Comparative transcriptomics
Dotaz
Zobrazit nápovědu
BACKGROUND: Understanding the genetic basis of novel traits is a central topic in evolutionary biology. Two novel pigmentation phenotypes, egg-spots and blotches, emerged during the rapid diversification of East African cichlid fishes. Egg-spots are circular pigmentation markings on the anal fins of hundreds of derived haplochromine cichlids species, whereas blotches are patches of conspicuous anal fin pigmentation with ill-defined boundaries that occur in few species that belong to basal cichlid lineages. Both traits play an important role in the breeding behavior of this group of fishes. Knowledge about the origin, homology and underlying genetics of these pigmentation traits is sparse. RESULTS: Here, we present a comparative transcriptomic and differential gene expression analysis of egg-spots and blotches. We first conducted an RNA sequencing experiment where we compared egg-spot tissue with the remaining portion of egg-spot-free fin tissue using six individuals of Astatotilapia burtoni. We identified 1229 differentially expressed genes between the two tissue types. We then showed that rates of evolution of these genes are higher than average estimated on whole transcriptome data. Using quantitative real-time PCR, we found that 29 out of a subset of 46 differentially expressed genes showed an analogous expression pattern in another haplochromine species' egg-spots, Cynotilapia pulpican, strongly suggesting that these genes are involved in the egg-spot phenotype. Among these are the previously identified egg-spot gene fhl2a, two known patterning genes (hoxC12a and bmp3) as well as other pigmentation related genes such as asip. Finally, we analyzed the expression patterns of the same gene subset in two species that feature blotches instead of egg-spots, one haplochromine species (Pseudocrenilabrus philander) and one ectodine species (Callochromis macrops), revealing that the expression patterns in blotches and egg-spots are rather distinct. CONCLUSIONS: We identified several candidate genes that will serve as an important and useful resource for future research on the emergence and diversification of cichlid fishes' egg-spots. Only a limited degree of conservation of gene expression patterns was detected between the egg-spots of the derived haplochromines and blotches from ancestral haplochromines, as well as between the two types of blotches, suggesting an independent origin of these traits.
- MeSH
- anální kanál fyziologie MeSH
- cichlidy genetika MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- molekulární evoluce MeSH
- pigmentace kůže genetika MeSH
- ploutve zvířat fyziologie MeSH
- regulace genové exprese MeSH
- rybí proteiny genetika MeSH
- sekvenční analýza RNA metody MeSH
- stanovení celkové genové exprese metody MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development.
- MeSH
- algoritmy MeSH
- buněčný cyklus genetika MeSH
- lidé MeSH
- nádorové buněčné linie MeSH
- nádory genetika metabolismus patologie MeSH
- proteiny buněčného cyklu genetika metabolismus MeSH
- transkripční faktory metabolismus MeSH
- transkriptom * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
- validační studie MeSH
This review defines limits of currently used techniques to assess developmental capacity of human embryos in assisted reproduction and provides an overview of techniques assessing embryo's physiology on levels of genomics, transcriptomics, proteomics and metabolomics. Basic principles of respective techniques are included. Discovered biomarkers are discussed with respect to biochemical functions and their prognostic values of embryonal development.
- Klíčová slova
- vývojový potenciál embrya,
- MeSH
- 2D gelová elektroforéza MeSH
- aneuploidie MeSH
- asistovaná reprodukce MeSH
- biologické markery analýza metabolismus MeSH
- biopsie MeSH
- embryo savčí * MeSH
- embryonální vývoj * genetika MeSH
- fertilizace in vitro MeSH
- hybridizace in situ fluorescenční metody MeSH
- lidé MeSH
- messenger RNA analýza MeSH
- metabolom MeSH
- metabolomika klasifikace metody MeSH
- polymerázová řetězová reakce metody MeSH
- preimplantační diagnóza metody MeSH
- proteom analýza MeSH
- sekvenční analýza DNA metody MeSH
- srovnávací genomová hybridizace metody MeSH
- transkriptom MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.
BACKGROUND: The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. RESULTS: Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. CONCLUSIONS: In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.
