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https://www.readbyqxmd.com/read/28549191/maintenance-of-phosphate-homeostasis-and-root-development-are-coordinately-regulated-by-myb1-an-r2r3-type-myb-transcription-factor-in-rice
#1
Mian Gu, Jun Zhang, Huanhuan Li, Daqian Meng, Ran Li, Xiaoli Dai, Shichao Wang, Wei Liu, Hongye Qu, Guohua Xu
The adaptive responses of plants to phosphate (Pi) starvation stress are fine-tuned by an elaborate regulatory network. In this study, we identified and characterized a novel Pi starvation-responsive gene, MYB1, encoding an R2R3-type transcription factor in rice. MYB1 was transcriptionally induced in leaf sheaths and old leaf blades. It was localized to the nucleus and expressed mainly in vascular tissues. Mutation of MYB1 led to an increase in Pi uptake and accumulation, accompanied by altered expression of a subset of Pi transporters and several genes involved in Pi starvation signaling...
May 26, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28548630/tenogenic-differentiation-of-human-embryonic-stem-cells
#2
Tina P Dale, Shazia Mazher, William R Webb, Jing Zhou, Nicola Maffulli, G-Q Chen, Alicia J El Haj, Nicholas R Forsyth
Tendon healing is complex to manage because of the limited regeneration capacity of tendon tissue; stem cell-based tissue engineering approaches may provide alternative healing strategies. We sought to determine whether human embryonic stem cells (hESC) could be induced to differentiate into tendon-like cells by the addition of exogenous bone morphogenetic protein (BMP)12 (growth differentiation factor(GDF)7) and BMP13 (GDF6). hESC (SHEF-1) were maintained with or without BMP12/13 supplementation, or supplemented with BMP12/13 and the SMAD signalling cascade blocking agent, dorsomorphin...
May 26, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28540426/genetic-analysis-of-heterogeneous-sub-clones-in-recombinant-chinese-hamster-ovary-cells
#3
Kaiming Chen, Dong Li, Hongwen Li, Bing Li, Jie Li, Lei Huang, Renhao Li, Xiaoqing Xu, Lingxiao Jiang, Cizhong Jiang, Hua Gu, Jianmin Fang
Chinese hamster ovary (CHO) cells have been widely used for production of recombinant proteins and therapeutic antibodies. However, owing to the instability and heterogeneity of CHO cells, the development of stable and high-expression recombinant CHO cell lines is often time-consuming. To investigate the mechanisms associated with heterogeneity in protein productivity, we performed transcriptome analysis on the subclones derived from a stable parental CHO clone. Two high-expression subclones and one low-expression subclone were selected based on their similar genomic background and subjected to RNA-seq analysis...
May 24, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28539408/temporal-regulation-of-epithelium-formation-mediated-by-foxa-mklp1-mgcracgap-and-par-6
#4
Stephen E Von Stetina, Jennifer Liang, Georgios Marnellos, Susan E Mango
To establish the animal body plan, embryos link the external epidermis to the internal digestive tract. In Caenorhabditis elegans, this linkage is achieved by the Arcade Cells, which form an epithelial bridge between the foregut and epidermis, but little is known about how development of these three epithelia is coordinated temporally. The Arcade Cell epithelium is generated after the epidermis and digestive tract epithelia have matured, ensuring that both organs can withstand the mechanical stress of embryo elongation; mis-timing of epithelium formation leads to defects in morphogenesis...
May 24, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28537551/rna-dependent-chromatin-association-of-transcription-elongation-factors-and-pol-ii-ctd-kinases
#5
Sofia Battaglia, Michael Lidschreiber, Carlo Baejen, Phillipp Torkler, Seychelle M Vos, Patrick Cramer
For transcription through chromatin, RNA polymerase (Pol) II associates with elongation factors (EFs). Here we show that many EFs crosslink to RNA emerging from transcribing Pol II in the yeast Saccharomyces cerevisiae. Most EFs crosslink preferentially to mRNAs, rather than unstable non-coding RNAs. RNA contributes to chromatin association of many EFs, including the Pol II serine 2 kinases Ctk1 and Bur1 and the histone H3 methyltransferases Set1 and Set2. The Ctk1 kinase complex binds RNA in vitro, consistent with direct EF-RNA interaction...
