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a cis-acting acting element in the promoter

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https://www.readbyqxmd.com/read/29778840/identification-of-a-novel-promoter-from-banana-aquaporin-family-gene-matip1-2-which-responses-to-drought-and-salt-stress-in-transgenic-arabidopsis-thaliana
#1
Shun Song, Yi Xu, Dongmei Huang, Hongxia Miao, Juhua Liu, Caihong Jia, Wei Hu, Ana Valeria Valarezo, Biyu Xu, Zhiqiang Jin
Drought and salt stresses often affect plant growth and crop yields. Identification of promoters involved in drought and salt stress responses is of great significance for genetic improvement of crop resistance. Our previous studies showed that aquaporin can respond to drought and salt stresses, but its promoter has not yet been reported in plants. In the present study, cis-acting elements of MaAQP family member promoters were systematically analyzed in banana. Expression of MaTIP1; 2 was induced by drought and salt stresses but not sensitive to cold stress, waterlogging stress, or mechanical damage, and its promoter contained five stress-related cis-acting elements...
May 17, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#2
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29772251/advances-of-dnase-seq-for-mapping-active-gene-regulatory-elements-across-the-genome-in-animals
#3
REVIEW
Ailing Chen, Daozhen Chen, Ying Chen
Expression of the eukaryotic genome is a highly complex and tightly regulated process, and its regulation depends on interactions among cis-acting elements and transcription factors. Identification of active gene regulatory elements is key to understanding transcriptional control of biological processes including differentiation, development, proliferation, cell-type specificity, and responses to the environment. DNase I hypersensitive sites (DHSs) are markers of open chromatin that provide a very effective method of targeting all types of cis-regulatory elements (CREs) including enhancers, promoters, insulators, silencers, and locus control regions...
May 14, 2018: Gene
https://www.readbyqxmd.com/read/29764390/delineation-of-condition-specific-cis-and-trans-acting-elements-in-plant-promoters-under-various-endo-and-exogenous-stimuli
#4
Chi-Nga Chow, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Han-Qin Zheng, Tzong-Yi Lee, Nai-Yun Wu, Kuan-Chieh Tseng, Ping-Fu Hou, Wen-Chi Chang
BACKGROUND: Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. RESULTS: Here, we developed a series of bioinformatics analysis methods to infer transcriptional regulation by using numerous gene expression data from abiotic stresses and hormones treatments...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29763523/role-of-basic-pentacysteiene-transcription-factors-in-a-sub-set-of-cytokinin-signaling-responses
#5
Carly M Shanks, Andreas Hecker, Chia-Yi Cheng, Luise Brand, Silvio Collani, Markus Schmid, G Eric Schaller, Dierk Wanke, Klaus Harter, Joseph J Kieber
Cytokinin plays diverse roles in plant growth and development, generally acting by modulating gene transcription in target tissues. The type-B ARR transcription factors have emerged as primary targets of cytokinin signaling and are required for essentially all cytokinin-mediated changes in gene expression. The diversity of cytokinin function is likely imparted by the activity of various transcription factors working with the type-B ARRs to alter specific sets of target genes. One potential set of co-regulators modulating the cytokinin response are the BARLEY B-RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC) family of plant-specific transcription factors...
May 15, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29743358/the-chromatin-remodeling-factor-spoc1-acts-as-a-cellular-restriction-factor-against-human-cytomegalovirus-by-repressing-the-major-immediate-early-promoter
#6
Anna Reichel, Anne-Charlotte Stilp, Myriam Scherer, Nina Reuter, Sören Lukassen, Bahram Kasmapour, Sabrina Schreiner, Luka Cicin-Sain, Andreas Winterpacht, Thomas Stamminger
The cellular protein SPOC1 (survival time-associated PHD finger protein in ovarian cancer 1) acts as a regulator of chromatin structure and DNA damage response. It binds H3K4me2/3 containing chromatin and promotes DNA condensation by recruiting corepressors such as KAP-1 and H3K9 methyltransferases. Previous studies identified SPOC1 as a restriction factor against human adenovirus (HAdV) infection that is antagonized by E1B-55K/E4orf6-dependent proteasomal degradation. Here, we demonstrate that, in contrast to HAdV-infected cells, SPOC1 is transiently upregulated during the early phase of HCMV replication...
