505 research outputs found
Gene expression drives the evolution of dominance.
Dominance is a fundamental concept in molecular genetics and has implications for understanding patterns of genetic variation, evolution, and complex traits. However, despite its importance, the degree of dominance in natural populations is poorly quantified. Here, we leverage multiple mating systems in natural populations of Arabidopsis to co-estimate the distribution of fitness effects and dominance coefficients of new amino acid changing mutations. We find that more deleterious mutations are more likely to be recessive than less deleterious mutations. Further, this pattern holds across gene categories, but varies with the connectivity and expression patterns of genes. Our work argues that dominance arises as a consequence of the functional importance of genes and their optimal expression levels
Law of Genome Evolution Direction : Coding Information Quantity Grows
The problem of the directionality of genome evolution is studied. Based on
the analysis of C-value paradox and the evolution of genome size we propose
that the function-coding information quantity of a genome always grows in the
course of evolution through sequence duplication, expansion of code, and gene
transfer from outside. The function-coding information quantity of a genome
consists of two parts, p-coding information quantity which encodes functional
protein and n-coding information quantity which encodes other functional
elements except amino acid sequence. The evidences on the evolutionary law
about the function-coding information quantity are listed. The needs of
function is the motive force for the expansion of coding information quantity
and the information quantity expansion is the way to make functional innovation
and extension for a species. So, the increase of coding information quantity of
a genome is a measure of the acquired new function and it determines the
directionality of genome evolution.Comment: 16 page
Ultraviolet Survey of CO and H_2 in Diffuse Molecular Clouds: The Reflection of Two Photochemistry Regimes in Abundance Relationships
(Abridged) We carried out a comprehensive far-ultraviolet (UV) survey of
^12CO and H_2 column densities along diffuse molecular Galactic sight lines in
order to explore in detail the relationship between CO and H_2. We measured new
CO abundances from HST spectra, new H_2 abundances from FUSE data, and new CH,
CH^+, and CN abundances from the McDonald and European Southern Observatories.
A plot of log N(CO) versus log N(H_2) shows that two power-law relationships
are needed for a good fit of the entire sample, with a break located at log
N(CO, cm^-2) = 14.1 and log N(H_2) = 20.4, corresponding to a change in
production route for CO in higher-density gas. Similar logarithmic plots among
all five diatomic molecules allow us to probe their relationships, revealing
additional examples of dual slopes in the cases of CO versus CH (break at log N
= 14.1, 13.0), CH^+ versus H_2 (13.1, 20.3), and CH^+ versus CO (13.2, 14.1).
These breaks are all in excellent agreement with each other, confirming the
break in the CO versus H_2 relationship, as well as the one-to-one
correspondence between CH and H_2 abundances. Our new sight lines were selected
according to detectable amounts of CO in their spectra and they provide
information on both lower-density (< 100 cm^-3) and higher-density diffuse
clouds. The CO versus H_2 correlation and its intrinsic width are shown to be
empirically related to the changing total gas density among the sight lines of
the sample. We employ both analytical and numerical chemical schemes in order
to derive details of the molecular environments. In the low-density gas, where
equilibrium-chemistry studies have failed to reproduce the abundance of CH^+,
our numerical analysis shows that nonequilibrium chemistry must be employed for
correctly predicting the abundances of both CH^+ and CO.Comment: 40 pages in emulateapj style, to appear in the Astrophysical Journa
Primate TNF Promoters Reveal Markers of Phylogeny and Evolution of Innate Immunity
Background. Tumor necrosis factor (TNF) is a critical cytokine in the immune response whose transcriptional activation is controlled by a proximal promoter region that is highly conserved in mammals and, in particular, primates. Specific single nucleotide polymorphisms (SNPs) upstream of the proximal human TNF promoter have been identified, which are markers of human ancestry.
Methodology/Principal findings. Using a comparative genomics approach we show that certain fixed genetic differences in the TNF promoter serve as markers of primate speciation. We also demonstrate that distinct alleles of most human TNF promoter SNPs are identical to fixed nucleotides in primate TNF promoters. Furthermore, we identify fixed genetic differences within the proximal TNF promoters of Asian apes that do not occur in African ape or human TNF promoters. Strikingly, protein-DNA binding assays and gene reporter assays comparing these Asian ape TNF promoters to African ape and human TNF promoters demonstrate that, unlike the fixed differences that we define that are associated with primate phylogeny, these Asian ape-specific fixed differences impair transcription factor binding at an Sp1 site and decrease TNF transcription induced by bacterial stimulation of macrophages.
Conclusions/significance. Here, we have presented the broadest interspecies comparison of a regulatory region of an innate immune response gene to date. We have characterized nucleotide positions in Asian ape TNF promoters that underlie functional changes in cell type- and stimulus-specific activation of the TNF gene. We have also identified ancestral TNF promoter nucleotide states in the primate lineage that correspond to human SNP alleles. These findings may reflect evolution of Asian and African apes under a distinct set of infectious disease pressures involving the innate immune response and TNF
A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues
The modification of DNA by methylation is an important epigenetic mechanism that affects the spatial and temporal regulation of gene expression. Methylation patterns have been described in many contexts within and across a range of species. However, the extent to which changes in methylation might underlie inter-species differences in gene regulation, in particular between humans and other primates, has not yet been studied. To this end, we studied DNA methylation patterns in livers, hearts, and kidneys from multiple humans and chimpanzees, using tissue samples for which genome-wide gene expression data were also available. Using the multi-species gene expression and methylation data for 7,723 genes, we were able to study the role of promoter DNA methylation in the evolution of gene regulation across tissues and species. We found that inter-tissue methylation patterns are often conserved between humans and chimpanzees. However, we also found a large number of gene expression differences between species that might be explained, at least in part, by corresponding differences in methylation levels. In particular, we estimate that, in the tissues we studied, inter-species differences in promoter methylation might underlie as much as 12%–18% of differences in gene expression levels between humans and chimpanzees
Quantum dash mode-locked lasers for millimeter wave signal generation and transmission
In this paper we present the remarkable characteristics of quantum dash mode-locked lasers and how they could be used for low phase noise signal generation, for high data rate wireless transmission and radar in the millimeter wave frequency range
Characterization and Comparison of the Tissue-Related Modules in Human and Mouse
BACKGROUND: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches. RESULTS: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity," a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse. CONCLUSIONS: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions
Human and Non-Human Primate Genomes Share Hotspots of Positive Selection
Among primates, genome-wide analysis of recent positive selection is currently
limited to the human species because it requires extensive sampling of genotypic
data from many individuals. The extent to which genes positively selected in
human also present adaptive changes in other primates therefore remains unknown.
This question is important because a gene that has been positively selected
independently in the human and in other primate lineages may be less likely to
be involved in human specific phenotypic changes such as dietary habits or
cognitive abilities. To answer this question, we analysed heterozygous Single
Nucleotide Polymorphisms (SNPs) in the genomes of single human, chimpanzee,
orangutan, and macaque individuals using a new method aiming to identify
selective sweeps genome-wide. We found an unexpectedly high number of
orthologous genes exhibiting signatures of a selective sweep simultaneously in
several primate species, suggesting the presence of hotspots of positive
selection. A similar significant excess is evident when comparing genes
positively selected during recent human evolution with genes subjected to
positive selection in their coding sequence in other primate lineages and
identified using a different test. These findings are further supported by
comparing several published human genome scans for positive selection with our
findings in non-human primate genomes. We thus provide extensive evidence that
the co-occurrence of positive selection in humans and in other primates at the
same genetic loci can be measured with only four species, an indication that it
may be a widespread phenomenon. The identification of positive selection in
humans alongside other primates is a powerful tool to outline those genes that
were selected uniquely during recent human evolution
Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq
Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq) to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20–28% of non-ribosomal transcripts correspond to annotated exons and 20–23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40–48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20%) represents 3′UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits
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