Structure of regulatory networks and diversity of gene expression patterns

Complexity of gene regulatory network has been considered to be responsible for diversity of cells. Different types of cells, characterized by the expression patterns of genes, are produced in early development through the dynamics of gene activities based on the regulatory network. However, very little is known about relationship between the structure of regulatory networks and the dynamics of gene activities. In this paper, I introduce new idea of “steady-state compatibility” by which the diversity of possible gene activities can be determined from the topological structure of gene regulatory networks. The basic premise is very simple: the activity of a gene should be a function of the controlling genes. Thus, a gene should always show unique expression activity if the activities of the controlling genes are unique. Based on this, the maximum possible diversity of steady states is determined using only information regarding regulatory linkages without knowing the regulatory functions of genes. By extending this idea, some general properties were derived. For example, multiple loop structures in regulatory networks are necessary for increasing the diversity of gene activity. On the other hand, connected multiple loops sharing the same genes do not increase the diversity. The method was applied to a gene regulatory network responsible for early development in a sea urchin species. A set of important genes responsible for generating diversities of gene activities was derived based on the concept of compatibility of steady states.     

Periodic oscillation in delayed gene networks with SUM regulatory logic and small perturbations

In this paper, we derive new criteria for evaluating the global stability of periodic oscillation in delayed gene networks with SUM regulatory logic and small perturbation, which appear in many biological systems at biomolecular or cellular levels due to the weak coupling and signal diffusion (or transport) process. Our results rely on the Lipschtiz conditions of Hill function, topology of gene networks and delay kernels. In particular, Our method based on the proposed model transforms the original network into matrix analysis problem, thereby not only significantly reducing the computational complexity but also making analysis of periodic oscillation tractable for even large-scale nonlinear networks.     

Insights into the dynamics of hind leg development in honey bee (Apis mellifera L.) queen and worker larvae - A morphology/differential gene expression analysis

Phenotypic plasticity is a hallmark of the caste systems of social insects, expressed in their life history and morphological traits. These are best studied in bees. In their co-evolution with angiosperm plants, the females of corbiculate bees have acquired a specialized structure on their hind legs for collecting pollen. In the highly eusocial bees (Apini and Meliponini), this structure is however only present in workers and absent in queens. By means of histological sections and cell proliferation analysis we followed the developmental dynamics of the hind legs of queens and workers in the fourth and fifth larval instars. In parallel, we generated subtractive cDNA libraries for hind leg discs of queen and worker larvae by means of a Representational Difference Analysis (RDA). From the total of 135 unique sequences we selected 19 for RT-qPCR analysis, where six of these were confirmed as differing significantly in their expression between the two castes in the larval spinning stage. The development of complex structures such as the bees’ hind legs, requires diverse patterning mechanisms and signaling modules, as indicated by the set of differentially expressed genes related with cell adhesion and signaling pathways.     

PCBP1在基因表达过程中的功能和作用机理

Poly（C）-binding protein 1 （PCBP 1）是一种RNA结合蛋白,其蛋白质相对分子质量约为38000。PCBP1含三个KH（hnRNP K homology）结构域,这些结构域对其结合RNA有重要作用。PCBP1的功能主要是参与基因转录及转录后调节,如前体mRNA的剪切、mRNA稳定性、mRNA翻译过程的沉默或增强等。本文主要对PCBP1参与的信号通路以及与人类疾病的关系进行综述,试图阐明PCBP1的生物学功能和作用机理。     

Molecular mapping of a rice gene conditioning thermosensitive genic male sterility using AFLP, RFLP and SSR techniques

