keyword
MENU ▼
Read by QxMD icon Read
search

cis-regulatory elements

keyword
https://www.readbyqxmd.com/read/28713404/genome-wide-identification-and-analysis-of-genes-conserved-between-japonica-and-indica-rice-cultivars-that-respond-to-low-temperature-stress-at-the-vegetative-growth-stage
#1
Manu Kumar, Yun-Shil Gho, Ki-Hong Jung, Seong-Ryong Kim
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28712775/simple-sequence-repeats-showing-length-preference-have-regulatory-functions-in-humans
#2
Jaya Krishnan, Fathima Athar, Tirupaati Swaroopa Rani, Rakesh Kumar Mishra
Simple sequence repeats (SSRs), simple tandem repeats (STRs) or microsatellites are short tandem repeats of 1-6 nucleotide motifs. They are twice as abundant as the protein coding DNA in the human genome and yet little is known about their functional relevance. Analysis of genomes across various taxa show that despite the instability associated with longer stretches of repeats, few SSRs with specific longer repeat lengths are enriched in the genomes indicating a positive selection. This conserved feature of length dependent enrichment hints at not only sequence but also length dependent functionality for SSRs...
July 13, 2017: Gene
https://www.readbyqxmd.com/read/28711355/characterization-of-the-foxl2-proximal-promoter-and-coding-sequence-from-the-common-snapping-turtle-chelydra-serpentina
#3
Lei Guo, Turk Rhen
Sex is determined by temperature during embryogenesis in snapping turtles, Chelydra serpentina. Previous studies in this species show that dihydrotestosterone (DHT) induces ovarian development at temperatures that normally produce males or mixed sex ratios. The feminizing effect of DHT is associated with increased expression of FoxL2, suggesting that androgens regulate transcription of FoxL2. To test this hypothesis, we cloned the proximal promoter (1.6kb) and coding sequence for snapping turtle FoxL2 (tFoxL2) in frame with mCherry to produce a fluorescent reporter...
July 12, 2017: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
https://www.readbyqxmd.com/read/28701416/eukaryotic-transcription-factors-paradigms-of-protein-intrinsic-disorder
#4
REVIEW
Lasse Staby, Charlotte O'Shea, Martin Willemoës, Frederik Theisen, Birthe B Kragelund, Karen Skriver
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from 'negative noodles' to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities...
July 12, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28695512/approaches-for-investigating-translational-regulation-controlled-by-parp1-biotin-based-uv-cross-linking-and-luciferase-reporter-assay
#5
Yingbiao Ji
The RNA-binding proteins (RBPs) play a pivotal role in controlling gene expression through posttranscriptional processes. As the trans-acting factors, RBPs interact with the cis-regulatory elements located within mRNAs to regulate mRNA translational efficiency. Adding a new-layer regulation, recent studies suggest that poly(ADP-ribosyl)ation of the RNA-binding proteins often inhibit the RNA-binding ability of RBPs, thus regulating RBP-dependent mRNA metabolism including translational control. Here, we describe a biotin-based UV cross-linking method to determine if excessive accumulation of pADPr in the cell disrupts the interaction between RBPs and their target mRNAs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28693485/three-members-of-medicago-truncatula-st-family-are-ubiquitous-during-development-and-modulated-by-nutritional-status-mtst1-and-dehydration-mtst2-and-mtst3
#6
Lucía Albornos, Ignacio Martín, Emilia Labrador, Berta Dopico
BACKGROUND: ShooT specific/Specific Tissue (ST) belong to a protein family of unknown function characterized by the DUF2775 domain and produced in specific taxonomic plant families, mainly Fabaceae and Asteraceae, with the Medicago truncatula ST family being the largest. The putative roles proposed for this family are cell elongation, biotic interactions, abiotic stress and N reserve. The aim of this work was to go deeper into the role of three M. truncatula ST proteins, namely ST1, ST2 and ST3...
