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https://www.readbyqxmd.com/read/27866166/variability-in-a-short-tandem-repeat-mediates-complex-epistatic-interactions-in-arabidopsis-thaliana
#1
Maximilian Oliver Press, Christine Queitsch
Short tandem repeats are hypervariable genetic elements that occur frequently in coding regions. Their high mutation rate readily generates genetic variation contributing to adaptive evolution and human diseases. We previously reported that natural ELF3 polyglutamine variants cause reciprocal genetic incompatibilities in two divergent Arabidopsis thaliana backgrounds. Here, we dissect the genetic architecture of this incompatibility, revealing as many as four loci putatively interacting with ELF3 We were able to specifically identify one such ELF3-interacting gene, LSH9 We further used a yeast two-hybrid strategy to identify proteins whose physical interactions with ELF3 were affected by polyglutamine tract length...
November 18, 2016: Genetics
https://www.readbyqxmd.com/read/27426928/molecular-cloning-and-functional-characterization-of-porcine-e74-like-factor-4-elf4
#2
Yanling Shi, Dang Wang, Xinyu Zhu, Qiong Wu, Huanchun Chen, Shaobo Xiao, Liurong Fang
E74-like factor 4 (ELF4) is a novel transcription factor that initiates transcription of type I interferon (IFN) genes to control diverse pathogens. Here, porcine ELF4 (poELF4) was cloned and its role in type I IFN signaling was investigated in different porcine cell lines. Full-length cDNA of poELF4 encodes 663 amino acid residues and ectopic expression of poELF4 significantly induced IFN-β production. Interestingly, difference from the human ELF4 (huELF4), poELF4 mutants lacking the serine/threonine rich domain, which has been demonstrated to be responsible for the phosphorylation of huELF4, were still capable of activating IFN-β promoter...
December 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27274533/data-on-the-identification-of-protein-interactors-with-the-evening-complex-and-pch1-in-arabidopsis-using-tandem-affinity-purification-and-mass-spectrometry-tap-ms
#3
He Huang, Sophie Alvarez, Dmitri A Nusinow
Tandem affinity purification coupled with mass spectrometry (TAP-MS) analysis is a powerful biochemical approach to identify protein-protein associations. Here we describe two datasets generated by a series of TAP-MS analyses to co-purify proteins associated with either ELF3 or ELF4 of the Evening Complex (EC) ("Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry" (Huang et al., 2016a) [1]) or proteins associated with PCH1, which is a newly identified output of the circadian clock to regulate photoperiodic growth in Arabidopsis thaliana ("PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis" (Huang et al...
September 2016: Data in Brief
https://www.readbyqxmd.com/read/27040637/the-ets-factor-myeloid-elf-1-like-factor-mef-elf4-is-transcriptionally-and-functionally-activated-by-hypoxia
#4
Mary Ann Suico, Manabu Taura, Eriko Kudo, Kumiko Gotoh, Tsuyoshi Shuto, Seiji Okada, Hirofumi Kai
Hypoxia-inducible factor (HIF)-1α is a transcription factor belonging to the HIF family that is activated in mammalian cells during conditions of low oxygen tension or hypoxia to induce an adaptive response and promote cell survival. Some of the genes targeted by HIF-1α are important for angiogenesis and proliferation. Here, we found that the E26 transformation-specific (ETS) transcription factor myeloid elf-1-like factor (MEF)/Elf4 is activated by HIF-1α. MEF induces genes such as human beta-defensin 2 (HβD2) and perforin (PRF1), and is known to affect the cell cycle...
