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cis-regulatory elements

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https://www.readbyqxmd.com/read/28550013/an-essential-regulatory-system-originating-from-polygenic-transcriptional-rewiring-of-phop-phoq-of-xanthomonas-campestris
#1
Bao-Yu Peng, Yue Pan, Ru-Jiao Li, Jin-Wei Wei, Fang Liang, Li Wang, Fang-Fang Wang, Wei Qian
How essential, regulatory genes originate and evolve is intriguing because mutations of these genes not only lead to lethality in organisms, but also have pleiotropic effects since they control the expression of multiple downstream genes. Therefore, the evolution of essential, regulatory genes is not only determined by genetic variations of their own sequences, but also by the biological function of downstream genes and molecular mechanisms of regulation. To understand the origin of essential, regulatory genes, experimental dissection of the complete regulatory cascade is needed...
May 26, 2017: Genetics
https://www.readbyqxmd.com/read/28549169/regulatory-dynamics-of-11p13-suggest-a-role-for-ehf-in-modifying-cf-lung-disease-severity
#2
Lindsay R Stolzenburg, Rui Yang, Jenny L Kerschner, Sara Fossum, Matthew Xu, Andrew Hoffmann, Kay-Marie Lamar, Sujana Ghosh, Sarah Wachtel, Shih-Hsing Leir, Ann Harris
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), but are not good predictors of lung phenotype. Genome-wide association studies (GWAS) previously identified additional genomic sites associated with CF lung disease severity. One of these, at chromosome 11p13, is an intergenic region between Ets homologous factor (EHF) and Apaf-1 interacting protein (APIP). Our goal was to determine the functional significance of this region, which being intergenic is probably regulatory...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28542178/uncovering-direct-and-indirect-molecular-determinants-of-chromatin-loops-using-a-computational-integrative-approach
#3
Raphaël Mourad, Lang Li, Olivier Cuvier
Chromosomal organization in 3D plays a central role in regulating cell-type specific transcriptional and DNA replication timing programs. Yet it remains unclear to what extent the resulting long-range contacts depend on specific molecular drivers. Here we propose a model that comprehensively assesses the influence on contacts of DNA-binding proteins, cis-regulatory elements and DNA consensus motifs. Using real data, we validate a large number of predictions for long-range contacts involving known architectural proteins and DNA motifs...
May 23, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28541183/pausing-guides-rna-folding-to-populate-transiently-stable-rna-structures-for-riboswitch-based-transcription-regulation
#4
Hannah Steinert, Florian Sochor, Anna Wacker, Janina Buck, Christina Helmling, Fabian Hiller, Sara Keyhani, Jonas Noeske, Steffen Kaspar Grimm, Martin M Rudolph, Heiko Keller, Rachel Anne Mooney, Robert Landick, Beatrix Suess, Boris Fürtig, Jens Wöhnert, Harald Schwalbe
In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element...
May 25, 2017: ELife
https://www.readbyqxmd.com/read/28536883/identification-of-genes-related-to-skin-development-in-potato
#5
Vijaya K R Vulavala, Edna Fogelman, Lior Rozental, Adi Faigenboim, Zachariah Tanami, Oded Shoseyov, Idit Ginzberg
Newly identified genes that are preferentially expressed in potato skin include genes that are associated with the secondary cell wall and stress-related activities and contribute to the skin's protective function. Microarrays were used to compare the skin and tuber-flesh transcriptomes of potato, to identify genes that contribute to the unique characteristics of the skin as a protective tissue. Functional gene analysis indicated that genes involved in developmental processes such as cell division, cell differentiation, morphogenesis and secondary cell wall formation (lignification and suberization), and stress-related activities, are more highly expressed in the skin than in the tuber flesh...