May 9, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29739903/identification-of-the-intragenomic-promoter-controlling-hepatitis-e-virus-subgenomic-rna-transcription
#7
Qiang Ding, Ila Nimgaonkar, Nicholas F Archer, Yaron Bram, Brigitte Heller, Robert E Schwartz, Alexander Ploss
Approximately 20 million hepatitis E virus (HEV) infections occur annually in both developing and industrialized countries. Most infections are self-limiting, but they can lead to chronic infections and cirrhosis in immunocompromised patients, and death in pregnant women. The mechanisms of HEV replication remain incompletely understood due to scarcity of adequate experimental platforms. HEV undergoes asymmetric genome replication, but it produces an additional subgenomic (SG) RNA encoding the viral capsid and a viroporin in partially overlapping open reading frames...
May 8, 2018: MBio
https://www.readbyqxmd.com/read/29719500/valproic-acid-attenuates-traumatic-brain-injury-induced-inflammation-in-vivo-involvement-of-autophagy-and-the-nrf2-are-signaling-pathway
#8
Xiangrong Chen, Handong Wang, Mengliang Zhou, Xiang Li, Zhongning Fang, Hongzhi Gao, Yasong Li, Weipeng Hu
Microglial activation and the inflammatory response in the central nervous system (CNS) play important roles in secondary damage after traumatic brain injury (TBI). Transcriptional activation of genes that limit secondary damage to the CNS are mediated by a cis-acting element called the antioxidant responsive element (ARE). ARE is known to associate with the transcription factor NF-E2-related factor 2 (Nrf2), a transcription factor that is associated with histone deacetylases (HDACs). This pathway, known as the Nrf2/ARE pathway, is a critical antioxidative factor pathway that regulates the balance of oxygen free radicals and the inflammatory response, and is also related to autophagic activities...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29706982/an-apetala2-homolog-rcap2-regulates-the-number-of-rose-petals-derived-from-stamens-and-response-to-temperature-fluctuations
#9
Yu Han, Aoying Tang, Huihua Wan, Tengxun Zhang, Tangren Cheng, Jia Wang, Weiru Yang, Huitang Pan, Qixiang Zhang
Rosa chinensis , which is a famous traditional flower in China, is a major ornamental plant worldwide. Long-term cultivation and breeding have resulted in considerable changes in the number of rose petals, while most wild Rosaceae plants have only one whorl consisting of five petals. The petals of double flowers reportedly originate from stamens, but the underlying molecular mechanism has not been fully characterized. In this study, we observed that the number of petals of R. chinensis 'Old Blush' flowers increased and decreased in response to low- and high-temperature treatments, respectively, similar to previous reports...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29705570/three-members-of-medicago-truncatula-st-family-mtst4-mtst5-and-mtst6-are-specifically-induced-by-hormones-involved-in-biotic-interactions
#10
Lucía Albornos, Ignacio Martín, Josefina Hernández-Nistal, Emilia Labrador, Berta Dopico
In this work, we study the function of the Medicago truncatula ST4, ST5 and ST6 proteins that belong to a protein family of unknown function characterized by the DUF2775 domain. Thus, we analyse their promoter sequence and activity, their transcript accumulation, and their subcellular location. The analysis of the three promoters showed different combination of cis-acting regulatory elements and they presented different activity pattern. Throughout development only ST6 mRNAs have been detected in most of the stages analysed, while ST4 was faintly detected in the roots and in the flowers and ST5 was always absent...
