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a cis-acting acting element in the promoter

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https://www.readbyqxmd.com/read/28407294/altered-tert-promoter-and-other-genomic-regulatory-elements-occurrence-and-impact
#1
Barbara Heidenreich, Rajiv Kumar
Study of genetic alterations, inherited or acquired, that increase the risk or drive cancers and many other diseases had remained mostly confined to coding sequences of the human genome. Data from genome wide associations studies, development of the Encyclopedia of DNA Elements (ENCODE), and a spurt in detection of driver somatic mutations have shifted focus towards noncoding regions of the human genome. The majority of genetic variants robustly associated with cancers and other syndromes identified through genome wide studies are located within noncoding regulatory regions of the genome...
April 13, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28389698/evolution-of-the-duplicated-intracellular-lipid-binding-protein-genes-of-teleost-fishes
#2
REVIEW
Ananda B Venkatachalam, Manoj B Parmar, Jonathan M Wright
Increasing organismal complexity during the evolution of life has been attributed to the duplication of genes and entire genomes. More recently, theoretical models have been proposed that postulate the fate of duplicated genes, among them the duplication-degeneration-complementation (DDC) model. In the DDC model, the common fate of a duplicated gene is lost from the genome owing to nonfunctionalization. Duplicated genes are retained in the genome either by subfunctionalization, where the functions of the ancestral gene are sub-divided between the sister duplicate genes, or by neofunctionalization, where one of the duplicate genes acquires a new function...
April 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28367152/genome-wide-identification-evolution-and-expression-analysis-of-the-atp-binding-cassette-transporter-gene-family-in-brassica-rapa
#3
Chao Yan, Weike Duan, Shanwu Lyu, Ying Li, Xilin Hou
ATP-binding cassette (ABC) proteins can act as transporters of different substrates across biological membranes by hydrolyzing ATP. However, little information is available about ABC transporters in Brassica rapa, an important leafy vegetable. In the present study, we carried out genome-wide identification, characterization and molecular evolution analyses of ABC gene family in B. rapa and 9 other plant species. A total of 179 B. rapa ABC genes (BraABCs) were identified. Among them, 173 BraABCs were identified on 10 chromosomes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28363779/genome-wide-analysis-and-expression-profiling-of-the-grf-gene-family-in-oilseed-rape-brassica-napus-l
#4
Jin-Qi Ma, Hong-Ju Jian, Bo Yang, Kun Lu, Ao-Xiang Zhang, Pu Liu, Jia-Na Li
Growth regulating-factors (GRFs) are plant-specific transcription factors that help regulate plant growth and development. Genome-wide identification and evolutionary analyses of GRF gene families have been performed in Arabidopsis thaliana, Zea mays, Oryza sativa, and Brassica rapa, but a comprehensive analysis of the GRF gene family in oilseed rape (Brassica napus) has not yet been reported. In the current study, we identified 35 members of the BnGRF family in B. napus. We analyzed the chromosomal distribution, phylogenetic relationships (Bayesian Inference and Neighbor Joining method), gene structures, and motifs of the BnGRF family members, as well as the cis-acting regulatory elements in their promoters...
March 28, 2017: Gene
https://www.readbyqxmd.com/read/28345627/heterologous-protein-dna-interactions-lead-to-biased-allelic-expression-of-circadian-clock-genes-in-interspecific-hybrids
#5
Danny W-K Ng, Helen H Y Chen, Z Jeffrey Chen
Genomic interactions in allopolyploids create expression variation of homoeologous alleles through protein-protein and protein-DNA interactions. However, the molecular basis for this is largely unknown. Here we investigated the protein-protein and protein-DNA interactions among homoeologous transcription factors in the circadian-clock feedback loop, consisting of CCA1 HIKING EXPEDITION (CHE), CIRCADIAN CLOCK ASSOCIATED1 (CCA1), and TIMING OF CAB EXPRESSION1 (TOC1), plus the interaction with a chromatin factor, HISTONE DEACETYLASE1 (HD1)...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28341984/combinatorial-requirement-of-w-and-wt-boxes-in-microbe-associated-molecular-pattern-responsive-synthetic-promoters
#6
Konstantin Kanofsky, Ann-Kathrin Bahlmann, Reinhard Hehl, Do Xuan Dong
The WT-box GGACTTTC belongs to a novel class of MAMP-responsive cis-regulatory sequences that are part of combinatorial elements. Microbe-associated molecular pattern (MAMP)-responsive synthetic promoters were generated with two cis-regulatory modules (CRM1 and CRM2) from the Arabidopsis thaliana WRKY30 promoter. Both modules harbour two W-boxes and one WT-box. Mutation analysis of the synthetic promoters and transient gene expression analysis in parsley protoplasts underline the importance of the W- and WT-boxes for MAMP-responsive gene expression and reveal the combinatorial requirement of at least two boxes for full MAMP responsivity...
