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https://www.readbyqxmd.com/read/29145496/insights-into-soybean-transcriptome-reconfiguration-under-hypoxic-stress-functional-regulatory-structural-and-compositional-characterization
#1
Thiago J Nakayama, Fabiana A Rodrigues, Norman Neumaier, Juliana Marcolino-Gomes, Hugo B C Molinari, Thaís R Santiago, Eduardo F Formighieri, Marcos F Basso, José R B Farias, Beatriz M Emygdio, Ana C B de Oliveira, Ângela D Campos, Aluízio Borém, Frank G Harmon, Liliane M Mertz-Henning, Alexandre L Nepomuceno
Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits...
2017: PloS One
https://www.readbyqxmd.com/read/29125227/pichia-pastoris-alcohol-oxidase-1-aox1-core-promoter-engineering-by-high-resolution-systematic-mutagenesis
#2
Rui M C Portela, Thomas Vogl, Katharina Ebner, Rui Oliveira, Anton Glieder
Unravelling the core promoter sequence-function relationship is fundamental for engineering transcription initiation and thereby a feasible 'tuning knob' for fine-tuning expression in synthetic biology and metabolic engineering applications. Here a systematic replacement studies of the core promoter and 5' untranslated region (5'UTR) of the exceptionally strong and tightly methanol regulated Komagataella phaffii (syn. Pichia pastoris) alcohol oxidase 1 (AOX1) promoter at unprecedented resolution was performed...
November 10, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/29122971/poly-a-site-choice-and-pol2-ctd-serine-5-status-govern-lncrna-control-of-phosphate-responsive-tgp1-gene-expression-in-fission-yeast
#3
Ana M Sanchez, Stewart Shuman, Beate Schwer
Expression of fission yeast glycerophosphate transporter Tgp1 is repressed in phosphate-rich medium and induced during phosphate starvation. Repression is enforced by transcription of the nc-tgp1 locus upstream of tgp1 to produce a long noncoding (lnc) RNA. Here we identify two essential elements of the nc-tgp1 promoter: a TATA box (-30)TATATATA(-23) and a HomolD box (-64)CAGTCACA(-57), mutations of which inactivate the nc-tgp1 promoter and de-repress the downstream tgp1 promoter under phosphate-replete conditions...
November 9, 2017: RNA
https://www.readbyqxmd.com/read/29116140/valid-gene-expression-normalization-by-rt-qpcr-in-studies-on-hpdl-fibroblasts-with-focus-on-orthodontic-tooth-movement-and-periodontitis
#4
Christian Kirschneck, Sarah Batschkus, Peter Proff, Josef Köstler, Gerrit Spanier, Agnes Schröder
Meaningful, reliable and valid mRNA expression analyses by real-time quantitative PCR (RT-qPCR) can only be achieved, if suitable reference genes are chosen for normalization and if appropriate RT-qPCR quality standards are met. Human periodontal ligament (hPDL) fibroblasts play a major mediating role in orthodontic tooth movement and periodontitis. Despite corresponding in-vitro gene expression studies being a focus of interest for many years, no information is available for hPDL fibroblasts on suitable reference genes, which are generally used in RT-qPCR experiments to normalize variability between samples...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29111974/architecture-of-taf11-taf13-tbp-complex-suggests-novel-regulation-properties-of-general-transcription-factor-tfiid
#5
Kapil Gupta, Aleksandra A Watson, Tiago Baptista, Elisabeth Scheer, Anna L Chambers, Christine Koehler, Juan Zou, Ima Obong-Ebong, Eaazhisai Kandiah, Arturo Temblador, Adam Round, Eric Forest, Petr Man, Christoph Bieniossek, Ernest D Laue, Edward A Lemke, Juri Rappsilber, Carol V Robinson, Didier Devys, Làszlò Tora, Imre Berger
General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the histone fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry...
