Analysis of metagenomes in extreme environments

Samo je malen broj bakterija prisutnih u biosferi moguće uzgojiti u laboratorijskim uvjetima, i stoga sve veća količina znanja o raznolikosti genoma prokariota dolaze iz direktne analize DNA iz okoliša pomoću visokoprotočnih metoda skupnog naziva Metagenomika. Metagenomom se naziva skup svih gena nekog mikrobnog okoliša. Poznato je da prokariotski genomi pokazuju značajnu nejednakost u korištenju sinonimnih kodona (CUB) (prema eng. codon usage bias). CUB je izravno povezan s razinom ekspresije gena stoga što su kodoni koje koriste visokoeksprimirani geni komplementarni s najrasprostranjenijim tRNA u organizmu. Dakle, CUB gena se može povezati s razinom ekspresije gena kroz translacijsku optimizaciju. Analizom različitih metagenomskih uzoraka pokazali smo da je moguće primijetiti nejednako iskorištenje kodona unutar pojedinog mikrobnog okoliša, kao i da je takvo svojstvo moguće iskoristiti za predviđanje razine ekspresije gena na razini cjelokupnog mikrobnog ekosustava. Primjena ovog pristupa omogućuje istraživanje genske adaptacije mikrobnih organizama na okoliš.Not all prokaryotes are amenable to cultivation in laboratory conditions, and increasing amounts of knowledge about microbial diversity is gained from direct sampling of DNA from environments. A rapidly developing field that studies whole microbial communities is metagenomics, the culture‐independent genomic study of organisms extracted directly from an ecological niche. Prokaryotic genomes show strong codon usage bias (CUB). CUB is directly correlated with expression levels of genes because codons used by genes expressed at high levels are encoded for by the most abundant tRNAs. Therefore, the CUB of a gene can be linked to its expression level through translational optimization. We show that metagenomes, much like genomes, also show CUB and that this phenomenon can be used to predict the expression level of genes at the level of the entire microbial community. We analyzed adaptation of organisms in metagenomes to their extreme environments through this approach

Analysis of metagenomes in extreme environments

Samo je malen broj bakterija prisutnih u biosferi moguće uzgojiti u laboratorijskim uvjetima, i stoga sve veća količina znanja o raznolikosti genoma prokariota dolaze iz direktne analize DNA iz okoliša pomoću visokoprotočnih metoda skupnog naziva Metagenomika. Metagenomom se naziva skup svih gena nekog mikrobnog okoliša. Poznato je da prokariotski genomi pokazuju značajnu nejednakost u korištenju sinonimnih kodona (CUB) (prema eng. codon usage bias). CUB je izravno povezan s razinom ekspresije gena stoga što su kodoni koje koriste visokoeksprimirani geni komplementarni s najrasprostranjenijim tRNA u organizmu. Dakle, CUB gena se može povezati s razinom ekspresije gena kroz translacijsku optimizaciju. Analizom različitih metagenomskih uzoraka pokazali smo da je moguće primijetiti nejednako iskorištenje kodona unutar pojedinog mikrobnog okoliša, kao i da je takvo svojstvo moguće iskoristiti za predviđanje razine ekspresije gena na razini cjelokupnog mikrobnog ekosustava. Primjena ovog pristupa omogućuje istraživanje genske adaptacije mikrobnih organizama na okoliš.Not all prokaryotes are amenable to cultivation in laboratory conditions, and increasing amounts of knowledge about microbial diversity is gained from direct sampling of DNA from environments. A rapidly developing field that studies whole microbial communities is metagenomics, the culture‐independent genomic study of organisms extracted directly from an ecological niche. Prokaryotic genomes show strong codon usage bias (CUB). CUB is directly correlated with expression levels of genes because codons used by genes expressed at high levels are encoded for by the most abundant tRNAs. Therefore, the CUB of a gene can be linked to its expression level through translational optimization. We show that metagenomes, much like genomes, also show CUB and that this phenomenon can be used to predict the expression level of genes at the level of the entire microbial community. We analyzed adaptation of organisms in metagenomes to their extreme environments through this approach