March 24, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28339724/three-cis-regulatory-motifs-auxre-mycrs1-and-mycrs2-are-required-for-modulating-the-auxin-and-mycorrhiza-responsive-expression-of-a-tomato-gh3-gene
#7
Xiao Chen, Dehua Liao, Xiaofeng Yang, Minjie Ji, Shuangshuang Wang, Mian Gu, Aiqun Chen, Guohua Xu
Auxin is well known to be a key regulator that acts in almost all physiological processes during plant growth, and in interactions between plants and microbes. However, to date, the regulatory mechanisms underlying auxin-mediated plant-arbuscular mycorrhizal (AM) fungi symbiosis have not been well deciphered. Previously we identified a GH3 gene, SlGH3.4, strongly responsive to both auxin induction and mycorrhizal symbiosis. Here, we reported a refined dissection of the SlGH3.4 promoter activity using the β-glucuronidase (GUS) reporter...
April 1, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28332702/the-mtp1-promoters-from-arabidopsis-halleri-reveal-cis-regulating-elements-for-the-evolution-of-metal-tolerance
#8
Elisa Fasani, Giovanni DalCorso, Claudio Varotto, Mingai Li, Giovanna Visioli, Monica Mattarozzi, Antonella Furini
In the hyperaccumulator Arabidopsis halleri, the zinc (Zn) vacuolar transporter MTP1 is a key component of hypertolerance. Because protein sequences and functions are highly conserved between A. halleri and Arabidopsis thaliana, Zn tolerance in A. halleri may reflect the constitutively higher MTP1 expression compared with A. thaliana, based on copy number expansion and different cis regulation. Three MTP1 promoters were characterized in A. halleri ecotype I16. The comparison with the A. thaliana MTP1 promoter revealed different expression profiles correlated with specific cis-acting regulatory elements...
March 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28293251/an-active-mitochondrial-complex-ii-present-in-mature-seeds-contains-an-embryo-specific-iron-sulfur-subunit-regulated-by-aba-and-bzip53-and-is-involved-in-germination-and-seedling-establishment
#9
Franko Restovic, Roberto Espinoza-Corral, Isabel Gómez, Jesús Vicente-Carbajosa, Xavier Jordana
Complex II (succinate dehydrogenase) is an essential mitochondrial enzyme involved in both the tricarboxylic acid cycle and the respiratory chain. In Arabidopsis thaliana, its iron-sulfur subunit (SDH2) is encoded by three genes, one of them (SDH2.3) being specifically expressed during seed maturation in the embryo. Here we show that seed SDH2.3 expression is regulated by abscisic acid (ABA) and we define the promoter region (-114 to +49) possessing all the cis-elements necessary and sufficient for high expression in seeds...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28265276/abscisic-acid-signaling-and-abiotic-stress-tolerance-in-plants-a-review-on-current-knowledge-and-future-prospects
#10
REVIEW
Kanchan Vishwakarma, Neha Upadhyay, Nitin Kumar, Gaurav Yadav, Jaspreet Singh, Rohit K Mishra, Vivek Kumar, Rishi Verma, R G Upadhyay, Mayank Pandey, Shivesh Sharma
Abiotic stress is one of the severe stresses of environment that lowers the growth and yield of any crop even on irrigated land throughout the world. A major phytohormone abscisic acid (ABA) plays an essential part in acting toward varied range of stresses like heavy metal stress, drought, thermal or heat stress, high level of salinity, low temperature, and radiation stress. Its role is also elaborated in various developmental processes including seed germination, seed dormancy, and closure of stomata. ABA acts by modifying the expression level of gene and subsequent analysis of cis- and trans-acting regulatory elements of responsive promoters...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28263861/proximity-of-radiation-desiccation-response-motif-to-the-core-promoter-is-essential-for-basal-repression-as-well-as-gamma-radiation-induced-gyrb-gene-expression-in-deinococcus-radiodurans
#11
Narasimha Anaganti, Bhakti Basu, Rita Mukhopadhyaya, Shree Kumar Apte
The radioresistant D. radiodurans regulates its DNA damage regulon (DDR) through interaction between a 17bp palindromic cis-regulatory element called the Radiation Desiccation Response Motif (RDRM), the DdrO repressor and a protease IrrE. The role of RDRM in regulation of DDR was dissected by constructing RDRM sequence-, position- or deletion-variants of Deinococcal gyrB gene (DR0906) promoter and by RDRM insertion in the non-RDRM groESL gene (DR0606) promoter, and monitoring the effect of such modifications on the basal as well as gamma radiation inducible promoter activity by quantifying fluorescence of a GFP reporter...