The discovery and application of the thermosensitive genic male sterility (TGMS) system has great potential for revolutionizing hybrid seed production technology in rice. Use of the TGMS system in two-line breeding is simple, inexpensive, efficient, and eliminates the limitations associated with the cytoplasmic-genetic male sterility (CMS) system. An F₂ population developed from a cross between a TGMS indica mutant, TGMS–VN1, and a fertile indica line, CH1, was used to identify molecular markers linked to the TGMS gene and to subsequently determine its chromosomal location on the linkage map of rice. Bulk segregant analysis was performed using the AFLP technique. From the survey of 200 AFLP primer combinations, four AFLP markers (E2/M5–600, E3/M16–400, E5/M12–600, and E5/M12–200) linked to the TGMS gene were identified. All the markers were linked to the gene in the coupling phase. All except E2/M5–200 were found to be low-copy sequences. However, the marker E5/M12–600 showed polymorphism in RFLP analysis and was closely linked to the TGMS gene at a distance of 3.3 cM. This marker was subsequently mapped on chromosome 2 using doubled-haploid mapping populations derived from the crosses IR64×Azucena and CT9993×IR62666, available at IRRI, Philippines, and Texas Tech University, respectively. Linkage of microsatellite marker RM27 with the TGMS gene further confirmed its location on chromosome 2. The closest marker, E5/M12–600, was sequenced so that a PCR marker can be developed for the marker-assisted transfer of this gene to different genetic backgrounds. The new TGMS gene is tentatively designated as tms4(t). Received: 13 July 1999 / Accepted: 27 July 1999     

TPH2 5′‐ and 3′‐regulatory polymorphisms are differentially associated with HPA axis function and self‐injurious behavior in rhesus monkeys

Tryptophan hydroxylase‐2 (TPH2) synthesizes neuronal serotonin and is linked to numerous behavioral traits. We have previously characterized the functionality of polymorphisms (especially 2051A>C) in 3’‐untranslated region (3’‐UTR) of rhesus monkey TPH2 (rhTPH2). This study further assessed the functionality of additional polymorphisms (–1605T>C, –1491Tn, –1485(AT)n, –1454A>G, –1325In>Del and –363T>G) in rhTPH2 5’‐flanking region (5’‐FR), and evaluated the effects of rhTPH2 5’ and 3’ genotypes on central serotonin turnover, hypothalamic–pituitary–adrenal (HPA) axis function and self‐injurious behavior (SIB) in 32 unrelated adult male monkeys of Indian origin. Haplotypes of the rhTPH2 5’‐FR polymorphisms exert a significant, cell‐dependent effect on reporter gene expression, primarily conferred by –1485(AT)n. The –1485(AT)n and 2051A>C polymorphisms interact to influence cerebrospinal fluid (CSF) 5‐HIAA and plasma adrenocorticotropic hormone (ACTH) in the afternoon. While –1485(AT)n exerts significant main effects on the afternoon cortisol level and nocturnal HPA negative feedback, 2051A>C has significant main effects on the morning cortisol level and cortisol response to ACTH challenge, as well as marginally significant main effects on the daytime HPA negative feedback and self‐biting rate. In addition, the genotype/allele frequency of the 5’‐FR –1325Ins>Del differed significantly between the self‐wounders and non‐wounders, whereas 3’‐UTR 2128S>L polymorphism differed significantly in genotype/allele frequency between the high‐ and low‐frequency biters. This study shows the functionality of rhTPH2 5’‐FR polymorphisms, and provides evidence for the differential association of rhTPH2 5’‐FR and 3’‐UTR polymorphisms with HPA axis function and SIB. Our findings shed light on the role of TPH2 gene variance in physiology and behavioral traits, and also contribute to the understanding of the pathophysiology and genetics of SIB     

Adaptive evolution of a key gene affecting queen and worker traits in the honey bee, Apis mellifera

The vitellogenin egg yolk precursor protein represents a well-studied case of social pleiotropy in the model organism Apis mellifera. Vitellogenin is associated with fecundity in queens and plays a major role in controlling division of labour in workers, thereby affecting both individual and colony-level fitness. We studied the molecular evolution of vitellogenin and seven other genes sequenced in a large population panel of Apis mellifera and several closely related species to investigate the role of social pleiotropy on adaptive protein evolution. We found a significant excess of nonsynonymous fixed differences between A. mellifera, A. cerana and A. florea relative to synonymous sites indicating high rates of adaptive evolution at vitellogenin. Indeed, 88% of amino acid changes were fixed by selection in some portions of the gene. Further, vitellogenin exhibited hallmark signatures of selective sweeps in A. mellifera, including a significant skew in the allele frequency spectrum, extreme levels of genetic differentiation and linkage disequilibrium. Finally, replacement polymorphisms in vitellogenin were significantly enriched in parts of the protein involved in binding lipid, establishing a link between the gene's structure, function and effects on fitness. Our case study provides unequivocal evidence of historical and ongoing bouts of adaptive evolution acting on a key socially pleiotropic gene in the honey bee.     