- MeSH
- genomika MeSH
- modely nemocí na zvířatech MeSH
- myši MeSH
- Naegleria fowleri * genetika MeSH
- transkriptom MeSH
- trogocytóza MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidium hominis. In contrast, data on the invertebrate-infecting gregarines remains sparse and their evolutionary relationship to other apicomplexans remains obscure. Most apicomplexans retain a highly modified plastid, while their mitochondria remain metabolically conserved. Cryptosporidium spp. inhabit an anaerobic host-gut environment and represent the known exception, having completely lost their plastid while retaining an extremely reduced mitochondrion that has lost its genome. Recent advances in single-cell sequencing have enabled the first broad genome-scale explorations of gregarines, providing evidence of differential plastid retention throughout the group. However, little is known about the retention and metabolic capacity of gregarine mitochondria. RESULTS: Here, we sequenced transcriptomes from five species of gregarines isolated from cockroaches. We combined these data with those from other apicomplexans, performed detailed phylogenomic analyses, and characterized their mitochondrial metabolism. Our results support the placement of Cryptosporidium as the earliest diverging lineage of apicomplexans, which impacts our interpretation of evolutionary events within the phylum. By mapping in silico predictions of core mitochondrial pathways onto our phylogeny, we identified convergently reduced mitochondria. These data show that the electron transport chain has been independently lost three times across the phylum, twice within gregarines. CONCLUSIONS: Apicomplexan lineages show variable functional restructuring of mitochondrial metabolism that appears to have been driven by adaptations to parasitism and anaerobiosis. Our findings indicate that apicomplexans are rife with convergent adaptations, with shared features including morphology, energy metabolism, and intracellularity.
'Omics' technologies have facilitated the identification of hundreds to thousands of tick molecules that mediate tick feeding and play a role in the transmission of tick-borne diseases. Deep sequencing methodologies have played a key role in this knowledge accumulation, profoundly facilitating the study of the biology of disease vectors lacking reference genomes. For example, the nucleotide sequences of the entire set of tick salivary effectors, the so-called tick 'sialome', now contain at least one order of magnitude more transcript sequences compared to similar projects based on Sanger sequencing. Tick feeding is a complex and dynamic process, and while the dynamic 'sialome' is thought to mediate tick feeding success, exactly how transcriptome dynamics relate to tick-host-pathogen interactions is still largely unknown. The identification and, importantly, the functional analysis of the tick 'sialome' is expected to shed light on this 'black box'. This information will be crucial for developing strategies to block pathogen transmission, not only for anti-tick vaccine development but also the discovery and development of new, pharmacologically active compounds for human diseases.
- MeSH
- genom fyziologie MeSH
- interakce hostitele a patogenu MeSH
- klíšťata genetika fyziologie MeSH
- lidé MeSH
- proteomika * MeSH
- slinné žlázy fyziologie MeSH
- transkriptom fyziologie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
Východiska: Současná protinádorová terapie se vyznačuje vysokou nespecifitou, a to Východiska: Současná protinádorová terapie se vyznačuje vysokou nespecifitou, a to z důvodu různorodé povahy nádorů, která významně snižuje účinnost léčby. Masivní rozvoj genomických, transkriptomických a proteomických metod v posledních desetiletích umožnil detailní charakterizaci nádorů na genomové, transkriptomové a proteomové úrovni a jejich vzájemná kombinace tak představuje potenciál, jak zvýšit efektivitu procesu detekce neopeptidů a následného navržení specifické terapie. Mezi v současné době široce používané genomické a transkriptomické metody patří zejména celogenomové, celotranskriptomové, příp. exomové sekvenování, která umožňují detekovat jednonukleotidové polymorfi zmy. V případě proteomických metod, pokud je k dispozici peptidová knihovna, je možné detekovat mutované proteiny v biologickém vzorku. Nedílnou součástí kooperace těchto metod jsou softwary, které umožní interpretovat získané výsledky, jejich vizualizaci, příp. zprostředkují konverzi mezi datovými formáty často specifickými pro použitou metodu/ přístroj. Cíl: Článek primárně popisuje bio informatickou analýzu vzorků v rámci genomických a transkriptomických metod a jejich možné limitace a související problémy, které musí být zváženy v průběhu analýzy, zejména týkající se kvality vstupních dat. V textu je rovněž věnována pozornost problémům vycházejícím ze zarovnání sekvencí na referenční genom. Součástí publikace je popis softwaru TransPEM, který byl vytvořen za účelem konverze výsledků analýzy jednonukleotidových polymorfizmů do podoby peptidové knihovny sekvencí využitelné k detekci neopeptidů pomocí proteomických metod. Nechybí ani stručný popis proteomických metod využívajících tuto knihovnu a představení jejich omezení.
