keyword
MENU ▼
Read by QxMD icon Read
search

cis-regulatory elements

keyword
https://www.readbyqxmd.com/read/29329783/comparative-genome-based-cis-elements-analysis-in-the-5-upstream-and-3-downstream-region-of-cell-wall-invertase-and-phenylalanine-ammonia-lyase-in-nicotiana-benthamiana
#1
S A Sheshadri, M J Nishanth, N Harita, P Brindha, S Bindu
Plant secondary metabolites are widely used in human disease treatment; though primary metabolism provides precursors for secondary metabolism, not much has been studied to unravel the link connecting both the processes. Most common form of gene regulation interconnecting diverse metabolism occurs at the transcriptional and/or posttranscriptional level mediated by regulatory cis-elements. The present study aims at understanding the common cis-elements network connecting the major primary metabolic enzyme, cell wall invertase (CWIN) and secondary metabolism genes in Nicotiana benthamiana (N...
November 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29327227/structural-characterization-of-a-novel-full-length-transcript-promoter-from-horseradish-latent-virus-hrlv-and-its-transcriptional-regulation-by-multiple-stress-responsive-transcription-factors
#2
Ahamed Khan, Ankita Shrestha, Kashyap Bhuyan, Indu B Maiti, Nrisingha Dey
The promoter fragment described in this study can be employed for strong transgene expression under both biotic and abiotic stress conditions. Plant-infecting Caulimoviruses have evolved multiple regulatory mechanisms to address various environmental stimuli during the course of evolution. One such mechanism involves the retention of discrete stress responsive cis-elements which are required for their survival and host-specificity. Here we describe the characterization of a novel Caulimoviral promoter isolated from Horseradish Latent Virus (HRLV) and its regulation by multiple stress responsive Transcription factors (TFs) namely DREB1, AREB1 and TGA1a...
January 11, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/29324742/functional-characterization-of-adaptive-variation-within-a-cis-regulatory-element-influencing-drosophila-melanogaster-growth
#3
Amanda Glaser-Schmitt, John Parsch
Gene expression variation is a major contributor to phenotypic diversity within species and is thought to play an important role in adaptation. However, examples of adaptive regulatory polymorphism are rare, especially those that have been characterized at both the molecular genetic level and the organismal level. In this study, we perform a functional analysis of the Drosophila melanogaster CG9509 enhancer, a cis-regulatory element that shows evidence of adaptive evolution in populations outside the species' ancestral range in sub-Saharan Africa...
January 11, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29313187/allelic-variants-of-ossub1a-cause-differential-expression-of-transcription-factor-genes-in-response-to-submergence-in-rice
#4
Niharika Sharma, Trang Minh Dang, Namrata Singh, Slobodan Ruzicic, Bernd Mueller-Roeber, Ute Baumann, Sigrid Heuer
BACKGROUND: Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2...
January 8, 2018: Rice
https://www.readbyqxmd.com/read/29305858/identification-of-a-candidate-enhancer-for-dmrt3-involved-in-spastic-cerebral-palsy-pathogenesis
#5
Naoto Kubota, Toshifumi Yokoyama, Nobuhiko Hoshi, Mikita Suyama
Cerebral palsy (CP) is a major neuronal disease and the most common movement disorder in children. Although environmental factors leading to CP have been greatly investigated, the genetic mechanism underlying CP is not well understood. Here we focused on two clinical reports that characterized a deletion involving the KANK1 gene locus in the 9p24.3 region. One report shows spastic CP and the other shows no spastic CP phenotype. Based on the epigenetic status and evolutionary conservation, we first found a functional genomic element at the noncoding region that was deleted only in patients with spastic CP...
January 3, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29304737/rnaseq-analysis-of-%C3%AE-proteobacterium-gluconobacter-oxydans-621h
#6
Angela Kranz, Tobias Busche, Alexander Vogel, Björn Usadel, Jörn Kalinowski, Michael Bott, Tino Polen
BACKGROUND: The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. The metabolism of this α-proteobacterium has been characterized to some extent, yet little is known about its transcriptomes and related data. In this study, we applied two different RNAseq approaches. Primary transcriptomes enriched for 5'-ends of transcripts were sequenced to detect transcription start sites, which allow subsequent analysis of promoter motifs, ribosome binding sites, and 5´-UTRs...
January 6, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29304382/transcriptional-regulation-of-chickpea-ferritin-cafer1-influences-its-role-in-iron-homeostasis-and-stress-response
#7
Shaista Parveen, Aarti Pandey, Neha Jameel, Subhra Chakraborty, Niranjan Chakraborty
Ferritin, ubiquitous among all living organisms except yeast, exhibits iron-regulated expression. In plants, this regulation is applied through transcriptional control. Previous studies established the presence of two types of cis-acting elements in the promoter region: the iron regulatory element (FRE) in soybean and the iron-dependent regulatory sequence (IDRS) in maize and Arabidopsis. Adverse environmental conditions (e.g. water-deficit and oxidative stress) are known to modulate the expression of phytoferritin genes...
