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Gene network evolution

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https://www.readbyqxmd.com/read/29339519/evidence-for-convergent-evolution-of-sine-directed-staufen-mediated-mrna-decay
#1
Bronwyn A Lucas, Eitan Lavi, Lily Shiue, Hana Cho, Sol Katzman, Keita Miyoshi, Mikiko C Siomi, Liran Carmel, Manuel Ares, Lynne E Maquat
Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3'-untranslated regions (3'-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29337961/how-the-evolution-of-multicellularity-set-the-stage-for-cancer
#2
REVIEW
Anna S Trigos, Richard B Pearson, Anthony T Papenfuss, David L Goode
Neoplastic growth and many of the hallmark properties of cancer are driven by the disruption of molecular networks established during the emergence of multicellularity. Regulatory pathways and molecules that evolved to impose regulatory constraints upon networks established in earlier unicellular organisms enabled greater communication and coordination between the diverse cell types required for multicellularity, but also created liabilities in the form of points of vulnerability in the network that when mutated or dysregulated facilitate the development of cancer...
January 16, 2018: British Journal of Cancer
https://www.readbyqxmd.com/read/29335803/contribution-of-transposable-elements-and-distal-enhancers-to-evolution-of-human-specific-features-of-interphase-chromatin-architecture-in-embryonic-stem-cells
#3
Gennadi V Glinsky
Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs...
January 15, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29331019/cis-regulator-runaway-and-divergence-in-asexuals
#4
Frédéric Fyon, Thomas Lenormand
With the advent of new sequencing technologies, the evolution of gene expression is becoming a subject of intensive genomic research, with sparking debates upon the role played by these kinds of changes in adaptive evolution and speciation. In this paper, we model expression evolution in species differing by their reproductive systems. We consider different rates of sexual versus asexual reproduction and the different type of parthenogenesis (apomixis and the various modes of automixis). We show that competition for expression leads to two selective processes on cis-regulatory regions that act independently to organism-level adaptation...
January 13, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29320604/reconstruction-of-molecular-network-evolution-from-cross-sectional-omics-data
#5
Mehran Aflakparast, Mathisca C M de Gunst, Wessel N van Wieringen
Cross-sectional studies may shed light on the evolution of a disease like cancer through the comparison of patient traits among disease stages. This problem is especially challenging when a gene-gene interaction network needs to be reconstructed from omics data, and, in addition, the patients of each stage need not form a homogeneous group. Here, the problem is operationalized as the estimation of stage-wise mixtures of Gaussian graphical models (GGMs) from high-dimensional data. These mixtures are fitted by a (fused) ridge penalized EM algorithm...
January 10, 2018: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/29320496/bayesian-inference-of-phylogenetic-networks-from-bi-allelic-genetic-markers
#6
Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M Meudt, Luay Nakhleh
Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence alignments of multiple unlinked loci. Bi-allelic markers, most notably single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs), provide a powerful source of genome-wide data. In a recent paper, a method called SNAPP was introduced for statistical inference of species trees from unlinked bi-allelic markers...
January 10, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29318384/small-but-powerful-function-of-micrornas-in-plant-development
#7
REVIEW
Haiping Liu, Hongyang Yu, Guiliang Tang, Tengbo Huang
MicroRNAs (miRNAs) are a group of endogenous noncoding small RNAs frequently 21 nucleotides long. miRNAs act as negative regulators of their target genes through sequence-specific mRNA cleavage, translational repression, or chromatin modifications. Alterations of the expression of a miRNA or its targets often result in a variety of morphological and physiological abnormalities, suggesting the strong impact of miRNAs on plant development. Here, we review the recent advances on the functional studies of plant miRNAs...
January 9, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29311454/-development-of-plant-metabolomics-and-medicinal-plant-genomics
#8
Kazuki Saito
 A variety of chemicals produced by plants, often referred to as 'phytochemicals', have been used as medicines, food, fuels and industrial raw materials. Recent advances in the study of genomics and metabolomics in plant science have accelerated our understanding of the mechanisms, regulation and evolution of the biosynthesis of specialized plant products. We can now address such questions as how the metabolomic diversity of plants is originated at the levels of genome, and how we should apply this knowledge to drug discovery, industry and agriculture...