The influence of male age on within‐pair and extra‐pair paternity in passerines

Although male age has often been found to predict success in gaining extra‐pair paternity, it is unclear whether this gain is associated with an individual’s success in avoiding cuckoldry. We examined the relationship between male age and both within‐ and extra‐pair paternity in passerines using a meta‐analytical approach. There was a positive correlation between male age and success in extra‐pair paternity but little evidence for an association between male age and within‐pair paternity. In addition, effect sizes for male within‐pair paternity and male extra‐pair paternity were not significantly correlated. Thus, factors that predict success in obtaining extra‐pair paternity, such as male age, may not necessarily predict success in avoiding cuckoldry.     

Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients

Fragile X‐associated Tremor/Ataxia Syndrome (FXTAS) is a neurodegenerative disorder caused by expansion of 55–200 CGG repeats in the 5′‐UTR of the FMR1 gene. FXTAS is characterized by action tremor, gait ataxia and impaired executive cognitive functioning. It has been proposed that FXTAS is caused by titration of RNA‐binding proteins by the expanded CGG repeats. Sam68 is an RNA‐binding protein involved in alternative splicing regulation and its ablation in mouse leads to motor coordination defects. Here, we report that mRNAs containing expanded CGG repeats form large and dynamic intranuclear RNA aggregates that recruit several RNA‐binding proteins sequentially, first Sam68, then hnRNP‐G and MBNL1. Importantly, Sam68 is sequestered by expanded CGG repeats and thereby loses its splicing‐regulatory function. Consequently, Sam68‐responsive splicing is altered in FXTAS patients. Finally, we found that regulation of Sam68 tyrosine phosphorylation modulates its localization within CGG aggregates and that tautomycin prevents both Sam68 and CGG RNA aggregate formation. Overall, these data support an RNA gain‐of‐function mechanism for FXTAS neuropathology, and suggest possible target routes for treatment options.     

Identification and development of long non‐coding RNA‐associated regulatory network in colorectal cancer

Colorectal cancer (CRC) is one of the leading causes of cancer‐associated death globally. Long non‐coding RNAs (lncRNAs) have been identified as micro RNA (miRNA) sponges in a competing endogenous RNA (ceRNA) network and are involved in the regulation of mRNA expression. This study aims to construct a lncRNA‐associated ceRNA network and investigate the prognostic biomarkers in CRC. A total of 38 differentially expressed (DE) lncRNAs, 23 DEmiRNAs and 27 DEmRNAs were identified by analysing the expression profiles of CRC obtained from The Cancer Genome Atlas (TCGA). These RNAs were chosen to develop a ceRNA regulatory network of CRC, which comprised 125 edges. Survival analysis showed that four lncRNAs, six miRNAs and five mRNAs were significantly associated with overall survival. A potential regulatory axis of ADAMTS9‐AS2/miR‐32/PHLPP2 was identified from the network. Experimental validation was performed using clinical samples by quantitative real‐time PCR (qRT‐PCR), which showed that expression of the genes in the axis was associated with clinicopathological features and the correlation among them perfectly conformed to the ‘ceRNA theory’. Overexpression of ADAMTS9‐AS2 in colon cancer cell lines significantly inhibited the miR‐32 expression and promoted PHLPP2 expression, while ADAMTS9‐AS2 knockdown had the opposite effects. The constructed novel ceRNA network may provide a comprehensive understanding of the mechanisms of CRC carcinogenesis. The ADAMTS9‐AS2/miR‐32/PHLPP2 regulatory axis may serve as a potential therapeutic target for CRC.     