December 27, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29298993/two-genetic-changes-in-cis-regulatory-elements-caused-evolution-of-petal-spot-position-in-clarkia
#8
Peng Jiang, Mark Rausher
A major premise in evolutionary developmental biology is that regulatory changes, often involving cis-regulatory elements, are responsible for much morphological evolution. This premise is supported by recent investigations of animal development, but information is just beginning to accumulate regarding whether it also applies to the evolution of plant morphology1-4. Here, we identify the genetic differences between species in the genus Clarkia that are responsible for evolutionary change in an ecologically important element of floral colour patterns: spot position...
January 3, 2018: Nature Plants
https://www.readbyqxmd.com/read/29298348/computational-exploration-of-cis-regulatory-modules-in-rhythmic-expression-data-using-the-exploration-of-distinctive-cres-and-crms-edcc-and-crm-network-generator-cng-programs
#9
Pavlos Stephanos Bekiaris, Tobias Tekath, Dorothee Staiger, Selahattin Danisman
Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, "Exploration of Distinctive CREs and CRMs" (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns...
2018: PloS One
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
#10
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/29285248/super-enhancer-associated-rai14-is-a-new-potential-biomarker-in-lung-adenocarcinoma
#11
Chongze Yuan, Hong Hu, Muyu Kuang, Zongwei Chen, Xiaoting Tao, Shengjian Fang, Yihua Sun, Yawei Zhang, Haiquan Chen
Purpose: Tyrosine kinase inhibitors (TKIs) are widely used to treat lung adenocarcinoma patients with EGFR mutations or ALK-fusions. However, patients with wild-type genes or TKIs-resistant mutations lack effective therapeutic targets. Extensive studies reveal that super enhancer (SE), a large cis-regulatory element, is associated with key oncogenes in a variety of cancers. By comparing the effect of SE on lung adenocarcinoma cell lines with normal cell line, this work attempts to find new biomarkers and potential therapeutic targets for lung adenocarcinoma...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29281032/zmwrky79-positively-regulates-maize-phytoalexin-biosynthetic-gene-expression-and-is-involved-in-stress-response
#12
Jingye Fu, Qin Liu, Chang Wang, Jin Liang, Lijun Liu, Qiang Wang
Maize (Zea mays) accumulates maize terpenoid phytoalexins (MTPs), kauralexins and zealexins in response to various elicitations. Although the key biosynthetic genes for these have been characterized, the regulatory mechanism remains unclear. Through co-correlation analysis, a transcription factor (TF), ZmWRKY79, was identified as highly correlated with expression of MTP biosynthetic genes. Gene expression analysis indicated that ZmWRKY79 was induced by Fusarium graminearum infection, phytohormone treatment, and multiple stresses...
December 21, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29277877/comparative-genomics-in-drosophila
#13
Martin Oti, Attilio Pane, Michael Sammeth
Since the pioneering studies of Thomas Hunt Morgan and coworkers at the dawn of the twentieth century, Drosophila melanogaster and its sister species have tremendously contributed to unveil the rules underlying animal genetics, development, behavior, evolution, and human disease. Recent advances in DNA sequencing technologies launched Drosophila into the post-genomic era and paved the way for unprecedented comparative genomics investigations. The complete sequencing and systematic comparison of the genomes from 12 Drosophila species represents a milestone achievement in modern biology, which allowed a plethora of different studies ranging from the annotation of known and novel genomic features to the evolution of chromosomes and, ultimately, of entire genomes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29274956/epigenetic-mechanisms-contribute-to-decrease-stearoyl-coa-desaturase-1-expression-in-the-liver-of-dairy-cows-after-prolonged-feeding-of-high-concentrate-diet
#14
T L Xu, H M Seyfert, X Z Shen
Subacute ruminal acidosis (SARA) of dairy cattle is a widely occurring but not very overt metabolic disorder thought to impair milk composition. The enzyme stearoyl-CoA desaturase 1 (SCD1) is rate-limiting for the formation of Δ-9 unsaturated fatty acids and thus crucially involved in controlling lipid metabolism in the liver. It is known that SCD1 expression is downregulated during SARA, but the underlying molecular mechanisms are unknown. To study these mechanisms, we enrolled 12 healthy multiparous mid-lactation Holstein cows into a diet-induced SARA experiment...
December 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29274230/crispr-cas9-and-active-genetics-based-trans-species-replacement-of-the-endogenous-drosophilakni-l2-crm-reveals-unexpected-complexity
#15
Xiang-Ru Shannon Xu, Valentino Matteo Gantz, Natalia Siomava, Ethan Bier
The knirps (kni) locus encodes transcription factors required for induction of the L2 wing vein in Drosophila. Here, we employ diverse CRISPR/Cas9 genome editing tools to generate a series of targeted lesions within the endogenous cis-regulatory module (CRM) required for kni expression in the L2 vein primordium. Phenotypic analysis of these 'in locus' mutations based on both expression of Kni protein and adult wing phenotypes, reveals novel unexpected features of L2-CRM function including evidence for a chromosome pairing-dependent process that promotes transcription...