April 21, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29703137/genome-wide-identification-of-the-auxin-response-factor-gene-family-in-cicer-arietinum
#11
Jose V Die, Juan Gil, Teresa Millan
BACKGROUND: Auxin Response Factors act as critical components of the auxin-signaling pathway by regulating the transcription of auxin-responsive genes. The release of the chickpea reference genome provides an opportunity to identify and characterize the ARF gene family in this important legume by a data mining coupled by comparative genomics approaches. RESULTS: We performed a comprehensive characterization and analysis of 24 ARF genes in the chickpea reference genome...
April 27, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29684486/contribution-of-transposable-elements-in-the-plant-s-genome
#12
REVIEW
Mahbod Sahebi, Mohamed M Hanafi, Andre J van Wijnen, David Rice, M Y Rafii, Parisa Azizi, Mohamad Osman, Sima Taheri, Mohd Faizal Abu Bakar, Mohd Noor Mat Isa, Yusuf Muhammad Noor
Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes...
April 20, 2018: Gene
https://www.readbyqxmd.com/read/29666351/sp1-is-an-important-transcriptional-regulation-factor-for-forkhead-box-n1-in-pig
#13
Dong Jie Zhang, Liang Wang, Zhong Qiu Li, Bo Fu, Guo Wei Yang
The transcription factor forkhead box N1 (Foxn1) plays an important role in the development and function of thymic epithelial cells (TECs) in vertebrates. However, the transcriptional regulation of Foxn1 is still unknown. A series of dual luciferase report vectors were constructed and their relative activities were also detected. The 5'-untranslated regions contains two cis-acting elements, Sp1 and GATA-1, as well as trans-acting elements between positions -332 to -438. Nevertheless, the relative activities of Foxn1 promoter were significantly increased in PK15 cells only when the Sp1 was overexpressed, suggesting that the Sp1 was the most important sequence for Foxn1 transcription activation in the pig...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29665088/gain-of-function-analysis-of-cis-acting-diversification-elements-in-dt40-cells
#14
Randolph B Caldwell, Herbert Braselmann, Steffen Heuer, Ulrike Schötz, Horst Zitzelsberger
Activation-induced cytidine deaminase (AID) is required for the immunoglobulin diversification processes of somatic hypermutation, gene conversion and class-switch recombination. The targeting of AID's deamination activity is thought to be a combination of cis- and trans-acting elements, but has not been fully elucidated. Deletion analysis of putative proximal cis-regulatory motifs, while helpful, fails to identify additive versus cumulative effects, redundancy, and may create new motifs where none previously existed...
April 17, 2018: Immunology and Cell Biology
https://www.readbyqxmd.com/read/29655791/overexpression-of-a-repressor-mdmyb15l-negatively-regulates-anthocyanin-and-cold-tolerance-in-red-fleshed-callus
#15
Haifeng Xu, Guanxian Yang, Jing Zhang, Yicheng Wang, Tianliang Zhang, Nan Wang, Shenghui Jiang, Zongying Zhang, Xuesen Chen
The cold-induced metabolic pathway and anthocyanin biosynthesis play important roles in plant growth. In this study, we identified a bHLH binding motif in the MdMYB15L protein using protein sequence analyses. Yeast two-hybrid and pull-down assays showed that MdMYB15L could interact with MdbHLH33. Overexpressing MdMYB15L in red-fleshed callus inhibited the expression of MdCBF2 and resulted in reduced cold tolerance but did not affect anthocyanin levels. Chip-PCR and EMSA analysis showed that MdMYB15L could bind the type II cis-acting element found in the MdCBF2 promoter...
April 12, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29650551/hnrnpa1-promotes-recognition-of-splice-site-decoys-by-u2af2-in-vivo
#16
Jonathan M Howard, Hai Lin, Andrew J Wallace, Garam Kim, Jolene M Draper, Maximilian Haeussler, Sol Katzman, Masoud Toloue, Yunlong Liu, Jeremy R Sanford
Alternative pre-mRNA splicing plays a major role in expanding the transcript output of human genes. This process is regulated, in part, by the interplay of trans -acting RNA binding proteins (RBPs) with myriad cis -regulatory elements scattered throughout pre-mRNAs. These molecular recognition events are critical for defining the protein-coding sequences (exons) within pre-mRNAs and directing spliceosome assembly on noncoding regions (introns). One of the earliest events in this process is recognition of the 3' splice site (3'ss) by U2 small nuclear RNA auxiliary factor 2 (U2AF2)...