June 5, 2017: Gene
https://www.readbyqxmd.com/read/28256531/repression-of-human-t-lymphotropic-virus-type-1-long-terminal-repeat-sense-transcription-by-sp1-recruitment-to-novel-sp1-binding-sites
#12
Sylvain Fauquenoy, Gwenaëlle Robette, Anna Kula, Caroline Vanhulle, Sophie Bouchat, Nadège Delacourt, Anthony Rodari, Céline Marban, Christian Schwartz, Arsène Burny, Olivier Rohr, Benoit Van Driessche, Carine Van Lint
Human T-lymphotropic Virus type 1 (HTLV-1) infection is characterized by viral latency in the majority of infected cells and by the absence of viremia. These features are thought to be due to the repression of viral sense transcription in vivo. Here, our in silico analysis of the HTLV-1 Long Terminal Repeat (LTR) promoter nucleotide sequence revealed, in addition to the four Sp1 binding sites previously identified, the presence of two additional potential Sp1 sites within the R region. We demonstrated that the Sp1 and Sp3 transcription factors bound in vitro to these two sites and compared the binding affinity for Sp1 of all six different HTLV-1 Sp1 sites...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28246387/functional-characterization-of-populus-psnshn2-in-coordinated-regulation-of-secondary-wall-components-in-tobacco
#13
Yingying Liu, Minjing Wei, Cong Hou, Tingting Lu, Lulu Liu, Hairong Wei, Yuxiang Cheng, Zhigang Wei
Wood formation is a biological process during which the most abundant lignocellulosic biomass on earth is produced. Although a number of transcription factors have been linked to the regulation of wood formation process, none of them has been demonstrated to be a higher hierarchical regulator that coordinately regulates secondary wall biosynthesis genes. Here, we identified a Populus gene, PsnSHN2, a counterpart of the Arabidopsis AP2/ERF type transcription factor, SHINE2. PsnSHN2 is predominantly expressed in xylem tissues and acted evidently as a high hierarchical transcriptional activator...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223997/melatonin-regulates-root-architecture-by-modulating-auxin-response-in-rice
#14
Chengzhen Liang, Aifu Li, Hua Yu, Wenzhen Li, Chengzhi Liang, Sandui Guo, Rui Zhang, Chengcai Chu
It has been suggested that melatonin acts as an important regulator in controlling root growth and development, but the underlying molecular mechanism driving this relationship remains undetermined. In this study, we demonstrated that melatonin acts as a potent molecule to govern root architecture in rice. Treatments with melatonin significantly inhibited embryonic root growth, and promoted lateral root formation and development. Genome-wide expression profiling by RNA-sequencing revealed auxin-related genes were significantly activated under melatonin treatment...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28216629/matrix-attachment-region-combinations-increase-transgene-expression-in-transfected-chinese-hamster-ovary-cells
#15
Chun-Peng Zhao, Xiao Guo, Si-Jia Chen, Chang-Zheng Li, Yun Yang, Jun-He Zhang, Shao-Nan Chen, Yan-Long Jia, Tian-Yun Wang
Matrix attachment regions (MARs) are cis-acting DNA elements that can increase transgene expression levels in a CHO cell expression system. To investigate the effects of MAR combinations on transgene expression and the underlying regulatory mechanisms, we generated constructs in which the enhanced green fluorescent protein (eGFP) gene flanked by different combinations of human β-interferon and β-globin MAR (iMAR and gMAR, respectively), which was driven by the cytomegalovirus (CMV) or simian virus (SV) 40 promoter...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28208770/splicing-and-polyadenylation-of-human-papillomavirus-type-16-mrnas
#16
REVIEW
Chengjun Wu, Naoko Kajitani, Stefan Schwartz
The human papillomavirus type 16 (HPV16) life cycle can be divided into an early stage in which the HPV16 genomic DNA is replicated, and a late stage in which the HPV16 structural proteins are synthesized and virions are produced. A strong coupling between the viral life cycle and the differentiation state of the infected cell is highly characteristic of all HPVs. The switch from the HPV16 early gene expression program to the late requires a promoter switch, a polyadenylation signal switch and a shift in alternative splicing...