Analysis of metagenomes in extreme environments

Samo je malen broj bakterija prisutnih u biosferi moguće uzgojiti u laboratorijskim uvjetima, i stoga sve veća količina znanja o raznolikosti genoma prokariota dolaze iz direktne analize DNA iz okoliša pomoću visokoprotočnih metoda skupnog naziva Metagenomika. Metagenomom se naziva skup svih gena nekog mikrobnog okoliša. Poznato je da prokariotski genomi pokazuju značajnu nejednakost u korištenju sinonimnih kodona (CUB) (prema eng. codon usage bias). CUB je izravno povezan s razinom ekspresije gena stoga što su kodoni koje koriste visokoeksprimirani geni komplementarni s najrasprostranjenijim tRNA u organizmu. Dakle, CUB gena se može povezati s razinom ekspresije gena kroz translacijsku optimizaciju. Analizom različitih metagenomskih uzoraka pokazali smo da je moguće primijetiti nejednako iskorištenje kodona unutar pojedinog mikrobnog okoliša, kao i da je takvo svojstvo moguće iskoristiti za predviđanje razine ekspresije gena na razini cjelokupnog mikrobnog ekosustava. Primjena ovog pristupa omogućuje istraživanje genske adaptacije mikrobnih organizama na okoliš.Not all prokaryotes are amenable to cultivation in laboratory conditions, and increasing amounts of knowledge about microbial diversity is gained from direct sampling of DNA from environments. A rapidly developing field that studies whole microbial communities is metagenomics, the culture‐independent genomic study of organisms extracted directly from an ecological niche. Prokaryotic genomes show strong codon usage bias (CUB). CUB is directly correlated with expression levels of genes because codons used by genes expressed at high levels are encoded for by the most abundant tRNAs. Therefore, the CUB of a gene can be linked to its expression level through translational optimization. We show that metagenomes, much like genomes, also show CUB and that this phenomenon can be used to predict the expression level of genes at the level of the entire microbial community. We analyzed adaptation of organisms in metagenomes to their extreme environments through this approach

Structural and Functional Characterization of Ribosomal Protein Gene Introns in Sponges

Ribosomal protein genes (RPGs) are a powerful tool for studying intron evolution. They exist in all three domains of life and are much conserved. Accumulating genomic data suggest that RPG introns in many organisms abound with non-protein-coding-RNAs (ncRNAs). These ancient ncRNAs are small nucleolar RNAs (snoRNAs) essential for ribosome assembly. They are also mobile genetic elements and therefore probably important in diversification and enrichment of transcriptomes through various mechanisms such as intron/exon gain/loss. snoRNAs in basal metazoans are poorly characterized. We examined 449 RPG introns, in total, from four demosponges: Amphimedon queenslandica, Suberites domuncula, Suberites ficus and Suberites pagurorum and showed that RPG introns from A. queenslandica share position conservancy and some structural similarity with “higher” metazoans. Moreover, our study indicates that mobile element insertions play an important role in the evolution of their size. In four sponges 51 snoRNAs were identified. The analysis showed discrepancies between the snoRNA pools of orthologous RPG introns between S. domuncula and A. queenslandica. Furthermore, these two sponges show as much conservancy of RPG intron positions between each other as between themselves and human. Sponges from the Suberites genus show consistency in RPG intron position conservation. However, significant differences in some of the orthologous RPG introns of closely related sponges were observed. This indicates that RPG introns are dynamic even on these shorter evolutionary time scales

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

Funder: European Molecular Biology Laboratory; doi: http://dx.doi.org/10.13039/100013060Abstract: Background: CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. Results: We carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. Conclusions: Dynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

Funder: European Molecular Biology Laboratory; doi: http://dx.doi.org/10.13039/100013060Abstract: Background: CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. Results: We carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. Conclusions: Dynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.

Funder: Helmholtz SocietyFunder: European Molecular Biology Laboratory; doi: http://dx.doi.org/10.13039/100013060BACKGROUND: To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals. RESULTS: The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching between promoters and enhancers were more common across species, and less common across tissues within a single species. Long Interspersed Nuclear Elements (LINEs) played recurrent evolutionary roles: LINE L1s were associated with tissue-specific regulatory regions, whereas more ancient LINE L2s were associated with tissue-shared regulatory regions and with those switching between promoter and enhancer signatures across species. CONCLUSIONS: Our analyses of the tissue-specificity and evolutionary stability among promoters and enhancers reveal how specific LINE families have helped shape the dynamic mammalian regulome

Environmental shaping of codon usage and functional adaptation across microbial communities.

Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology