Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes

Comparison of expression levels and breadth and evolutionary rates of intronless and intron-containing mammalian genes shows that intronless genes are expressed at lower levels, tend to be tissue specific, and evolve significantly faster than spliced genes. By contrast, monomorphic spliced genes that are not subject to detectable alternative splicing and polymorphic alternatively spliced genes show similar statistically indistinguishable patterns of expression and evolution. Alternative splicing is most common in ancient genes, whereas intronless genes appear to have relatively recent origins. These results imply tight coupling between different stages of gene expression, in particular, transcription, splicing, and nucleocytosolic transport of transcripts, and suggest that formation of intronless genes is an important route of evolution of novel tissue-specific functions in animals

Connections between Alternative Transcription and Alternative Splicing in Mammals

The majority of mammalian genes produce multiple transcripts resulting from alternative splicing (AS) and/or alternative transcription initiation (ATI) and alternative transcription termination (ATT). Comparative analysis of the number of alternative nucleotides, isoforms, and introns per locus in genes with different types of alternative events suggests that ATI and ATT contribute to the diversity of human and mouse transcriptome even more than AS. There is a strong negative correlation between AS and ATI in 5′ untranslated regions (UTRs) and AS in coding sequences (CDSs) but an even stronger positive correlation between AS in CDSs and ATT in 3′ UTRs. These observations could reflect preferential regulation of distinct, large groups of genes by different mechanisms: 1) regulation at the level of transcription initiation and initiation of translation resulting from ATI and AS in 5′ UTRs and 2) posttranslational regulation by different protein isoforms. The tight linkage between AS in CDSs and ATT in 3′ UTRs suggests that variability of 3′ UTRs mediates differential translational regulation of alternative protein forms. Together, the results imply coordinate evolution of AS and alternative transcription, processes that occur concomitantly within gene expression factories

Expansion of the human μ-opioid receptor gene architecture: novel functional variants

The μ-opioid receptor (OPRM1) is the principal receptor target for both endogenous and exogenous opioid analgesics. There are substantial individual differences in human responses to painful stimuli and to opiate drugs that are attributed to genetic variations in OPRM1. In searching for new functional variants, we employed comparative genome analysis and obtained evidence for the existence of an expanded human OPRM1 gene locus with new promoters, alternative exons and regulatory elements. Examination of polymorphisms within the human OPRM1 gene locus identified strong association between single nucleotide polymorphism (SNP) rs563649 and individual variations in pain perception. SNP rs563649 is located within a structurally conserved internal ribosome entry site (IRES) in the 5′-UTR of a novel exon 13-containing OPRM1 isoforms (MOR-1K) and affects both mRNA levels and translation efficiency of these variants. Furthermore, rs563649 exhibits very strong linkage disequilibrium throughout the entire OPRM1 gene locus and thus affects the functional contribution of the corresponding haplotype that includes other functional OPRM1 SNPs. Our results provide evidence for an essential role for MOR-1K isoforms in nociceptive signaling and suggest that genetic variations in alternative OPRM1 isoforms may contribute to individual differences in opiate responses

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

Catechol-O-methyltransferase (COMT) is a major enzyme controlling catecholamine levels that plays a central role in cognition, affective mood and pain perception. There are three common COMT haplotypes in the human population reported to have functional effects, divergent in two synonymous and one nonsynonymous position. We demonstrate that one of the haplotypes, carrying the non-synonymous variation known to code for a less stable protein, exhibits increased protein expression in vitro. This increased protein expression, which would compensate for lower protein stability, is solely produced by a synonymous variation (C166T) situated within the haplotype and located in the 5′ region of the RNA transcript. Based on mRNA secondary structure predictions, we suggest that structural destabilization near the start codon caused by the T allele could be related to the observed increase in COMT expression. Our folding simulations of the tertiary mRNA structures demonstrate that destabilization by the T allele lowers the folding transition barrier, thus decreasing the probability of occupying its native state. These data suggest a novel structural mechanism whereby functional synonymous variations near the translation initiation codon affect the translation efficiency via entropy-driven changes in mRNA dynamics and present another example of stable compensatory genetic variations in the human population

Expression Patterns of Protein Kinases Correlate with Gene Architecture and Evolutionary Rates