May 23, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28536440/genetic-variants-in-the-transcription-regulatory-region-of-megf10-are-associated-with-autism-in-chinese-han-population
#6
Zhiliu Wu, Jian Qin, Yang You, Yuanlin Ma, Meixiang Jia, Linyan Wang, Tianlan Lu, Weihua Yue, Yanyan Ruan, Dai Zhang, Jun Li, Lifang Wang
Multiple epidermal growth factor-like-domains 10 (MEGF10), a critical member of the apoptotic engulfment pathway, mediates axon pruning and synapse elimination during brain development. Previous studies indicated that synaptic pruning deficit was associated with autism-related phenotypes. However, the relationship between MEGF10 and autism remains poorly understood. Disease-associated variants are significantly enriched in the transcription regulatory regions. These include the transcription start site (TSS) and its cis-regulatory elements...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28533025/enhancer-derived-rna-a-primer
#7
REVIEW
Feng Liu
Enhancer-derived RNAs (eRNAs) are a group of RNAs transcribed by RNA polymerase II from the domain of transcription enhancers, a major type of cis-regulatory elements in the genome. The correlation between eRNA production and enhancer activity has stimulated studies on the potential role of eRNAs in transcriptional regulation. Additionally, eRNA has also served as a marker for global identification of enhancers. Here I review the brief history and fascinating properties of eRNAs.
May 19, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28529519/genome-wide-identification-of-sorghum-bicolor-laccases-reveals-potential-targets-for-lignin-modification
#8
Jinhui Wang, Juanjuan Feng, Weitao Jia, Pengxiang Fan, Hexigeduleng Bao, Shizhong Li, Yinxin Li
Laccase is a key enzyme in plant lignin biosynthesis as it catalyzes the final step of monolignols polymerization. Sweet sorghum [Sorghum bicolor (L.) Moench] is considered as an ideal feedstock for ethanol production, but lignin greatly limits the production efficiency. No comprehensive analysis on laccase has ever been conducted in S. bicolor, although it appears as the most promising target for engineering lignocellulosic feedstock. The aim of our work is to systematically characterize S. bicolor laccase gene family and to identify the lignin-specific candidates...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28527335/dissection-of-cis-regulatory-element-architecture-of-the-rice-oleosin-gene-promoters-to-assess-abscisic-acid-responsiveness-in-suspension-cultured-rice-cells
#9
Sol Kim, Soo-Bin Lee, Chae-Seong Han, Mi-Na Lim, Sung-Eun Lee, In Sun Yoon, Yong-Sic Hwang
Oleosins are the most abundant proteins in the monolipid layer surrounding neutral storage lipids that form oil bodies in plants. Several lines of evidence indicate that they are physiologically important for the maintenance of oil body structure and for mobilization of the lipids stored inside. Rice has six oleosin genes in its genome, the expression of all of which was found to be responsive to abscisic acid (ABA) in our examination of mature embryo and aleurone tissues. The 5'-flanking region of OsOle5 was initially characterized for its responsiveness to ABA through a transient expression assay system using the protoplasts from suspension-cultured rice cells...
May 1, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28526334/regulatory-cis-and-trans-elements-of-mitochondrial-d-loop-driven-reporter-genes-in-budding-tunicates
#10
Kaz Kawamura, Yuhya Saitoh, Loriano Ballarin, Takeshi Sunanaga
To unveil the underlying mechanism of mitochondrial gene regulation associated with ageing and budding in the tunicate Polyandrocarpa misakiensis, mitochondrial non-coding-region (NCR)-containing reporter genes were constructed. PmNCR2.3K/GFP was expressed spatiotemporally in a pattern quite similar to mitochondrial 16SrRNA. The reporter gene expression was sensitive to high dose of rifampicin similar to mitochondrial genes, suggesting that the transcription indeed occurs in mitochondria. However, the gene expression also occurred in vivo in the cell nucleus and in vitro in the nuclear extracts...