February 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28174683/post-translational-modifications-of-annexin-a2-are-linked-to-its-association-with-perinuclear-nonpolysomal-mrnp-complexes
#17
Ingvild Aukrust, Linn Andersen Rosenberg, Mia Madeleine Ankerud, Vibeke Bertelsen, Hanne Hollås, Jaakko Saraste, Ann Kari Grindheim, Anni Vedeler
Various post-translational modifications (PTMs) regulate the localisation and function of the multifunctional protein Annexin A2 (AnxA2). In addition to its various tasks as a cytoskeletal- and membrane-associated protein, AnxA2 can function as a trans-acting protein binding to cis-acting sequences of specific mRNAs. In the present study, we have examined the role of Ser25 phosphorylation in subcellular localisation of AnxA2 and its interaction with mRNP complexes. Subcellular fractionation and confocal microscopy of rat neuroendocrine PC12 cells showed that Ser25-phosphorylated AnxA2 (pSer25AnxA2) is absent from the nucleus and mainly localised to the perinuclear region, evidently associating with both membranes and cytoskeletal elements...
February 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28174576/comparative-analysis-of-agpase-genes-and-encoded-proteins-in-eight-monocots-and-three-dicots-with-emphasis-on-wheat
#18
Ritu Batra, Gautam Saripalli, Amita Mohan, Saurabh Gupta, Kulvinder S Gill, Pritish K Varadwaj, Harindra S Balyan, Pushpendra K Gupta
ADP-glucose pyrophosphorylase (AGPase) is a heterotetrameric enzyme with two large subunits (LS) and two small subunits (SS). It plays a critical role in starch biosynthesis. We are reporting here detailed structure, function and evolution of the genes encoding the LS and the SS among monocots and dicots. "True" orthologs of maize Sh2 (AGPase LS) and Bt2 (AGPase SS) were identified in seven other monocots and three dicots; structure of the enzyme at protein level was also studied. Novel findings of the current study include the following: (i) at the DNA level, the genes controlling the SS are more conserved than those controlling the LS; the variation in both is mainly due to intron number, intron length and intron phase distribution; (ii) at protein level, the SS genes are more conserved relative to those for LS; (iii) "QTCL" motif present in SS showed evolutionary differences in AGPase belonging to wheat 7BS, T...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28174238/functional-characterisation-of-cis-regulatory-elements-governing-dynamic-eomes-expression-in-the-early-mouse-embryo
#19
Claire S Simon, Damien J Downes, Matthew E Gosden, Jelena Telenius, Douglas R Higgs, Jim R Hughes, Ita Costello, Elizabeth K Bikoff, Elizabeth J Robertson
The T-box transcription factor (TF) Eomes is a key regulator of cell fate decisions during early mouse development. The cis-acting regulatory elements that direct expression in the anterior visceral endoderm (AVE), primitive streak (PS) and definitive endoderm (DE) have yet to be defined. Here, we identified three gene-proximal enhancer-like sequences (PSE_a, PSE_b and VPE) that faithfully activate tissue specific expression in transgenic embryos. However, targeted deletion experiments demonstrate that PSE_a and PSE_b are dispensable and only the VPE is required for optimal Eomes expression in vivo Embryos lacking this enhancer display variably penetrant defects in anterior-posterior axis orientation and DE formation...
February 7, 2017: Development
https://www.readbyqxmd.com/read/28168220/the-structurally-disordered-paramyxovirus-nucleocapsid-protein-tail-domain-is-a-regulator-of-the-mrna-transcription-gradient
#20
Robert M Cox, Stefanie A Krumm, Vidhi D Thakkar, Maximilian Sohn, Richard K Plemper
The paramyxovirus RNA-dependent RNA-polymerase (RdRp) complex loads onto the nucleocapsid protein (N)-encapsidated viral N:RNA genome for RNA synthesis. Binding of the RdRp of measles virus (MeV), a paramyxovirus archetype, is mediated through interaction with a molecular recognition element (MoRE) located near the end of the carboxyl-terminal Ntail domain. The structurally disordered central Ntail section is thought to add positional flexibility to MoRE, but the functional importance of this Ntail region for RNA polymerization is unclear...
February 2017: Science Advances
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