2016: Biological & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/26988076/identification-of-potential-drug-targets-in-cancer-signaling-pathways-using-stochastic-logical-models
#5
Peican Zhu, Hamidreza Montazeri Aliabadi, Hasan Uludağ, Jie Han
The investigation of vulnerable components in a signaling pathway can contribute to development of drug therapy addressing aberrations in that pathway. Here, an original signaling pathway is derived from the published literature on breast cancer models. New stochastic logical models are then developed to analyze the vulnerability of the components in multiple signalling sub-pathways involved in this signaling cascade. The computational results are consistent with the experimental results, where the selected proteins were silenced using specific siRNAs and the viability of the cells were analyzed 72 hours after silencing...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26961797/generation-of-a-novel-multi-stage-progressive-and-transplantable-model-of-plasma-cell-neoplasms
#6
Takashi Asai, Megan A Hatlen, Chen Lossos, Delphine Ndiaye-Lobry, Anthony Deblasio, Kazunori Murata, Martin Fleisher, Elena M Cortizas, Ramiro E Verdun, John Petrini, Stephen D Nimer
Multiple myeloma is a plasma cell neoplasm with an extremely variable clinical course. Animal models are needed to better understand its pathophysiology and for preclinical testing of potential therapeutic agents. Hematopoietic cells expressing the hypermorphic Rad50(s) allele show hematopoietic failure, which can be mitigated by the lack of a transcription factor, Mef/Elf4. However, we find that 70% of Mef(-/-)Rad50(s/s) mice die from multiple myeloma or other plasma cell neoplasms. These mice initially show an abnormal plasma cell proliferation and monoclonal protein production, and then develop anemia and a decreased bone mineral density...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26941752/fhy3-and-far1-act-downstream-of-light-stable-phytochromes
#7
Hamad Siddiqui, Safina Khan, Bruce M Rhodes, Paul F Devlin
FHY3 and FAR1 are positively acting transcription factors that directly regulate expression of a number of target genes in Arabidopsis thaliana. Here, we looked at the regulation of one specific target gene, ELF4. We demonstrate that the action of FHY3 and FAR1 in upregulation of ELF4 is light dependent. Furthermore, although FHY3 and FAR1 have been exclusively characterized as components of the phytochrome A signaling pathway because of their importance in regulating expression of phyA nuclear importers, we show that, as transcription factors in their own right, FHY3 and FAR1 act downstream of light stable phytochromes, phyB, phyD, and phyE...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/26921333/mutational-landscape-and-antiproliferative-functions-of-elf-transcription-factors-in-human-cancer
#8
Mizuo Ando, Masahito Kawazu, Toshihide Ueno, Daizo Koinuma, Koji Ando, Junji Koya, Keisuke Kataoka, Takahiko Yasuda, Hiroyuki Yamaguchi, Kazutaka Fukumura, Azusa Yamato, Manabu Soda, Eirin Sai, Yoshihiro Yamashita, Takahiro Asakage, Yasushi Miyazaki, Mineo Kurokawa, Kohei Miyazono, Stephen D Nimer, Tatsuya Yamasoba, Hiroyuki Mano
ELF4 (also known as MEF) is a member of the ETS family of transcription factors. An oncogenic role for ELF4 has been demonstrated in hematopoietic malignancies, but its function in epithelial tumors remains unclear. Here, we show that ELF4 can function as a tumor suppressor and is somatically inactivated in a wide range of human tumors. We identified a missense mutation affecting the transactivation potential of ELF4 in oral squamous cell carcinoma cells. Restoration of the transactivation activity through introduction of wild-type ELF4 significantly inhibited cell proliferation in vitro and tumor xenograft growth...
April 1, 2016: Cancer Research
https://www.readbyqxmd.com/read/26772990/evolution-of-duf1313-family-members-across-plant-species-and-their-association-with-maize-photoperiod-sensitivity
#9
Jia Li, Erliang Hu, Xueying Chen, Jie Xu, Hai Lan, Chuan Li, Yaodong Hu, Yanli Lu
Proteins of the DUF1313 family contain a highly conserved domain and are only found in plants; they play important roles in most plant functions. In this study, 269 DUF1313 genes from 81 photoautotrophic species were identified; they were classified into three major types based on the amino acid substitutions in the conserved region: IARV, I(S/T/F)(K/R)V, and IRRV. Phylogenic tree constructed from 51 DUF1313 genes from graminoids revealed three clades: A, B1, and B2. Clade B1 was found to have undergone episodic positive selection after a gene duplication event and included four amino acid sites under positive selection...
May 2016: Genomics
https://www.readbyqxmd.com/read/26545401/identification-of-evening-complex-associated-proteins-in-arabidopsis-by-affinity-purification-and-mass-spectrometry
#10
He Huang, Sophie Alvarez, Rebecca Bindbeutel, Zhouxin Shen, Michael J Naldrett, Bradley S Evans, Steven P Briggs, Leslie M Hicks, Steve A Kay, Dmitri A Nusinow
Many species possess an endogenous circadian clock to synchronize internal physiology with an oscillating external environment. In plants, the circadian clock coordinates growth, metabolism and development over daily and seasonal time scales. Many proteins in the circadian network form oscillating complexes that temporally regulate myriad processes, including signal transduction, transcription, protein degradation and post-translational modification. In Arabidopsis thaliana, a tripartite complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX), named the evening complex, modulates daily rhythms in gene expression and growth through transcriptional regulation...