May 16, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28521937/using-drosophila-pigmentation-traits-to-study-the-mechanisms-of-cis-regulatory-evolution
#11
REVIEW
Mark Rebeiz, Thomas M Williams
One primary agenda of the developmental evolution field is to elucidate molecular mechanisms governing differences in animal form. While mounting evidence has established an important role for mutations in transcription controlling cis-regulatory elements (CREs), the underlying mechanisms that translate these alterations into differences in gene expression are poorly understood. Emerging studies focused on pigmentation differences among closely related Drosophila species have provided many examples of phenotypically relevant CRE changes, and have begun to illuminate how this process works at the level of regulatory sequence function and transcription factor binding...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28518057/on-the-mechanistic-nature-of-epistasis-in-a-canonical-cis-regulatory-element
#12
Mato Lagator, Tiago Paixao, Nick Barton, Jonathan P Bollback, Călin C Guet
Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites...
May 18, 2017: ELife
https://www.readbyqxmd.com/read/28508170/viral-vector-based-evaluation-of-regulatory-regions-in-the-neuron-specific-enolase-nse-promoter-in-mouse-cerebellum-in-vivo
#13
Yoichiro Shinohara, Toshinori Ohtani, Ayumu Konno, Hirokazu Hirai
We investigated the neuron-specific enolase (NSE) promoter in terms of its promoter strength and neuronal specificity in the cerebellum in vivo. The 1.8 kb rat NSE promoter was divided into three regions, A (0.8 kb), B (0.7 kb), and C (0.3 kb), starting from the 5' side. Then, we made various deletion constructs and assessed them by virally expressing GFP under the control of one of the deleted promoters. Removing region A reduced GFP expression to ~6% of that of the original 1.8 kb promoter. Further deletion of region B (presence of region C alone) did not influence the promoter strength, but removing region B from the original 1...
May 15, 2017: Cerebellum
https://www.readbyqxmd.com/read/28505153/gene-duplication-and-co-evolution-of-g1-s-transcription-factor-specificity-in-fungi-are-essential-for-optimizing-cell-fitness
#14
Adi Hendler, Edgar M Medina, Anastasiya Kishkevich, Mehtap Abu-Qarn, Steffi Klier, Nicolas E Buchler, Robertus A M de Bruin, Amir Aharoni
Transcriptional regulatory networks play a central role in optimizing cell survival. How DNA binding domains and cis-regulatory DNA binding sequences have co-evolved to allow the expansion of transcriptional networks and how this contributes to cellular fitness remains unclear. Here we experimentally explore how the complex G1/S transcriptional network evolved in the budding yeast Saccharomyces cerevisiae by examining different chimeric transcription factor (TF) complexes. Over 200 G1/S genes are regulated by either one of the two TF complexes, SBF and MBF, which bind to specific DNA binding sequences, SCB and MCB, respectively...
May 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28497882/identification-of-the-2-tridecanone-cis-acting-element-in-the-promoter-of-cytochrome-p450-cyp6b7-in-helicoverpa-armigera
#15
Li Xu, Dong-Zhi Li, Yuan-Yuan Luo, Jian-Ying Qin, Li-Hong Qiu
The expression level of cytochrome P450 genes in insects can be induced by plant allelochemicals, which is important for insects to adapt to host plants. Cytochrome P450 CYP6B7 has been reported to be involved in pyrethroid insecticide resistance in Helicoverpa armigera, and its transcription level was induced by some inducers. Currently, the regulatory mechanism of the induced expression of CYP6B7 remains unknown, although it is very important for understanding the detoxification mechanism to allelochemicals in host plants...
May 12, 2017: Insect Science
https://www.readbyqxmd.com/read/28490839/higher-order-chromatin-regulation-of-inflammatory-gene-expression
#16
REVIEW
Jin-Wen Xu, Shuang Ling, Jun Liu
Whether it is caused by viruses and bacteria infection, or low-grade chronic inflammation of atherosclerosis and cellular senescence, the transcription factor (TF) NF-κB plays a central role in the inducible expression of inflammatory genes. Accumulated evidence has indicated that the chromatin environment is the main determinant of TF binding in gene expression regulation, including the stimulus-responsive NF-κB. Dynamic changes in intra- and interchromosomes are the key regulatory mechanisms promoting the binding of TFs...