May 24, 2017: ELife
https://www.readbyqxmd.com/read/28536436/functional-characterization-and-differential-nutritional-regulation-of-putative-elovl5-and-elovl4-elongases-in-large-yellow-croaker-larimichthys-crocea
#6
Songlin Li, Óscar Monroig, Tianjiao Wang, Yuhui Yuan, Juan Carlos Navarro, Francisco Hontoria, Kai Liao, Douglas R Tocher, Kangsen Mai, Wei Xu, Qinghui Ai
In the present study, two elongases, Elovl4 and Elovl5, were functionally characterized and their transcriptional regulation in response to n-3 LC-PUFA administration were investigated in vivo and in vitro. We previously described the molecular characterization of croaker elovl5. Here, we report the full-length cDNA sequence of croaker elovl4, which contained 1794 bp (excluding the polyA tail), including 909 bp of coding region that encoded a polypeptide of 302 amino acids possessing all the characteristic features of Elovl proteins...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28534718/jasmonate-suppresses-seedling-soil-emergence-in-arabidopsis-thaliana
#7
Lulu Yao, Yuyu Zheng, Ziqiang Zhu
In addition to defense response, phytohormone jasmonate participates in various plant growth and developmental processes. Nonetheless, its role in the seedling stage is not well defined. We recently report that jasmonate suppresses hypocotyl elongation and promotes cotyledon unfolding in etiolated Arabidopsis seedlings. The molecular basis underlying this phenotype is that jasmonate treatment reduces the biochemical activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) to stabilize several COP1-targetted transcription factors for eliciting a proportion of light responsive transcriptome...
May 23, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28533212/primitive-auxin-response-without-tir1-and-aux-iaa-in-the-charophyte-alga-klebsormidium-nitens
#8
Kinuka Ohtaka, Koichi Hori, Yuri Kanno, Mitsunori Seo, Hiroyuki Ohta
The phytohormone auxin regulates many aspects of growth and development in land plants, but the origin and evolution of auxin signaling and response mechanisms remain largely unknown. Indeed, it remains to be investigated whether auxin-related pathways diverged before the emergence of land plants. To address this knowledge deficit, we analyzed auxin responses in the charophyte alga Klebsormidium nitens NIES-2285, whose ancestor diverged from a green algal ancestor during the evolution of land plants. This strain is the same as K...
May 22, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28531235/rna-seq-analysis-of-gene-expression-for-floral-development-in-crested-wheatgrass-agropyron-cristatum-l
#9
Fangqin Zeng, Bill Biligetu, Bruce Coulman, Michael P Schellenberg, Yong-Bi Fu
Crested wheatgrass [Agropyron cristatum L. (Gaertn.)] is widely used for early spring grazing in western Canada and the development of late maturing cultivars which maintain forage quality for a longer period is desired. However, it is difficult to manipulate the timing of floral transition, as little is known about molecular mechanism of plant maturity in this species. In this study, RNA-Seq and differential gene expression analysis were performed to investigate gene expression for floral initiation and development in crested wheatgrass...
2017: PloS One
https://www.readbyqxmd.com/read/28526936/fingerprint-of-long-non-coding-rna-regulated-by-cyclic-mechanical-stretch-in-human-aortic-smooth-muscle-cells-implications-for-hypertension
#10
Laura-Eve Mantella, Krishna K Singh, Paul Sandhu, Crystal Kantores, Azza Ramadan, Nadiya Khyzha, Adrian Quan, Mohammed Al-Omran, Jason E Fish, Robert P Jankov, Subodh Verma
Emerging evidence suggests that long non-coding RNAs (lncRNAs) represent a cellular hub coordinating various cellular processes that are critical in health and disease. Mechanical stress triggers changes in vascular smooth muscle cells (VSMCs) that in turn contribute to pathophysiological changes within the vasculature. We sought to evaluate the role that lncRNAs play in mechanical stretch-induced alterations of human aortic smooth muscle cells (HASMCs). RNA (lncRNA and mRNA) samples isolated from HASMCs that had been subjected to 10 or 20% elongation (1 Hz) for 24 h were profiled with the Arraystar Human LncRNA Microarray V3...