Protein kinase (PK) genes comprise the third largest superfamily that occupy ∼2% of the human genome. They encode regulatory enzymes that control a vast variety of cellular processes through phosphorylation of their protein substrates. Expression of PK genes is subject to complex transcriptional regulation which is not fully understood.Our comparative analysis demonstrates that genomic organization of regulatory PK genes differs from organization of other protein coding genes. PK genes occupy larger genomic loci, have longer introns, spacer regions, and encode larger proteins. The primary transcript length of PK genes, similar to other protein coding genes, inversely correlates with gene expression level and expression breadth, which is likely due to the necessity to reduce metabolic costs of transcription for abundant messages. On average, PK genes evolve slower than other protein coding genes. Breadth of PK expression negatively correlates with rate of non-synonymous substitutions in protein coding regions. This rate is lower for high expression and ubiquitous PKs, relative to low expression PKs, and correlates with divergence in untranslated regions. Conversely, rate of silent mutations is uniform in different PK groups, indicating that differing rates of non-synonymous substitutions reflect variations in selective pressure. Brain and testis employ a considerable number of tissue-specific PKs, indicating high complexity of phosphorylation-dependent regulatory network in these organs. There are considerable differences in genomic organization between PKs up-regulated in the testis and brain. PK genes up-regulated in the highly proliferative testicular tissue are fast evolving and small, with short introns and transcribed regions. In contrast, genes up-regulated in the minimally proliferative nervous tissue carry long introns, extended transcribed regions, and evolve slowly.PK genomic architecture, the size of gene functional domains and evolutionary rates correlate with the pattern of gene expression. Structure and evolutionary divergence of tissue-specific PK genes is related to the proliferative activity of the tissue where these genes are predominantly expressed. Our data provide evidence that physiological requirements for transcription intensity, ubiquitous expression, and tissue-specific regulation shape gene structure and affect rates of evolution

Effect of Multiwalled Carbon Nanotubes on the Kinetics of the Aniline Polymerization: The Semi-Quantitative OCP Approach

We demonstrate applicability of the open-circuit potential (OCP) method for kinetic analysis of the oxidative chemical polymerization of aniline both in clear solution and in dispersions of multiwalled carbon nanotubes (MWCNT). The characteristic points and the shape of the OCP profile are used to estimate the kinetic parameters of the main stages of the known two-step polymerization mechanism of aniline. We have found that the reciprocal values of the duration of the main polymerization stages namely the induction period, pernigraniline (PN) accumulation and reduction of PN with residual aniline are the linear functions of the weight fraction of MWCNT. To compare the kinetic data of the proposed OCP and known approaches the last two stages have been considered as a single heterogeneous stage of emeraldine (EM) formation. The <i>k</i>_<i>EM</i> rate constant calculated by the OCP profiles for this EM stage in the solution and dispersion media is in a very good agreement with the known <i>k</i>₂ values

PVDF/poly(3-methylthiophene)/MWCNT nanocomposites for EMI shielding in the microwave range

This work presents a new approach to enhance EMI shielding efficiency of nanocomposites of dielectric polymers, multiwalled carbon nanotubes (MWCNTs) and intrinsically conducting polymers for account of using core-shell morphology for conducting components. To realize this approach new ternary nanocomposites of poly(vinylidene fluoride) (PVDF), MWCNTs and poly(3-methylthiophene) doped by Cl− anions (P3MT) were prepared through synthesis of thermally stable core/shell nanocomposites PVDF/P3MT and MWCNT/P3MT. These binary nanocomposites were mixed with pure MWCNTs or PVDF followed by compression molding to prepare the ternary nanocomposites of different morphology to discriminate their EMI shielding properties in a wide frequency range (1–67 GHz). Values of the tangent of dielectric loss angle, the efficiency of transmission, reflection and absorption of microwave radiation, and shielding efficiency (SE) of the specified materials were found from analysis of spectral dependences of their complex dielectric constants. It was shown that while the melt mixing of the binary PVDF/P3MT nanocomposite with MWCNTs both in a pure state and in the binary nanocomposite (MWCNT/P3MT) expectedly strongly enhances SE of the former, this effect is non-linear and depends on presence/absence of the P3MT shell on the MWCNT core. The ternary nanocomposite PVDF/P3MT/MWCNT made of the binary polymer-polymer nanocomposite PVDF/P3MT and pure MWCNTs showed highest SE values at the frequencies above 4.5 GHz up to 68.4 dB at 67 GHz in the case of the 1 mm thickness sample. However, below 4.5 GHz the SE was higher in the case of the ternary nanocomposites containing core/shell MWCNT/P3MT nanocomposite instead of pure MWCNT