July 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28687067/genome-wide-characterization-of-the-aldehyde-dehydrogenase-gene-superfamily-in-soybean-and-its-potential-role-in-drought-stress-response
#7
Wei Wang, Wei Jiang, Juge Liu, Yang Li, Junyi Gai, Yan Li
BACKGROUND: Aldehyde dehydrogenases (ALDHs) represent a group of enzymes that detoxify aldehydes by facilitating their oxidation to carboxylic acids, and have been shown to play roles in plant response to abiotic stresses. However, the comprehensive analysis of ALDH superfamily in soybean (Glycine max) has been limited. RESULTS: In present study, a total of 53 GmALDHs were identified in soybean, and grouped into 10 ALDH families according to the ALDH Gene Nomenclature Committee and phylogenetic analysis...
July 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28681587/functional-characterization-of-the-promoter-of-carbonyl-reductase-1-gene-in-porcine-endometrial-cells
#8
Ai-Ling Zhang, Xian-Yue Sun, Qi Yin, Jian-Hua Zeng, Zhe Zhang, Jia-Qi Li, Hao Zhang
Prostaglandins (PGs) play a critical role in porcine reproduction, of which prostaglandin E2 (PGE2) and prostaglandin F2α (PGF2α) exert antiluteolytic and luteolysis actions, respectively. As a rate-limiting enzyme, carbonyl reductase 1 (CBR1) catalyzes the conversion of PGE2 to PGF2α. A high ratio of PGE2:PGF2α is beneficial to the establishment and maintenance of porcine pregnancy. PG is essential for the establishment of pregnancy which resembles the proinflammatory response and nuclear factor κB (NF-κB) is involved in the process...
July 2017: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/28679357/genome-scale-analysis-of-regulatory-protein-acetylation-enzymes-from-photosynthetic-eukaryotes
#9
R Glen Uhrig, Pascal Schläpfer, Devang Mehta, Matthias Hirsch-Hoffmann, Wilhelm Gruissem
BACKGROUND: Reversible protein acetylation occurring on Lys-N(e) has emerged as a key regulatory post-translational modification in eukaryotes. It is mediated by two groups of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) that catalyze the addition and removal of acetyl groups from target proteins. Estimates indicate that protein acetylation is second to protein phosphorylation in abundance, with thousands of acetylated sites now identified in different subcellular compartments...
July 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28675662/separate-and-coincident-expression-of-hes1-and-hes5-in-the-developing-mouse-eye
#10
Amy N Riesenberg, Kevin W Conley, Tien T Le, Nadean L Brown
BACKGROUND: Notch signaling is broadly required during embryogenesis, frequently activating the transcription of two bHLH transcription factors, Hes1 and Hes5. But, it remains unresolved when and where Hes1 and Hes5 act alone or together during development. Here, we analyzed a Hes5-GFP BAC transgenic mouse, as a proxy for endogenous Hes5. We directly compared transgenic GFP expression with Hes1, and particular markers of embryonic lens and retina development. RESULTS: Hes5-GFP is dynamic within subsets of retinal and lens progenitor cells, and differentiating retinal ganglion neurons, in contrast to Hes1 found in all progenitor cells...
July 4, 2017: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/28673963/yeast-pah1-encoded-phosphatidate-phosphatase-controls-the-expression-of-cho1-encoded-phosphatidylserine-synthase-for-membrane-phospholipid-synthesis
#11
Gil-Soo Han, George M Carman
The PAH1-encoded phosphatidate phosphatase (PAP), which catalyzes the committed step for the synthesis of triacylglycerol in Saccharomyces cerevisiae, exerts a negative regulatory effect on the level of phosphatidate used for the de novo synthesis of membrane phospholipids. This raises the question whether PAP thereby affects the expression and activity of enzymes involved in phospholipid synthesis. Here, we examined the PAP-mediated regulation of CHO1-encoded phosphatidylserine synthase (PSS), which catalyzes the committed step for the synthesis of major phospholipids via the CDP-diacylglycerol pathway...