May 19, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28524697/emerging-functions-of-multi-protein-complex-mediator-with-special-emphasis-on-plants
#11
Naveen Malik, Pinky Agarwal, Akhilesh Tyagi
Mediator is a multi-subunit protein complex which is involved in transcriptional regulation in yeast and other eukaryotes. As a co-activator, it connects information from transcriptional activators/repressors to transcriptional machinery including RNA polymerase II and general transcription factors. It is not only involved in transcription initiation but also has important roles to play in transcription elongation and termination. Functional attributes of different Mediator subunits have been largely defined in yeast and mammalian systems earlier, while such studies in plants have gained momentum recently...
May 19, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28522413/microglia-support-atf3-positive-neurons-following-hypoglossal-nerve-axotomy
#12
Tatsuhide Tanaka, Koichi Murakami, Yoshio Bando, Taichi Nomura, Ayami Isonishi, Shoko Morita-Takemura, Kouko Tatsumi, Akio Wanaka, Shigetaka Yoshida
Microglia are essential in developmental processes and maintenance of neuronal homeostasis. Experimental axotomy of motor neurons results in neurodegeneration, and microglia in motor nuclei become activated and migrate towards injured neurons. However, whether these activated microglia are protective or destructive to neurons remains controversial. In the present study, we transected the hypoglossal nerve in BALB/c mice, causing activating transcription factor 3 (ATF3) and growth associated protein 43 (GAP43) induction, and partial neuronal death...
May 15, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28521739/drosophila-melanogaster-positive-transcriptional-elongation-factors-regulate-metabolic-and-sex-biased-expression-in-adults
#13
Haiwang Yang, Denis Basquin, Daniel Pauli, Brian Oliver
BACKGROUND: Transcriptional elongation is a generic function, but is also regulated to allow rapid transcription responses. Following relatively long initiation and promoter clearance, RNA polymerase II can pause and then rapidly elongate following recruitment of positive elongation factors. Multiple elongation complexes exist, but the role of specific components in adult Drosophila is underexplored. RESULTS: We conducted RNA-seq experiments to analyze the effect of RNAi knockdown of Suppressor of Triplolethal and lilliputian...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28521214/def1-and-dst1-play-distinct-roles-in-repair-of-ap-lesions-in-highly-transcribed-genomic-regions
#14
Norah Owiti, Christopher Lopez, Shivani Singh, Andrei Stephenson, Nayun Kim
Abasic or AP sites generated by spontaneous DNA damage accumulate at a higher rate in actively transcribed regions of the genome in S. cerevisiae and are primarily repaired by base excision repair (BER) pathway. We have demonstrated that transcription-coupled nucleotide excision repair (NER) pathway can functionally replace BER to repair those AP sites located on the transcribed strand much like the strand specific repair of UV-induced pyrimidine dimers. Previous reports indicate that Rad26, a yeast homolog of transcription-repair coupling factor CSB, partly mediates strand-specific repair of UV-dimers as well as AP lesions...
May 10, 2017: DNA Repair
https://www.readbyqxmd.com/read/28520979/the-dead-box-helicase-mss116-plays-distinct-roles-in-mitochondrial-ribogenesis-and-mrna-specific-translation
#15
Dasmanthie De Silva, Sarah Poliquin, Rui Zeng, Angelica Zamudio-Ochoa, Natalie Marrero, Xochitl Perez-Martinez, Flavia Fontanesi, Antoni Barrientos
Members of the DEAD-box family are often multifunctional proteins involved in several RNA transactions. Among them, yeast Saccharomyces cerevisiae Mss116 participates in mitochondrial intron splicing and, under cold stress, also in mitochondrial transcription elongation. Here, we show that Mss116 interacts with the mitoribosome assembly factor Mrh4, is required for efficient mitoribosome biogenesis, and consequently, maintenance of the overall mitochondrial protein synthesis rate. Additionally, Mss116 is required for efficient COX1 mRNA translation initiation and elongation...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28514748/a-transcriptional-complex-composed-of-er-%C3%AE-gata3-foxa1-and-ell3-regulates-il-20-expression-in-breast-cancer-cells
#16
Jae Yong Lee, Young Joon Park, Nuri Oh, Kyu Bum Kwack, Kyung-Soon Park
Interleukin-20 (IL-20) is a member of the IL-10 family. IL-20 expression is regulated by a transcription elongation factor, Ell3, in estrogen receptor-positive (ER(+)) breast cancer cells. In this study, we demonstrated that ER(α), GATA3 and FOXA1 form a transcriptional complex with Ell3 to regulate IL-20 expression in ER(+) breast cancer cells. We also determined that GATA3 and FOXA1 share a binding site with ER(α) in the interleukin-20 promoter. Furthermore, we found that FOXA1 represses IL-20 expression, whereas GATA3 and ER(α) activate it...