2018: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/29303971/molecular-epidemiology-and-evolution-of-european-bat-lyssavirus-2
#9
REVIEW
Lorraine M McElhinney, Denise A Marston, Emma L Wise, Conrad M Freuling, Hervé Bourhy, Reto Zanoni, Torfinn Moldal, Engbert A Kooi, Antonie Neubauer-Juric, Tiina Nokireki, Thomas Müller, Anthony R Fooks
Bat rabies cases in Europe are mainly attributed to two lyssaviruses, namely European Bat Lyssavirus 1 (EBLV-1) and European Bat Lyssavirus 2 (EBLV-2). Prior to the death of a bat worker in Finland in 1985, very few bat rabies cases were reported. Enhanced surveillance in the two subsequent years (1986-1987) identified 263 cases (more than a fifth of all reported cases to date). Between 1977 and 2016, 1183 cases of bat rabies were reported, with the vast majority (>97%) being attributed to EBLV-1. In contrast, there have been only 39 suspected cases of EBLV-2, of which 34 have been confirmed by virus typing and presently restricted to just two bat species; Myotis daubentonii and Myotis dasycneme...
January 5, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29300827/miic-online-a-web-server-to-reconstruct-causal-or-non-causal-networks-from-non-perturbative-data
#10
Nadir Sella, Louis Verny, Guido Uguzzoni, Séverine Affeldt, Hervé Isambert
Summary: We present a web server running the MIIC algorithm, a network learning method combining constraint-based and information-theoretic frameworks to reconstruct causal, non-causal or mixed networks from non-perturbative data, without the need for an a priori choice on the class of reconstructed network. Starting from a fully connected network, the algorithm first removes dispensable edges by iteratively subtracting the most significant information contributions from indirect paths between each pair of variables...
December 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29298909/evolution-of-the-spx-gene-family-in-plants-and-its-role-in-the-response-mechanism-to-phosphorus-stress
#11
REVIEW
Na Liu, Wenyan Shang, Chuang Li, Lihua Jia, Xin Wang, Guozhen Xing, WenMing Zheng
Molecular and genomic studies have shown the presence of a large number of SPX gene family members in plants, some of which have been proved to act in P signalling and homeostasis. In this study, the molecular and evolutionary characteristics of the SPX gene family in plants were comprehensively analysed, and the mechanisms underlying the function of SPX genes in P signalling and homeostasis in the model plant species Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), and in important crops, including wheat (Triticum aestivum), soya beans (Glycine max) and rapeseed (Brassica napus), were described...
January 2018: Open Biology
https://www.readbyqxmd.com/read/29297463/cis-regulatory-evolution-integrated-the-bric-%C3%A3-brac-transcription-factors-into-a-novel-fruit-fly-gene-regulatory-network
#12
Maxwell J Roeske, Eric M Camino, Sumant Grover, Mark Rebeiz, Thomas Michael Williams
Gene expression evolution through gene regulatory network (GRN) changes has gained appreciation as a driver of morphological evolution. However, understanding how GRNs evolve is hampered by finding relevant cis-regulatory element (CRE) mutations, and interpreting the protein-DNA interactions they alter. We investigated evolutionary changes in the duplicated Bric-à-brac (Bab) transcription factors and a key Bab target gene in a GRN underlying the novel dimorphic pigmentation of D. melanogaster and its relatives...
January 3, 2018: ELife
https://www.readbyqxmd.com/read/29297327/the-factors-affecting-the-evolution-of-the-anthocyanin-biosynthesis-pathway-genes-in-monocot-and-dicot-plant-species
#13
Olesya Yu Shoeva, Anastasiya Yu Glagoleva, Elena K Khlestkina
BACKGROUND: The available data demonstrate that even in universal metabolic pathways, some species-specific regulatory features of structural genes are present. For instance, in the anthocyanin biosynthesis pathway (ABP), genes may be regulated by ABP-specific regulatory factors, and their expression levels may be strongly associated with anthocyanin pigmentation, or they may be expressed independently of pigmentation. A dataset of orthologous ABP genes (Chs, Chi, F3h, F3'h, Dfr, Ans) from monocot and dicot plant species that have distinct gene regulation patterns and different types of pollination was constructed to test whether these factors affect the evolution of the genes...