January 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/26468131/defining-the-robust-behaviour-of-the-plant-clock-gene-circuit-with-absolute-rna-timeseries-and-open-infrastructure
#11
Anna Flis, Aurora Piñas Fernández, Tomasz Zielinski, Virginie Mengin, Ronan Sulpice, Kevin Stratford, Alastair Hume, Alexandra Pokhilko, Megan M Southern, Daniel D Seaton, Harriet G McWatters, Mark Stitt, Karen J Halliday, Andrew J Millar
Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI...
October 2015: Open Biology
https://www.readbyqxmd.com/read/26404688/-clinical-significance-of-the-expression-of-eukaryotic-initiation-factor-4-e-and-mammalian-target-of-rapamycin-in-esophageal-squamous-carcinoma-tissues
#12
Jianjun Lu, You Pan, Yiyan Lei, Yong Gu, Fotian Zhong
OBJECTIVE: To explore the clinical significance of eukaryotic initiation factor 4 E (eIF4E) and mammalian target of rapamycin (mTOR) expressions in esophageal squamous carcinoma tissues. METHODS: Clinicopathological data and paraffin samples of resected tumor tissue from 148 patients with esophageal squamous carcinoma undergoing resection in our department between January 2010 and December 2012 were collected retrospectively. Expressions of eIF4E and mTOR were detected in above carcinoma tissues, counterpart para-carcinoma tissues (1 cm distance to carcinoma) and normal tissues (5 cm distance to carcinoma) with Western blot and immunohistochemistry...
September 2015: Zhonghua Wei Chang Wai Ke za Zhi, Chinese Journal of Gastrointestinal Surgery
https://www.readbyqxmd.com/read/26382718/the-plant-circadian-clock-looks-like-a-traditional-japanese-clock-rather-than-a-modern-western-clock
#13
Takeshi Mizuno, Takafumi Yamashino
Life cycle adaptation to seasonal changes in photoperiod and ambient temperature is a major determinant of the ecological success behind the widespread domestication of flowering plants. The circadian clock plays a role in the underlying mechanism for adaptation through generating endogenous rhythms that allow plants to adapt and adjust to both the 24 h diurnal rotation and 365 d seasonal revolution. Nevertheless, the mechanism by which the circadian clock tracks seasonal changes in photoperiod and temperature is a longstanding subject in the field...
2015: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/26205509/dhefl2-3-and-4-the-three-early-flowering4-like-genes-in-a-doritaenopsis-hybrid-regulate-floral-transition
#14
Weiwei Chen, Qiaoping Qin, Chi Zhang, Yongping Zheng, Chun Wang, Mingbing Zhou, Yongyi Cui
DhEFL2, 3 and 4 regulate the flowering of Doritaenopsis . These genes could rescue elf4-1 phenotype in Arabidopsis while its overexpression delayed flowering. Phalaenopsis are popular floral plants, and studies on orchid flowering genes could help develop off-season cultivars. Early flowering 4 (ELF4) of A. thaliana has been shown to be involved in photoperiod perception and circadian regulation. We isolated two members of the ELF4 family from Doritaenopsis hybrid (Doritaenopsis 'Tinny Tender' (Doritaenopsis Happy Smile × Happy Valentine)), namely, DhEFL2 and DhEFL3 (DhEFL4 has been previously cloned)...
December 2015: Plant Cell Reports
https://www.readbyqxmd.com/read/26108788/insight-into-a-physiological-role-for-the-ec-night-time-repressor-in-the-arabidopsis-circadian-clock
#15
Takeshi Mizuno, Miki Kitayama, Chieko Takayama, Takafumi Yamashino
Life cycle adaptation to seasonal variation in photoperiod and temperature is a major determinant of ecological success of widespread domestication of Arabidopsis thaliana. The circadian clock plays a role in the underlying mechanism for adaptation. Nevertheless, the mechanism by which the circadian clock tracks seasonal changes in photoperiod and temperature is a longstanding subject of research in the field. We previously showed that a set of the target genes (i.e. GI, LNK1. PRR9 and PRR7) of the Evening Complex (EC) consisting of LUX-ELF3-ELF4 is synergistically induced in response to both warm-night and night-light signals...
