inversed response (a reduction in activation) to SIN in the same brain areas. These novel findings support the notion that the MTG can serve as a neural marker for speech understanding in CI patients.

•MALDI MSP/I can detect and map blood in enhanced marks over paint.•The application of MALDI MSP/I does not prevent subsequent DNA typing.•An alternative forensic workflow for suspected blood marks on painted walls integrating MALDI MSP/I is suggested.•MALDI MSP can detect blood in fingermarks concealed under a coat of paint. [Display omitted] Matrix Assisted Laser Desorption Ionization Mass Spectrometry Profiling and Imaging (MALDI MSP and MALDI MSI), in combination with bottom up proteomics, have proven to successfully detect and map blood-derived peptide signatures in blood fingermarks, with high specificity and compatibility with a number of blood enhancement techniques (BET). In the present study, the application of MALDI MSP and MSI to blood marks has been investigated further. In particular, the MALDI based detection and visualisation of blood has been explored in tandem with DNA typing. This investigation has been undertaken in a scenario simulating blood fingermarks on painted walls. In the present study, two sets of marks were analysed with each set comprising of a depletion series of four marks deposited on a surface treated to simulate painted walls: Set I - developed with Ninhydrin (NIN) and Set II- developed with Acid Black-1 (AB-1). For both sets, the application of MALDI MSP was successful in detecting haem and human specific haemoglobin peptide markers. MALDI MSI also provided molecular images by visualising haem on the ridge pattern enhanced by BET. The feasibility of successful and subsequent DNA profiling from the recovered fingermarks was also assessed for marks that had undergone enzymatic in situ digestion and MALDI MSI; it was observed that in 73% of the samples analysed, a DNA profile suitable for comparison was obtained. Based on these results, a possible operational workflow has been proposed incorporating the use of a MALDI MS based approach as a confirmatory test for human blood enabling subsequent DNA typing.

Protein abundance is controlled at the transcriptional, translational and post-translational levels, and its regulatory principles are starting to emerge. Investigating these principles requires large-scale proteomics data and cannot just be done with transcriptional outcomes that are commonly used as a proxy for protein abundance. Here, we determine proteome changes resulting from the individual knockout of 3308 nonessential genes in the yeast Schizosaccharomyces pombe . We use similarity clustering of global proteome changes to infer gene functionality that can be extended to other species, such as humans or baker’s yeast. Furthermore, we analyze a selected set of deletion mutants by paired transcriptome and proteome measurements and show that upregulation of proteins under stable transcript expression utilizes optimal codons. Protein abundance is controlled at the transcriptional, translational and posttranslational levels. Here, Öztürk et al. determine proteome changes resulting from individual knockout of 3308 nonessential genes in the yeast S. pombe , infer gene functionality, and show that protein upregulation under stable transcript expression utilizes optimal codons.

Mitochondrial metabolic remodeling is a hallmark of the Trypanosoma brucei digenetic life cycle because the insect stage utilizes a cost-effective oxidative phosphorylation (OxPhos) to generate ATP, while bloodstream cells switch to aerobic glycolysis. Due to difficulties in acquiring enough parasites from the tsetse fly vector, the dynamics of the parasite's metabolic rewiring in the vector have remained obscure. Here, we took advantage of in vitro-induced differentiation to follow changes at the RNA, protein, and metabolite levels. This multi-omics and cell-based profiling showed an immediate redirection of electron flow from the cytochrome-mediated pathway to an alternative oxidase (AOX), an increase in proline consumption, elevated activity of complex II, and certain tricarboxylic acid (TCA) cycle enzymes, which led to mitochondrial membrane hyperpolarization and increased reactive oxygen species (ROS) levels. Interestingly, these ROS molecules appear to act as signaling molecules driving developmental progression because ectopic expression of catalase, a ROS scavenger, halted the in vitro-induced differentiation. Our results provide insights into the mechanisms of the parasite's mitochondrial rewiring and reinforce the emerging concept that mitochondria act as signaling organelles through release of ROS to drive cellular differentiation.

Telomeres are nucleoprotein structures at the ends of linear chromosomes. In humans, they consist of TTAGGG repeats, which are bound by dedicated proteins such as the shelterin complex. This complex blocks unwanted DNA damage repair at telomeres, e.g. by suppressing nonhomologous end joining (NHEJ) through its subunit TRF2. Here, we describe ZNF524, a zinc finger protein that directly binds telomeric repeats with nanomolar affinity, and reveal base-specific sequence recognition by cocrystallization with telomeric DNA. ZNF524 localizes to telomeres and specifically maintains the presence of the TRF2/RAP1 subcomplex at telomeres without affecting other shelterin members. Loss of ZNF524 concomitantly results in an increase in DNA damage signaling and recombination events. Overall, ZNF524 is a direct telomere-binding protein involved in the maintenance of telomere integrity. ZNF524 is a newly described protein that binds to telomeres, the ends of linear chromosomes. ZNF524 promotes the presence of two members of the shelterin complex, TRF2/RAP1, at telomeres, and prevents genomic instability.