November 7, 2017: ELife
https://www.readbyqxmd.com/read/29102610/systematic-analysis-of-the-determinants-of-gene-expression-noise-in-embryonic-stem-cells
#6
Andre J Faure, Jörn M Schmiedel, Ben Lehner
Isogenic cells in a common environment show substantial cell-to-cell variation in gene expression, often referred to as "expression noise." Here, we use multiple single-cell RNA-sequencing datasets to identify features associated with high or low expression noise in mouse embryonic stem cells. These include the core promoter architecture of a gene, with CpG island promoters and a TATA box associated with low and high noise, respectively. High noise is also associated with "conflicting" chromatin states-the absence of transcription-associated histone modifications or the presence of repressive ones in active genes...
October 31, 2017: Cell Systems
https://www.readbyqxmd.com/read/29079779/reference-gene-selection-for-gene-expression-study-in-shell-gland-and-spleen-of-laying-hens-challenged-with-infectious-bronchitis-virus
#7
Samiullah Khan, Juliet Roberts, Shu-Biao Wu
Ten reference genes were investigated for normalisation of candidate target gene expression data in the shell gland and spleen of laying hens challenged with two strains of infectious bronchitis virus (IBV). Data were analysed with geNorm, NormFinder and BestKeeper, and a comprehensive ranking (geomean) was calculated. In the combined data set of IBV challenged shell gland samples, the comprehensive ranking showed TATA-box binding protein (TBP) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ) as the two most stable, and succinate dehydrogenase complex flavoprotein subunit A (SDHA) and albumin (ALB) as the two least stable reference genes...
October 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28992066/tfiia-transcriptional-activity-is-controlled-by-a-cleave-and-run-exportin-1-taspase-1-switch
#8
Christian Schrenk, Verena Fetz, Cecilia Vallet, Christina Heiselmayer, Elisabeth Schröder, Astrid Hensel, Angelina Hahlbrock, Désirée Wünsch, Dorothee Goesswein, Carolin Bier, Negusse Habtemichael, Günter Schneider, Roland H Stauber, Shirley K Knauer
Transcription factor TFIIA is controlled by complex regulatory networks including proteolysis by the protease Taspase 1, though the full impact of cleavage remains elusive. Here, we demonstrate that in contrast to the general assumption, de novo produced TFIIA is rapidly confined to the cytoplasm via an evolutionary conserved nuclear export signal (NES, amino acids 21VINDVRDIFL30), interacting with the nuclear export receptor Exportin-1/chromosomal region maintenance 1 (Crm1). Chemical export inhibition or genetic inactivation of the NES not only promotes TFIIA's nuclear localization but also affects its transcriptional activity...
August 10, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28979209/evolution-of-ucp1-transcriptional-regulatory-elements-across-the-mammalian-phylogeny
#9
Michael J Gaudry, Kevin L Campbell
Uncoupling protein 1 (UCP1) permits non-shivering thermogenesis (NST) when highly expressed in brown adipose tissue (BAT) mitochondria. Exclusive to placental mammals, BAT has commonly been regarded to be advantageous for thermoregulation in hibernators, small-bodied species, and the neonates of larger species. While numerous regulatory control motifs associated with UCP1 transcription have been proposed for murid rodents, it remains unclear whether these are conserved across the eutherian mammal phylogeny and hence essential for UCP1 expression...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28974698/characterization-of-the-promoter-region-of-the-bovine-six1-gene-roles-of-myod-pax7-creb-and-myog
#10
Da-Wei Wei, Xue-Yao Ma, Song- Zhang, Jie-Yun Hong, Lin-Sheng Gui, Chu-Gang Mei, Hong-Fang Guo, Li- Wang, Yue- Ning, Lin-Sen Zan
The SIX1 gene belongs to the family of six homeodomain transcription factors (TFs), that regulates the extracellular signal-regulated kinase 1/2 (ERK1/2) pathway and mediate skeletal muscle growth and regeneration. Previous studies have demonstrated that SIX1 is positively correlated with body measurement traits (BMTs). However, the transcriptional regulation of SIX1 remains unclear. In the present study, we determined that bovine SIX1 was highly expressed in the longissimus thoracis. To elucidate the molecular mechanisms involved in bovine SIX1 regulation, 2-kb of the 5' regulatory region were obtained...