2017: Mediators of Inflammation
https://www.readbyqxmd.com/read/28490275/genome-wide-sequential-evolutionary-organizational-and-expression-analyses-of-phenylpropanoid-biosynthesis-associated-myb-domain-transcription-factors-in-arabidopsis
#17
Sunil Kanti Mondal, Sujit Roy
The MYB gene family represents one of the largest groups of transcription factors in plants. Recent evidences have also demonstrated key role of MYB transcription factors in regulating the expression of major genes involved in the biosynthesis of phenylpropanoid compounds which confer biotic and abiotic stress tolerance in plant species. However, no comprehensive genome-wide analysis of the phenylpropanoid pathway associated MYB transcription factors has been reported thus far. In this study, 11 Arabidopsis MYB proteins, such as MYB3, MYB4, MYB7, MYB11, MYB12, MYB32, MYB75, MYB90, MYB111, MYB113 and MYB114 were initially identified considering their reported regulatory function in phenylpropanoid biosynthesis pathway...
May 10, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28487507/transcriptional-regulation-of-foxp3-requires-integrated-activation-of-both-promoter-and-cns-regions-in-tumor-induced-cd8-treg-cells
#18
Sreeparna Chakraborty, Abir K Panda, Sayantan Bose, Dia Roy, Kirti Kajal, Deblina Guha, Gaurisankar Sa
T-regulatory cells are an upsurge in the tumor microenvironment and induce immune-evasion. CD4(+) Treg cells are well characterized whereas the role of CD8(+) Tregs in cancer has recently started to crease attention. Here, we report an augmentation CD8(+)FOXP3(+) Tregs in breast tumor microenvironment. FOXP3, the lineage-specific transcription factor, is a dominant regulator of Treg cell development and function. FOXP3 is induced preferentially by divergent signaling in CD4(+) Treg cells. But how FOXP3 is induced and maintained in tumor-CD8(+) Tregs is the Cinderella of the investigation...
May 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28487406/set1a-compass-and-shadow-enhancers-in-the-regulation-of-homeotic-gene-expression
#19
Kaixiang Cao, Clayton K Collings, Stacy A Marshall, Marc A Morgan, Emily J Rendleman, Lu Wang, Christie C Sze, Tianjiao Sun, Elizabeth T Bartom, Ali Shilatifard
The homeotic (Hox) genes are highly conserved in metazoans, where they are required for various processes in development, and misregulation of their expression is associated with human cancer. In the developing embryo, Hox genes are activated sequentially in time and space according to their genomic position within Hox gene clusters. Accumulating evidence implicates both enhancer elements and noncoding RNAs in controlling this spatiotemporal expression of Hox genes, but disentangling their relative contributions is challenging...
May 9, 2017: Genes & Development
https://www.readbyqxmd.com/read/28481873/restoring-pu-1-induces-apoptosis-and-modulates-viral-transactivation-via-interferon-stimulated-genes-in-primary-effusion-lymphoma
#20
H Goto, R Kariya, E Kudo, Y Okuno, K Ueda, H Katano, S Okada
Primary effusion lymphoma (PEL), which is an aggressive subgroup of B-cell lymphoma associated with Kaposi sarcoma-associated herpes virus/human herpes virus-8, is refractory to the standard treatment, and exhibits a poor survival. Although PU.1 is downregulated in PEL, the potential role of its reduction remains to be elucidated. In this investigation, we analyzed the DNA methylation of PU.1 cis-regulatory elements in PEL and the effect of restoring PU.1 on PEL cells. The mRNA level of PU.1 was downregulated in PEL cells...
May 8, 2017: Oncogene
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