December 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29285397/divergent-evolutionary-patterns-of-the-mapk-cascade-genes-in-brassica-rapa-and-plant-phylogenetics
#14
Peng Wu, Wenli Wang, Ying Li, Xilin Hou
Mitogen-activated protein kinase (MAPK) cascade signal transduction modules play crucial roles in regulating many biological processes in plants. These cascades are composed of three classes of hierarchically organized protein kinases, MAPKKKs, MAPKKs and MAPKs. Here, we analyzed gene retention, phylogenetic, evolution and expression patterns of MAPK cascade genes in Brassica rapa. We further found that the MAPK branches, classes III and IV, appeared after the split of bryophytes and green algae after analyzing the MAPK cascade genes in 8 species, and their rapid expansion led to the great size of the families of MAPKs...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29276507/in-silico-analysis-of-the-small-molecule-content-of-outer-membrane-vesicles-produced-by-bacteroides-thetaiotaomicron-indicates-an-extensive-metabolic-link-between-microbe-and-host
#15
William A Bryant, Régis Stentz, Gwenaelle Le Gall, Michael J E Sternberg, Simon R Carding, Thomas Wilhelm
The interactions between the gut microbiota and its host are of central importance to the health of the host. Outer membrane vesicles (OMVs) are produced ubiquitously by Gram-negative bacteria including the gut commensal Bacteroides thetaiotaomicron. These vesicles can interact with the host in various ways but until now their complement of small molecules has not been investigated in this context. Using an untargeted high-coverage metabolomic approach we have measured the small molecule content of these vesicles in contrasting in vitro conditions to establish what role these metabolites could perform when packed into these vesicles...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29260295/expansion-of-gene-clusters-circular-orders-and-the-shortest-hamiltonian-path-problem
#16
Sonja J Prohaska, Sarah J Berkemer, Fabian Gärtner, Thomas Gatter, Nancy Retzlaff, Christian Höner Zu Siederdissen, Peter F Stadler
Clusters of paralogous genes such as the famous HOX cluster of developmental transcription factors tend to evolve by stepwise duplication of its members, often involving unequal crossing over. Gene conversion and possibly other mechanisms of concerted evolution further obfuscate the phylogenetic relationships. As a consequence, it is very difficult or even impossible to disentangle the detailed history of gene duplications in gene clusters. In this contribution we show that the expansion of gene clusters by unequal crossing over as proposed by Walter Gehring leads to distinctive patterns of genetic distances, namely a subclass of circular split systems...
December 19, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/29258880/aquatic-long-distance-dispersal-and-vicariance-shape-the-evolution-of-an-ostracod-species-complex-crustacea-in-four-major-brazilian-floodplains
#17
Isa Schön, Janet Higuti, Tasnim Patel, Koen Martens
Cladogenesis is often driven by the interplay of dispersal and vicariance. The importance of long-distance dispersal in biogeography and speciation is increasingly recognised, but still ill-understood. Here, we study faunal interconnectivity between four large Brazilian floodplains, namely the Amazon, Araguaia, Pantanal (on Paraguay River) and Upper Paraná River floodplains, investigating a species complex of the non-marine ostracod genus Strandesia. We use DNA sequence data from the mitochondrial COI and the nuclear Elongation Factor 1 alpha genes to construct molecular phylogenies and minimum spanning networks, to identify genetic species, analyse biogeographic histories and provide preliminary age estimates of this species complex...
December 16, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29258434/genome-wide-identification-characterization-and-evolutionary-analysis-of-flowering-genes-in-radish-raphanus-sativus-l
#18
Jinglei Wang, Yang Qiu, Feng Cheng, Xiaohua Chen, Xiaohui Zhang, Haiping Wang, Jiangping Song, Mengmeng Duan, Haohui Yang, Xixiang Li
BACKGROUND: Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus...
December 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29247320/time-dependent-propagators-for-stochastic-models-of-gene-expression-an-analytical-method
#19
Frits Veerman, Carsten Marr, Nikola Popović
The inherent stochasticity of gene expression in the context of regulatory networks profoundly influences the dynamics of the involved species. Mathematically speaking, the propagators which describe the evolution of such networks in time are typically defined as solutions of the corresponding chemical master equation (CME). However, it is not possible in general to obtain exact solutions to the CME in closed form, which is due largely to its high dimensionality. In the present article, we propose an analytical method for the efficient approximation of these propagators...
December 15, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/29240947/a-fth1-gene-pseudogene-microrna-network-regulates-tumorigenesis-in-prostate-cancer
#20
Jia Jia Chan, Zhi Hao Kwok, Xiao Hong Chew, Bin Zhang, Chao Liu, Tuck Wah Soong, Henry Yang, Yvonne Tay
Non-coding RNAs play a vital role in diverse cellular processes. Pseudogenes, which are non-coding homologs of protein-coding genes, were once considered non-functional evolutional relics. However, recent studies have shown that pseudogene transcripts can regulate their parental transcripts by sequestering shared microRNAs (miRNAs), thus acting as competing endogenous RNAs (ceRNAs). In this study, we utilize an unbiased screen to identify the ferritin heavy chain 1 (FTH1) transcript and multiple FTH1 pseudogenes as targets of several oncogenic miRNAs in prostate cancer (PCa)...
December 12, 2017: Nucleic Acids Research
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