genome complexity
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Nedávné zveřejnění předběžné sekvence lidského genomu a její první analýzy přinesly několik překvapivých zjištění. Lidský genom obsahuje pouze kolem 42 000 genů a nikoliv 100 000, jak se dlouho předpokládalo. Srovnání s dalšími sekvenovanými genomy naznačuje, že komplexity organizmu nemusí být dosahováno zvyšováním počtu genů, ale že může být založena na regulačních mechanizmech spojených s alternativní expresí genů a na složitých interakcích genů a/nebo jejich proteinových produktů. Pokroky genomiky a příbuzných moderních oborů začínají podstatně měnit biomedicínský výzkum a samotnou medicínu, kde se zájem přesouvá zejména k multifaktoriálním chorobám. Nové poznatky postupně povedou k mnohem efektivnější diagnostice, přesné prognóze průběhu chorob a prognóze odpovědi jedince na léky, cílené terapii s využitím nových farmak i terapie genové a především k cílené prevenci založené na detailní znalosti individuální predispozice k chorobám.
Recent publication of the working draft of the human genome and its first analyses revealed several surprising findings. The human genome contains only about 42 000 genes, contrary to previous estimates of about 100 000. Comparison with other genomes suggests that the complexity of an organism neednot result from increasing gene number, but it can be based on regulatory mechanisms associated with alternative gene expression and on complex interactions of genes and/or their protein products. The progress in genomics and related modern disciplines is influencing substantially the biomedical research and the medicine itself, where the main focus shifts towards multifactorial diseases. The new knowledge will lead to much more effective diagnosis, exact prognosis of the disease course and of individual drug response, to the targeted therapy using new drugs and gene therapy, and mainly towards targeted prevention based on the detailed knowledge of individual disease predisposition.
- MeSH
- genomová knihovna MeSH
- projekt Lidský genom MeSH
- rekombinantní DNA MeSH
- Publikační typ
- přehledy MeSH
Kinetoplastids are flagellated protozoans, whose members include the pathogens Trypanosoma brucei, T. cruzi and Leishmania species, that are considered among the earliest diverging eukaryotes with a mitochondrion. This organelle has become famous because of its many unusual properties, which are unique to the order Kinetoplastida, including an extensive kinetoplast DNA network and U-insertion/deletion type RNA editing of its mitochondrial transcripts. In the last decade, considerable progress has been made in elucidating the complex machinery of RNA editing. Moreover, our understanding of the structure and replication of kinetoplast DNA has also dramatically improved. Much less however, is known, about the developmental regulation of RNA editing, its integration with other RNA maturation processes, stability of mitochondrial mRNAs, or evolution of the editing process itself. Yet the profusion of genomic data recently made available by sequencing consortia, in combination with methods of reverse genetics, hold promise in understanding the complexity of this exciting organelle, knowledge of which may enable us to fight these often medically important protozoans.
- MeSH
- editace RNA MeSH
- exprese genu MeSH
- financování organizované MeSH
- genetická transkripce MeSH
- genom protozoální MeSH
- Kinetoplastida genetika MeSH
- kinetoplastová DNA chemie MeSH
- messenger RNA metabolismus MeSH
- mitochondriální geny MeSH
- mitochondrie genetika MeSH
- RNA protozoální metabolismus MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- přehledy MeSH
xxii, 1135 s., [32] s. obr. příl. : il., tab., grafy ; 30 cm
The identification of causal genomic loci and their interactions underlying various traits in plants has been greatly aided by progress in understanding the organization of the nuclear genome. This provides clues to the responses of plants to environmental stimuli at the molecular level. Apart from other uses, these insights are needed to fully explore the potential of new breeding techniques that rely on genome editing. However, genome analysis and sequencing is not straightforward in the many agricultural crops and their wild relatives that possess large and complex genomes. Chromosome genomics streamlines this task by dissecting the genome to single chromosomes whose DNA is then used instead of nuclear DNA. This results in a massive and lossless reduction in DNA sample complexity, reduces the time and cost of the experiment, and simplifies data interpretation. Flow cytometric sorting of condensed mitotic chromosomes makes it possible to purify single chromosomes in large quantities, and as the DNA remains intact this process can be coupled successfully with many techniques in molecular biology and genomics. Since the first experiments with flow cytometric sorting in the late 1980s, numerous applications have been developed, and chromosome genomics has been having a significant impact in many areas of research, including the sequencing of complex genomes of important crops and gene cloning. This review discusses these applications, describes their contribution to advancements in plant genome analysis and gene cloning, and outlines future directions.