April 12, 2018: Genome Research
https://www.readbyqxmd.com/read/29621331/a-gossypium-hirsutum-gdsl-lipase-hydrolase-gene-ghglip-appears-to-be-involved-in-promoting-seed-growth-in-arabidopsis
#17
Rendi Ma, Hali Yuan, Jing An, Xiaoyun Hao, Hongbin Li
GDSL lipase (GLIP) plays a pivotal role in plant cell growth as a multifunctional hydrolytic enzyme. Herein, a cotton (Gossypium hirsutum L. cv Xuzhou 142) GDSL lipase gene (GhGLIP) was obtained from developing ovules and fibers. The GhGLIP cDNA contained an open reading frame (ORF) of 1,143 base pairs (bp) and encodes a putative polypeptide of 380 amino acid residues. Sequence alignment indicated that GhGLIP includes four enzyme catalytic amino acid residue sites of Ser (S), Gly (G), Asn (N) and His (H), located in four conserved blocks...
2018: PloS One
https://www.readbyqxmd.com/read/29618383/high-efficiency-promoter-driven-coordinated-regulation-of-multiple-metabolic-nodes-elevates-lipid-accumulation-in-the-model-microalga-phaeodactylum-tricornutum
#18
Li-Gong Zou, Jia-Wen Chen, Dan-Lin Zheng, Srinivasan Balamurugan, Da-Wei Li, Wei-Dong Yang, Jie-Sheng Liu, Hong-Ye Li
BACKGROUND: Microalgal metabolic engineering holds great promise for the overproduction of a wide range of commercial bioproducts. It demands simultaneous manipulation of multiple metabolic nodes. However, high-efficiency promoters have been lacking. RESULTS: Here we report a strong constitutive promoter Pt211 in expressing multiple target genes in oleaginous microalga Phaeodactylum tricornutum. Pt211 was revealed to contain significant cis-acting elements. GUS reporter and principal genes glycerol-3-phosphate acyltransferase (GPAT) and diacylglycerol acyltransferase 2 (DGAT2) involved in triacylglycerol biosynthesis were tested under driven of Pt211 in P...
April 4, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29606212/review-plant-g-quadruplex-g4-motifs-in-dna-and-rna-abundant-intriguing-sequences-of-unknown-function
#19
REVIEW
Brianna D Griffin, Hank W Bass
DNA sequences capable of forming G-quadruplex (G4) structures can be predicted and mapped in plant genomes using computerized pattern search programs. Non-telomeric G4 motifs have recently been found to number in the thousands across many plant species and enriched around gene promoters, prompting speculation that they may represent a newly uncovered and ubiquitous family of cis-acting elements. Comparative analysis shows that monocots exhibit five to ten times higher G4 motif density than eudicots, but the significance of this difference has not been determined...
April 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29558271/phytoremediation-of-petroleum-contaminated-soil-by-salicornia-from-psy-activity-to-physiological-and-morphological-communications
#20
Tayebe Abdollahzadeh, Ali Niazi, Ali Moghadam, Zohreh Heydarian, Reza Ghasemi-Fasaei, Elina Kaviani, Neda Pourdad
Petroleum compounds are considered as one of the critical environmental pollutants. Salicornia can grow in petroleum-contaminated soil. Therefore, the potential of two Iranian Salicornia species, S. persica Akhani and S. iranica Akhani, for phytoremediation of soils contaminated with 0.2% and 2% petroleum contaminations was evaluated over the short (1 and 10 h) and long (100 days) periods of time. In addition, some key factors involved in phytoremediation including the expression analysis of phytoene synthase, physiological and morphological factors were studied...
March 20, 2018: Environmental Technology
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