Single nucleotide polymorphisms in the insulin‐like growth factor 1 (IGF1) gene are associated with growth‐related traits in farmed Atlantic salmon

Understanding the genetic basis of variation in traits related to growth and fillet quality in Atlantic salmon is of importance to the aquaculture industry. Several growth‐related QTL have been identified via the application of genetic markers. The IGF1 gene is considered a highly conserved and crucial growth‐regulating gene in salmonid species. However, the association between polymorphisms in the IGF1 gene and growth‐related traits in Atlantic salmon is unknown. Therefore, in this study, regions of the Atlantic salmon IGF1 gene were sequenced, aligned and compared across individuals. Three SNPs were identified in the putative promoter (SNP1, g.5763G>T; GenBank no. AGKD01012745 ), intron 1 (SNP2, g.7292C>T; GenBank no. AGKD01012745 ) and intron 3 (SNP3, g.4671A>C; GenBank no. AGKD01133398 ) regions respectively. These SNPs were genotyped in a population of 4800 commercial Atlantic salmon with data on several weight and fillet traits measured at harvest (at approximately 3 years of age). In a mixed model, association analysis of individual SNPs, SNP1 and SNP3 were both significantly associated with several weight traits (P < 0.05). The estimated additive effect on overall harvest weight was approximately 35 and 110 g for SNPs 1 and 3 respectively. A haplotype analysis confirmed the association between genetic variation in the IGF1 gene with overall body weight (P < 0.05) and fillet component traits (P < 0.05). Our findings suggest the identified nucleotide polymorphisms of the IGF1 gene may either affect farmed Atlantic salmon growth directly or be in population‐wide linkage disequilibrium with causal variation, highlighting their possible utility as candidates for marker‐assisted selection in the aquaculture industry.     

Routes to indirect fitness in cooperatively breeding vertebrates: kin discrimination and limited dispersal

Hamilton demonstrated that the evolution of cooperative behaviour is favoured by high relatedness, which can arise through kin discrimination or limited dispersal (population viscosity). These two processes are likely to operate with limited overlap: kin discrimination is beneficial when variation in relatedness is higher, whereas limited dispersal results in less variable and higher average relatedness, reducing selection for kin discrimination. However, most empirical work on eukaryotes has focused on kin discrimination. To address this bias, we analysed how kin discrimination and limited dispersal interact to shape helping behaviour across cooperatively breeding vertebrates. We show that kin discrimination is greater in species where the: (i) average relatedness in groups is lower and more variable; (ii) effect of helpers on breeders reproductive success is greater; and (iii) probability of helping was measured, rather than the amount of help provided. There was also an interaction between these effects with the correlation between the benefits of helping and kin discrimination being stronger in species with higher variance in relatedness. Overall, our results suggest that kin discrimination provides a route to indirect benefits when relatedness is too variable within groups to favour indiscriminate cooperation.     

Characterizing the role of mechanical signals in gene regulatory networks using Long SAGE

A systems understanding of mechanical regulation is critical for determining how cells proliferate and differentiate. To better understand the biological process in which mechanical signals regulate cells, we globally investigated the gene expression profiling via long serial analysis of gene expression (Long SAGE) in osteoblasts after exposure to mechanical stretching. The analysis showed that the differentially expressed genes were related with many physiological processes, including signal transduction, cell proliferation and apoptosis. Several genes that were seldom or never studied in osteoblasts have been found in this study. We further analyzed the signal pathways and provided gene regulatory networks activated by mechanical signals. Many changed genes in our data were contributed to ECM-integrin-FAK mediated pathway and mainly influenced actin-cytoskeleton dynamic remodeling, cell proliferation and differentiation. We also provided evidence supporting the hypothesis that endoplasmic reticulum and mitochondrion were combined to dedicate to calcium regulation. Taken together, our experiments provided a systemic view on biological processes and mechanotransduction network in osteoblasts, suggesting that mechanical signals regulate osteoblast through a greater diversity of interactions and pathways than previously appreciated.