October 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28956216/creb-nf-y-and-meis1-conserved-binding-sites-are-essential-to-balance-myostatin-promoter-enhancer-activity-during-early-myogenesis
#11
Carla Vermeulen Carvalho Grade, Carolina Stefano Mantovani, Marina Alves Fontoura, Faisal Yusuf, Beate Brand-Saberi, Lúcia Elvira Alvares
Myostatin (MSTN) is a strong inhibitor of skeletal muscle growth in human and other vertebrates. Its transcription is controlled by a proximal promoter/enhancer (Mstn P/E) containing a TATA box besides CREB, NF-Y, MEIS1 and FXR transcription factor binding sites (TFBSs), which are conserved throughout evolution. The aim of this work was to investigate the role of these TFBSs on Mstn P/E activity and evaluate the potential of their putative ligands as Mstn trans regulators. Mstn P/E mutant constructs were used to establish the role of conserved TFBSs using dual-luciferase assays...
October 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28955749/structure-organization-and-tissue-expression-of-the-pig-slc13a1-and-slc13a4-sulfate-transporter-genes
#12
Samuel K Barnes, Yvonne A Eiby, Soohyun Lee, Barbara E Lingwood, Paul A Dawson
Sulfate is an obligate nutrient for fetal growth and development. In mice, the renal Slc13a1 sulfate transporter maintains high maternal circulating levels of sulfate in pregnancy, and the placental Slc13a4 sulfate transporter mediates sulfate supply to the fetus. Both of these genes have been linked to severe embryonal defects and fetal loss in mice. However, the clinical significance of SLC13A1 and SLC13A4 in human gestation is unknown. One approach towards understanding the potential involvement of these genes in human fetal pathologies is to use an animal model, such as the pig, which mimics the developmental trajectory of the human fetus more closely than the previously studied mouse models...
July 2017: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/28945323/identification-of-genes-alternatively-spliced-in-developing-maize-endosperm
#13
S Xie, X Zhang, Z Zhou, X Li, Y Huang, J Zhang, J Weng
The process of alternative splicing is critical for the regulation of growth and development of plants. Thus far, little is known about the role of alternative splicing in the regulation of maize (Zea mays L.) endosperm development. RNA sequencing (RNA-seq) data of endosperms from two maize inbred lines, Mo17 and Ji419, at 15 and 25 days after pollination (DAP), respectively, were used to identify genes that were alternatively spliced during endosperm development. Intron retention (IR) in GRMZM2G005887 was further validated using PCR and re-sequencing technologies...
September 25, 2017: Plant Biology
https://www.readbyqxmd.com/read/28890398/functional-characterization-of-pol-iii-u6-promoters-for-gene-knockdown-and-knockout-in-plutella-xylostella
#14
Yuping Huang, Yajun Wang, Baosheng Zeng, Zhaoxia Liu, Xuejiao Xu, Qian Meng, Yongping Huang, Guang Yang, Liette Vasseur, Geoff M Gurr, Minsheng You
RNA polymerase type III (Pol-III) promoters such as U6 are commonly used to express small RNAs, including short hairpin RNAs (shRNAs) and single guide RNAs (sgRNAs). Functional U6 promoters are widely used in CRISPR systems, and their characterization can facilitate genome editing of non-model organisms. In the present study, six U6 small nuclear RNA (snRNA) promoters containing two conserved elements of a proximal sequence element (PSEA) and a TATA box, were identified and characterized in the diamondback moth (Plutella xylostella) genome...
October 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28870864/counter-regulation-of-ecrg4-gene-expression-by-hypermethylation-dependent-inhibition-and-the-sp1-transcription-factor-dependent-stimulation-of-the-c2orf40-promoter
#15
Xitong Dang, Xiaorong Zeng, Raul Coimbra, Brian P Eliceiri, Andrew Baird
The human cytokine precursor ECRG4 has been associated with multiple physiological, developmental and pathophysiological processes involving cell proliferation, cell migration, innate immunity, inflammation, cancer progression and metastases. Although down-regulation of ECRG4 gene expression has been largely attributed to hypermethylation of CpG islands in the 5'untranslated region of the ECRG4 promoter, the mechanisms that underlie the dynamics of its regulation have never been systematically described. Here we show that the ECRG4 gene is widely expressed in human tissues and report that its core promoter lies between the -780 to +420 base pairs relative to the ATG start codon of the ECRG4 open reading frame...