Complex karyotype (CK) identified by chromosome-banding analysis (CBA) has shown prognostic value in chronic lymphocytic leukemia (CLL). Genomic arrays offer high-resolution genome-wide detection of copy-number alterations (CNAs) and could therefore be well equipped to detect the presence of a CK. Current knowledge on genomic arrays in CLL is based on outcomes of single center studies, in which different cutoffs for CNA calling were used. To further determine the clinical utility of genomic arrays for CNA assessment in CLL diagnostics, we retrospectively analyzed 2293 arrays from 13 diagnostic laboratories according to established standards. CNAs were found outside regions captured by CLL FISH probes in 34% of patients, and several of them including gains of 8q, deletions of 9p and 18p (p<0.01) were linked to poor outcome after correction for multiple testing. Patients (n=972) could be divided in three distinct prognostic subgroups based on the number of CNAs. Only high genomic complexity (high-GC), defined as ≥5 CNAs emerged as an independent adverse prognosticator on multivariable analysis for time to first treatment (Hazard ratio: 2.15, 95% CI: 1.36-3.41; p=0.001) and overall survival (Hazard ratio: 2.54, 95% CI: 1.54-4.17; p<0.001; n=528). Lowering the size cutoff to 1 Mb in 647 patients did not significantly improve risk assessment. Genomic arrays detected more chromosomal abnormalities and performed at least as well in terms of risk stratification compared to simultaneous chromosome banding analysis as determined in 122 patients. Our findings highlight genomic array as an accurate tool for CLL risk stratification.
The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less "reduced" than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organization of endomembrane systems, and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent preadaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe-S cluster assembly and the loss of glycine cleavage system. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.
Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.
- MeSH
- chromozomy chemie genetika MeSH
- fyzikální mapování chromozomů metody MeSH
- genom lidský MeSH
- genomika metody MeSH
- genová knihovna MeSH
- karyotyp MeSH
- lidé MeSH
- malování chromozomů metody MeSH
- mitóza MeSH
- průtoková cytometrie metody MeSH
- rostliny chemie genetika MeSH
- sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů metody MeSH
- struktury chromozomu chemie genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
BACKGROUND: Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date. RESULTS: In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids. CONCLUSIONS: As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.
Fenotyp člověka je ovládán genotypem – souborem genetických informací uložených v DNA. Pokud si pomůžeme s tradiční terminologií, jde o něco přes 20 000 genů, jejichž vliv na utváření fenotypu je různě „silný“ a uplatňuje se většinou v rámci celého genomu, tedy v prostředí plném působení ostatních genů. Výsledný efekt je závislý nejen na pevně stanovených programech, které jsme zdědili od svých předků (a jejichž minulost bychom mohli sledovat do samého počátku života na zemi, který začal používat informační molekuly nukleových kyselin), ale i na vnějších vlivech, které na organismus působily od okamžiku jeho vzniku jako individua. I když se úspěšně propracováváme k porozumění, co je nám dáno do vínku v podobě zděděných genetických informací, stále máme příliš veliký zmatek v hodnocení toho, co na nás působilo během našeho života a jen málo víme, jaký měl ten který vliv význam. Proto jakákoliv predikce toho, co nás čeká a nemine, by měla být omezena na „nesporné“ situace a v každém případě – tzv. vysoce kvalifikovaná a odpovědná.
Human phenotype is governed by its genotype – a set of genetic information materialized in DNA. Using traditional terminology we speak about a little more than 20 thousands genes that differ in strength to become realized and their effect is modified by a large number of other genes. The result originates from firmly established programmes we obtained from our ancestors. Development and activity of such molecules selected for maintenance, copying and transfer of information i.e. nucleic acids can be followed back to the very origin of the life. Nevertheless the final result is achieved not only by confrontation of the original information with other genetic information but largely also by external influences – environment. Though we are relatively successful in understanding what we have inherited from our parents, our knowledge of environmental factors and their effects on formation of the phenotype is still limited. From this point of view medical prediction has always to be very cautious and interpretations at the probability level must be done by a very experienced and responsible professional. Key words: genome, genotype, phenotype, toxicogenomics, epigenetics, mutation, penetrance, pleiotropy, monogenic inheritance, multifactorial inheritance, genetic risk.
- Klíčová slova
- DNA genom, toxikogenomika, epigenetika, pleiotropie, monogenní dědičnost, genetické riziko,
- MeSH
- dědičnost MeSH
- DNA MeSH
- epigenomika MeSH
- fenotyp MeSH
- financování organizované MeSH
- genetická pleiotropie MeSH
- genetická predispozice k nemoci MeSH
- genetické testování etika metody využití MeSH
- genom MeSH
- genotyp MeSH
- interakce genů a prostředí MeSH
- lékařská genetika metody trendy MeSH
- lidé MeSH
- multifaktoriální dědičnost MeSH
- mutace MeSH
- penetrance MeSH
- toxikogenetika MeSH
- životní prostředí MeSH
- Check Tag
- lidé MeSH