July 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28662576/social-aggression-experience-and-brain-gene-expression-in-a-subsocial-bee
#12
Jacob R Withee, Sandra M Rehan
The genetic mechanisms behind aggressive behaviors are important for understanding the formation of dominance hierarchies, and thus social systems in general. Studies into the effects of social experience and agonistic contest outcomes have shown significant changes in brain gene expression resulting from repeated winning and losing, as well as changing dominance rank, primarily in obligately social species. However, our knowledge of the genetic underpinnings of behavior in subsocial organisms is relatively poor, yet understanding the behavioral genetics of this simplest form of sociality provides the basis for understanding all other forms of social living...
June 28, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28659956/identification-of-genes-associated-with-lemon-floral-transition-and-flower-development-during-floral-inductive-water-deficits-a-hypothetical-model
#13
Jin-Xue Li, Xiao-Jin Hou, Jiao Zhu, Jing-Jing Zhou, Hua-Bin Huang, Jian-Qiang Yue, Jun-Yan Gao, Yu-Xia Du, Cheng-Xiao Hu, Chun-Gen Hu, Jin-Zhi Zhang
Water deficit is a key factor to induce flowering in many woody plants, but reports on the molecular mechanisms of floral induction and flowering by water deficit are scarce. Here, we analyzed the morphology, cytology, and different hormone levels of lemon buds during floral inductive water deficits. Higher levels of ABA were observed, and the initiation of floral bud differentiation was examined by paraffin sections analysis. A total of 1638 differentially expressed genes (DEGs) were identified by RNA sequencing...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28653245/muscadinia-rotundifolia-noble-defense-response-to-plasmopara-viticola-inoculation-by-inducing-phytohormone-mediated-stilbene-accumulation
#14
Chaoxia Wang, Jiao Wu, Yali Zhang, Jiang Lu
Downy mildew (DM), one of the most devastating grape diseases worldwide, is caused by the biotrophic oomycete Plasmopara viticola (Pv). In general, grapevine responds to Pv infection with the accumulation of phytoalexins as part of the innate immune system, and diverse phytoalexins are induced on grapevines with different DM-resistance levels in response to Pv invasion. However, the regulation of phytoalexin biosynthesis during grapevine against Pv is still unclear. Herein, we detected stilbenes by UPLC-ESI-MS/MS and found that resveratrol was accumulated to higher level and earlier in the DM-immune Muscadinia rotundifolia 'Noble' than that in the DM-susceptible Vitis vinifera 'Thompson Seedless' after Pv inoculation...
June 26, 2017: Protoplasma
https://www.readbyqxmd.com/read/28647924/comparative-expression-analysis-of-rice-and-arabidopsis-peroxiredoxin-genes-suggests-conserved-or-diversified-roles-between-the-two-species-and-leads-to-the-identification-of-tandemly-duplicated-rice-peroxiredoxin-genes-differentially-expressed-in-seeds
#15
Yun-Shil Gho, Sun-A Park, Sung-Ruyl Kim, Anil Kumar Nalini Chandran, Gynheung An, Ki-Hong Jung
BACKGROUND: Peroxiredoxins (PRXs) have recently been identified as plant antioxidants. Completion of various genome sequencing projects has provided genome-wide information about PRX genes in major plant species. Two of these -- Oryza sativa (rice) and Arabidopsis -- each have 10 PRX members. Although significant progress has been made in understanding their biological roles in Arabidopsis, those functions in rice, a model crop plant, have not been well studied. RESULTS: We performed a comparative expression analysis of rice and Arabidopsis PRXs...