December 15, 2017: Gene
https://www.readbyqxmd.com/read/28857320/identification-of-heteromolecular-binding-sites-in-transcription-factors-sp1-and-taf4-using-high-resolution-nuclear-magnetic-resonance-spectroscopy
#16
Emi Hibino, Rintaro Inoue, Masaaki Sugiyama, Jun Kuwahara, Katsumi Matsuzaki, Masaru Hoshino
The expression of eukaryotic genes is precisely controlled by interactions between general transcriptional factors and promoter-specific transcriptional activators. The fourth element of TATA-box binding protein-associated factor (TAF4), an essential subunit of the general transcription factor TFIID, serves as a coactivator for various promoter-specific transcriptional regulators. Interactions between TAF4 and site-specific transcriptional activators, such as Sp1, are important for regulating the expression levels of genes of interest...
November 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28847004/a-heterochromatin-dependent-transcription-machinery-drives-pirna-expression
#17
Peter Refsing Andersen, Laszlo Tirian, Milica Vunjak, Julius Brennecke
Nuclear small RNA pathways safeguard genome integrity by establishing transcription-repressing heterochromatin at transposable elements. This inevitably also targets the transposon-rich source loci of the small RNAs themselves. How small RNA source loci are efficiently transcribed while transposon promoters are potently silenced is not understood. Here we show that, in Drosophila, transcription of PIWI-interacting RNA (piRNA) clusters-small RNA source loci in animal gonads-is enforced through RNA polymerase II pre-initiation complex formation within repressive heterochromatin...
September 7, 2017: Nature
https://www.readbyqxmd.com/read/28810828/suitable-reference-gene-for-quantitative-real-time-pcr-analysis-of-gene-expression-in-gonadal-tissues-of-minnow-puntius-sophore-under-high-temperature-stress
#18
Arabinda Mahanty, Gopal Krishna Purohit, Sasmita Mohanty, Nihar Ranjan Nayak, Bimal Prasanna Mohanty
BACKGROUND: High ambient temperature is known to affect fish gonadal development and physiology in a variety of ways depending on the severity and duration of exposure; however, the underlying molecular mechanisms are poorly understood. Gonadal gene expression influence the gonadal development, physiology and the quality of egg/sperm produced in teleosts and the mechanistic understanding of spatio-temporal changes in the gonadal gene expression could be instrumental in controlling the fate of egg/sperm and the quality of seed produced...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28806956/mirnas-regulate-oxidative-stress-related-genes-via-binding-to-the-3-utr-and-tata-box-regions-a-new-hypothesis-for-cataract-pathogenesis
#19
Changrui Wu, Zhao Liu, Le Ma, Cheng Pei, Li Qin, Ning Gao, Jun Li, Yue Yin
BACKGROUND: Age-related cataracts are related to oxidative stress. However, the genome-wide screening of cataract related oxidative stress related genes are not thoroughly investigated. Our study aims to identify cataract regulated miRNA target genes that are related to oxidative stress and to propose a new possible mechanism for cataract formation. METHODS: Microarrays were used to determine the mRNA expression profiles of both transparent and cataractous lenses...
August 14, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/28806616/parvovirus-b19-integration-into-human-cd36-erythroid-progenitor-cells
#20
Tyler Janovitz, Susan Wong, Neal S Young, Thiago Oliveira, Erik Falck-Pedersen
The pathogenic autonomous human parvovirus B19 (B19V) productively infects erythroid progenitor cells (EPCs). Functional similarities between B19V nonstructural protein (NS1), a DNA binding endonuclease, and the Rep proteins of Adeno-Associated Virus (AAV) led us to hypothesize that NS1 may facilitate targeted nicking of the human genome and B19 vDNA integration. We adapted an integration capture sequencing protocol (IC-Seq) to screen B19V infected human CD36+ EPCs for viral integrants, and discovered 40,000 unique B19V integration events distributed throughout the human genome...
November 2017: Virology
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