Background: Current anti-tumour therapy is characterised by high non-specificity due to the diverse nature of tumours, which can significantly reduce its efficiency. The massive development of genomic, transcriptomic, and proteomic methods has enabled the detailed characterisation of individual tumours at the genome, transcriptome and proteome levels. Whole-genome sequencing, whole-transcriptome sequencing and exome sequencing can be listed as examples of genomics and transcriptomics methods. Those methods are suitable for detecting single- -nucleotide polymorphisms. In the case of proteomic methods, where a peptide library is available, it is possible to detect mutated proteins in a biological sample. Also important is software that interprets and visualises the results or facilitates conversion between data formats that are specific to the method. The combination of methods can in principle increase the likelihood of detecting new neoantigens and design-specific anti-tumour therapy. Aim: The article primarily describes the bioinformatics analysis of samples using the methods of genomics, transcriptomics and proteomics, and the possible problems which must be considered during the analysis. The article includes a description of TransPEM software designed to convert the results from the analysis of single nucleotide polymorphisms into a peptide library of sequences useful for the detection of neopeptides using proteomic methods. The publication is accompanied by a brief description of the proteomics methods using this peptide library and the summary of its limitations.
- Klíčová slova
- transkriptomika,
- MeSH
- genomika * metody MeSH
- lidé MeSH
- nádory diagnóza MeSH
- navrhování softwaru MeSH
- proteomika * metody MeSH
- výpočetní biologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
During SARS-CoV-2 infection, the virus transforms the infected host cell into factories that produce new viral particles. As infection progresses, the infected cells undergo numerous changes in various pathways. One of these changes is the occurrence of a cytokine storm, which leads to severe symptoms. In this study, we examined the transcriptomic changes caused by COVID-19 by analyzing RNA-seq data obtained from COVID-19-positive patients as well as COVID-19-negative donors. RNA-seq data were collected for the purpose of identification of potential biomarkers associated with a different course of the disease. We analyzed the first datasets, consisting of 96 samples to validate our methods. The objective of this publication is to report the pilot results. To explore potential biomarkers related to disease severity, we conducted a differential expression analysis of human transcriptome, focusing on COVID-19 positivity and symptom severity. Given the large number of potential biomarkers we identified, we further performed pathway enrichment analysis with terms from Kyoto Encyclopedia of Genes and Genomics (KEGG) to obtain a more profound understanding of altered pathways. Our results indicate that pathways related to immune processes, response to infection, and multiple signaling pathways were affected. These findings align with several previous studies that also reported the influence of SARS-CoV-2 infection on these pathways.
- MeSH
- biologické markery MeSH
- COVID-19 * genetika MeSH
- genomika MeSH
- lidé MeSH
- SARS-CoV-2 genetika MeSH
- stanovení celkové genové exprese MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
PURPOSE: Missing heritability in human diseases represents a major challenge, and this is particularly true for ABCA4-associated Stargardt disease (STGD1). We aimed to elucidate the genomic and transcriptomic variation in 1054 unsolved STGD and STGD-like probands. METHODS: Sequencing of the complete 128-kb ABCA4 gene was performed using single-molecule molecular inversion probes (smMIPs), based on a semiautomated and cost-effective method. Structural variants (SVs) were identified using relative read coverage analyses and putative splice defects were studied using in vitro assays. RESULTS: In 448 biallelic probands 14 known and 13 novel deep-intronic variants were found, resulting in pseudoexon (PE) insertions or exon elongations in 105 alleles. Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions and flanking exon deletions. Eleven distinct large deletions were found, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. CONCLUSION: Deep sequencing of ABCA4 and midigene-based splice assays allowed the identification of SVs and causal deep-intronic variants in 25% of biallelic STGD1 cases, which represents a model study that can be applied to other inherited diseases.
- MeSH
- ABC transportéry genetika MeSH
- genomika MeSH
- introny MeSH
- lidé MeSH
- makulární degenerace * genetika MeSH
- mutace MeSH
- rodokmen MeSH
- Stargardtova nemoc MeSH
- transkriptom * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