December 2017: Rice
https://www.readbyqxmd.com/read/28639191/promoter-targeted-small-activating-rnas-alter-nucleosome-positioning
#16
Bin Wang, Yunzhang Hu
Epigenetic modification of target promoters has been identified as a mechanism underlying RNA activation (RNAa) induced by promoter-targeting small activating RNAs (saRNAs), but it is unclear how the chromosomal environment influences gene expression. In a study of the activation of the OCT4, SOX2, and NANOG genes by saRNAs, we found that saRNA targeting induced nucleosome-depleted region (NDRs) and the accumulation of RNA polymerase II (RNAPII) near or at the saRNA target sites. Additionally, promoters containing certain cis-regulatory elements such as the TATA box and CpG islands (CGIs) appeared to be more susceptible to RNAa...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28634199/characterising-cis-regulatory-variation-in-the-transcriptome-of-histologically-normal-and-tumour-derived-pancreatic-tissues
#17
Mingfeng Zhang, Soren Lykke-Andersen, Bin Zhu, Wenming Xiao, Jason W Hoskins, Xijun Zhang, Lauren M Rost, Irene Collins, Martijn van de Bunt, Jinping Jia, Hemang Parikh, Tongwu Zhang, Lei Song, Ashley Jermusyk, Charles C Chung, Bin Zhu, Weiyin Zhou, Gail L Matters, Robert C Kurtz, Meredith Yeager, Torben Heick Jensen, Kevin M Brown, Halit Ongen, William R Bamlet, Bradley A Murray, Mark I McCarthy, Stephen J Chanock, Nilanjan Chatterjee, Brian M Wolpin, Jill P Smith, Sara H Olson, Gloria M Petersen, Jianxin Shi, Laufey Amundadottir
OBJECTIVE: To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN: We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS: We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0...
June 20, 2017: Gut
https://www.readbyqxmd.com/read/28630892/disruption-of-the-axonal-trafficking-of-tyrosine-hydroxylase-mrna-impairs-catecholamine-biosynthesis-in-the-axons-of-sympathetic-neurons
#18
Armaz Aschrafi, Anthony E Gioio, Lijin Dong, Barry B Kaplan
Tyrosine hydroxylase (TH) is the enzyme that catalyzes the rate-limiting step in the biosynthesis of the catecholamine neurotransmitters. In a previous communication, evidence was provided that TH mRNA is trafficked to the axon, where it is locally translated. In addition, a 50-bp sequence element in the 3'untranslated region (3'UTR) of TH mRNA was identified that directs TH mRNA to distal axons (i.e., zip-code). In the present study, the hypothesis was tested that local translation of TH plays an important role in the biosynthesis of the catecholamine neurotransmitters in the axon and/or presynaptic nerve terminal...
May 2017: ENeuro
https://www.readbyqxmd.com/read/28630007/rna-localization-making-its-way-to-the-center-stage
#19
REVIEW
Ashley Chin, Eric Lécuyer
Cells are highly organized entities that rely on intricate addressing mechanisms to sort their constituent molecules to precise subcellular locations. These processes are crucial for cells to maintain their proper organization and carry out specialized functions in the body, consequently genetic perturbations that clog up these addressing systems can contribute to disease aetiology. The trafficking of RNA molecules represents an important layer in the control of cellular organization, a process that is both highly prevalent and for which features of the regulatory machineries have been deeply conserved evolutionarily...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28626890/transcriptomic-analysis-of-rice-aleurone-cells-identified-a-novel-abscisic-acid-response-element
#20
Kenneth A Watanabe, Arielle Homayouni, Lingkun Gu, Kuan-Ying Huang, Tuan-Hua David Ho, Qingxi J Shen
Seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (ABA). The ABA responsive element (ABRE) is a key cis-regulatory element in ABA signaling. However, its consensus sequence, (ACGTG(G/T)C), is present in the promoters of only about 40% of ABA induced genes in rice aleurone cells, suggesting other ABREs may exist. To identify novel ABREs, RNA-sequencing was performed on aleurone cells of rice seeds treated with 20 μM ABA. Gibbs sampling was used to identify enriched elements and particle bombardment-mediated transient expression studies were performed to verify the function...
June 18, 2017: Plant, Cell & Environment
keyword
keyword
68261
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"