April 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28514164/the-non-bulky-dna-lesions-spiroiminodihydantoin-and-5-guanidinohydantoin-significantly-block-human-rna-polymerase-ii-elongation-in-vitro
#17
Marina Kolbanovskiy, Moinuddin A Chowdhury, Aditi Nadkarni, Suse Broyde, Nicholas E Geacintov, David A Scicchitano, Vladimir Shafirovich
The most common, oxidatively generated lesion in cellular DNA is 8-oxo-7,8-dihydroguanine, which can be oxidized further to yield highly mutagenic spiroiminodihydantoin (Sp) and 5-guanidinohydantoin (Gh) in DNA. In human cell-free extracts, both lesions can be excised by base excision repair and global genomic nucleotide excision repair. However, it is not known if these lesions can be removed by transcription-coupled DNA repair (TCR), a pathway that clears lesions from DNA that impede RNA synthesis. To determine if Sp or Gh impede transcription, which could make them viable substrates for TCR, either an Sp or a Gh lesion was positioned on the transcribed strand of DNA under the control of a promoter that supports transcription by human RNA polymerase II...
May 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28513325/developmental-transitions-in-arabidopsis-are-regulated-by-antisense-rnas-resulting-from-bidirectionally-transcribed-genes
#18
Katarzyna Krzyczmonik, Agata Wroblewska-Swiniarska, Szymon Swiezewski
Transcription terminators are DNA elements located at the 3' end of genes that ensure efficient cleavage of nascent RNA generating the 3' end of mRNA, as well as facilitating disengagement of elongating DNA-dependent RNA polymerase II. Surprisingly, terminators are also a potent source of antisense transcription. We have recently described an Arabidopsis antisense transcript originating from the 3' end of a master regulator of Arabidopsis thaliana seed dormancy DOG1. In this review, we discuss the broader implications of our discovery in light of recent developments in yeast and Arabidopsis...
May 17, 2017: RNA Biology
https://www.readbyqxmd.com/read/28507243/modular-organization-of-the-nusa-and-nusg-stimulated-rna-polymerase-pause-signal-that-participates-in-the-bacillus-subtilis-trp-operon-attenuation-mechanism
#19
Smarajit Mondal, Alexander V Yakhnin, Paul Babitzke
The Bacillus subtilis trpEDCFBA operon is regulated by a transcription attenuation mechanism in which tryptophan-activated TRAP binds to the nascent transcript and blocks formation of an antiterminator structure such that formation of an overlapping intrinsic terminator causes termination in the 5' untranslated region (5' UTR). In the absence of bound TRAP the antiterminator forms and transcription continues into the trp genes. RNA polymerase pauses at positions U107 and U144 in the 5' UTR. The general transcription elongation factors NusA and NusG stimulate pausing at both positions...
May 15, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28506636/multiple-dna-interactions-contribute-to-the-initiation-of-telomerase-elongation
#20
Ahu Karademir Andersson, Cecilia Gustafsson, Roopesh Krishnankutty, Marita Cohn
Telomerase maintains telomere length and chromosome integrity by adding short tandem repeats of single-stranded DNA to the 3' ends, via reverse transcription of a defined template region of its RNA subunit. To further understand the telomerase elongation mechanism, we studied the primer utilization and extension activity of the telomerase from the budding yeast Naumovozyma castellii (Saccharomyces castellii), which displays a processive nucleotide and repeat addition polymerization. For the efficient initiation of canonical elongation, telomerase required 4nt primer 3' end complementarity to the template RNA...
May 12, 2017: Journal of Molecular Biology
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