December 23, 2017: ELife
https://www.readbyqxmd.com/read/29273966/molecular-characterization-of-amic-a-positive-regulator-in-acetamidase-operon-of-mycobacterium-smegmatis
#16
Arunkumar Venkatesan, Kannan Palaniyandi, Sujatha Narayanan
Mycobacterium smegmatis, a rapidly growing non-pathogenic mycobacterium, is currently used as a model organism to study mycobacterial genetics. Acetamidase of M. smegmatis is the highly inducible enzyme of Mycobacteria, which utilizes several amide compounds as sole carbon and nitrogen sources. The acetamidase operon has a complex regulatory mechanism, which involves three regulatory proteins, four promoters, and three operator elements. In our previous study, we showed that over-expression of AmiA leads to a negative regulation of acetamidase by blocking the P2 promoter...
December 22, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/29259885/isolation-and-characterization-of-systemic-acquired-resistance-marker-gene-pr1-and-its-promoter-from-brassica-juncea
#17
Sajad Ali, Zahoor Ahmad Mir, Javaid Akhter Bhat, Anshika Tyagi, N Chandrashekar, Prashant Yadav, Sandhya Rawat, Mazher Sultana, Anita Grover
Systemic acquired resistance (SAR) is an inducible defense response in plants that provides enhanced resistance against a variety of pathogens. In this regard, SAR marker gene PR1 (pathogenesis-related gene 1) was isolated from Brassica juncea and was named as BjPR1. The amino acid sequence of BjPR1 protein showed 99, 92, and 78% similarity with known PR1 proteins of Brassica rapa, Brassica napus, and Arabidopsis thaliana, respectively. Quantitative real-time PCR (qRT-PCR) analysis showed increased expression of BjPR1 gene both in local (infected) and distal (non-infected) leaves of B...
January 2018: 3 Biotech
https://www.readbyqxmd.com/read/29250708/identification-characterization-expression-profiling-and-virus-induced-gene-silencing-of-armadillo-repeat-containing-proteins-in-tomato-suggest-their-involvement-in-tomato-leaf-curl-new-delhi-virus-resistance
#18
Arunava Mandal, Awdhesh Kumar Mishra, Priya Dulani, Mehanathan Muthamilarasan, Shweta Shweta, Manoj Prasad
Armadillo repeat family is well-characterized in several plant species for their involvement in multiple regulatory processes including growth, development, and stress response. We have previously shown a three-fold higher expression of ARM protein-encoding in tomato cultivar tolerant to tomato leaf curl New Delhi virus (ToLCNDV) compared to susceptible cultivar upon virus infection. This suggests the putative involvement of ARM proteins in defense response against virus infection; however, no comprehensive investigation has been performed to address this inference...
December 17, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29246441/roquin-suppresses-the-pi3k-mtor-signaling-pathway-to-inhibit-t-helper-cell-differentiation-and-conversion-of-treg-to-tfr-cells
#19
Katharina Essig, Desheng Hu, Joao C Guimaraes, Dominik Alterauge, Stephanie Edelmann, Timsse Raj, Jan Kranich, Gesine Behrens, Alexander Heiseke, Stefan Floess, Juliane Klein, Andreas Maiser, Susan Marschall, Martin Hrabĕ de Angelis, Heinrich Leonhardt, Cornelis F Calkhoven, Elfriede Noessner, Thomas Brocker, Jochen Huehn, Anne B Krug, Mihaela Zavolan, Dirk Baumjohann, Vigo Heissmeyer
Roquin proteins preclude spontaneous T cell activation and aberrant differentiation of T follicular helper (Tfh) or T helper 17 (Th17) cells. Here we showed that deletion of Roquin-encoding alleles specifically in regulatory T (Treg) cells also caused the activation of conventional T cells. Roquin-deficient Treg cells downregulated CD25, acquired a follicular Treg (Tfr) cell phenotype, and suppressed germinal center reactions but could not protect from colitis. Roquin inhibited the PI3K-mTOR signaling pathway by upregulation of Pten through interfering with miR-17∼92 binding to an overlapping cis-element in the Pten 3' UTR, and downregulated the Foxo1-specific E3 ubiquitin ligase Itch...
December 12, 2017: Immunity
https://www.readbyqxmd.com/read/29241563/two-metallocarboxypeptidase-inhibitors-are-implicated-in-tomato-fruit-development-and-regulated-by-the-inner-no-outer-transcription-factor
#20
B Molesini, G L Rotino, V Dusi, R Chignola, T Sala, G Mennella, G Francese, T Pandolfini
The TCMP-1 and TCMP-2 genes of tomato code for metallocarboxypeptidase inhibitors and show sequential, tightly regulated expression patterns during flower and fruit development. In particular, TCMP-1 is highly expressed in flower buds before anthesis, while TCMP-2 in ripe fruits. Their expression pattern suggests that they might play a role in fruit development. Here, to investigate their function, we altered their endogenous levels by generating transgenic plants harbouring a chimeric gene expressing the TCMP-1 coding sequence under the control of the TCMP-2 promoter...
January 2018: Plant Science: An International Journal of Experimental Plant Biology
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"