September 2015: Plant & Cell Physiology
https://www.readbyqxmd.com/read/26091701/quantitative-circadian-phosphoproteomic-analysis-of-arabidopsis-reveals-extensive-clock-control-of-key-components-in-physiological-metabolic-and-signaling-pathways
#16
Mani Kant Choudhary, Yuko Nomura, Lei Wang, Hirofumi Nakagami, David E Somers
The circadian clock provides adaptive advantages to an organism, resulting in increased fitness and survival. The phosphorylation events that regulate circadian-dependent signaling and the processes which post-translationally respond to clock-gated signals are largely unknown. To better elucidate post-translational events tied to the circadian system we carried out a survey of circadian-regulated protein phosphorylation events in Arabidopsis seedlings. A large-scale mass spectrometry-based quantitative phosphoproteomics approach employing TiO2-based phosphopeptide enrichment techniques identified and quantified 1586 phosphopeptides on 1080 protein groups...
August 2015: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/26025321/splice-variants-and-regulatory-networks-associated-with-host-resistance-to-the-intestinal-worm-cooperia-oncophora-in-cattle
#17
Robert W Li, Sitao Wu, Cong-Jun Li, Weizhong Li, Steven G Schroeder
To elucidate the molecular mechanism of host resistance, we characterized the jejunal transcriptome of Angus cattle selected for parasite resistance for over 20 years in response to infection caused by the intestinal worm Cooperia oncophora. The transcript abundance of 56 genes, such as that of mucin 12 (MUC12) and intestinal alkaline phosphatase (ALPI), was significantly higher in resistant cattle. Novel splicing variants, exon skipping events, and gene fusion events, were also detected. An algorithm for the reconstruction of accurate cellular networks (ARACNE) was used to infer de novo regulatory molecular networks in the interactome between the parasite and host...
July 30, 2015: Veterinary Parasitology
https://www.readbyqxmd.com/read/25860116/comparative-transcriptome-analysis-of-the-petal-degeneration-mutant-pdm-in-chinese-cabbage-brassica-campestris-ssp-pekinensis-using-rna-seq
#18
COMPARATIVE STUDY
Shengnan Huang, Zhiyong Liu, Runpeng Yao, Danyang Li, Hui Feng
Flowering, which plays a crucial role in the growth and development of flowering plants, is a crucial point from vegetative growth to reproductive growth. The goal of this study was to examine the differences between the transcriptomes of the Chinese cabbage mutant pdm and the corresponding wild-type line 'FT'. We performed transcriptome analysis on mRNA isolated from flower buds of pdm and 'FT' using Illumina RNA sequencing (RNA-Seq) data. A total of 117 differentially expressed genes (DEGs) were detected...
October 2015: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/25752595/nature-and-nurture-a-case-of-transcending-haematological-pre-malignancies-in-a-pair-of-monozygotic-twins-adding-possible-clues-on-the-pathogenesis-of-b-cell-proliferations
#19
Marcus C Hansen, Charlotte G Nyvold, Anne S Roug, Eigil Kjeldsen, Palle Villesen, Line Nederby, Peter Hokland
We describe a comprehensive molecular analysis of a pair of monozygotic twins, who came to our attention when one experienced amaurosis fugax and was diagnosed with JAK2+ polycythaemia vera. He (Twin A) was also found to have an asymptomatic B-cell chronic lymphocytic leukaemia (B-CLL). Although JAK2-, Twin B was subsequently shown to have a benign monoclonal B-cell lymphocytosis (MBL). Flow cytometric and molecular analyses of the B-cell compartments revealed different immunoglobulin light and heavy chain usage in each twin...
May 2015: British Journal of Haematology
https://www.readbyqxmd.com/read/25729255/p70s6k-and-elf4e-dual-inhibition-is-essential-to-control-bladder-tumor-growth-and-progression-in-orthotopic-mouse-non-muscle-invasive-bladder-tumor-model
#20
Byung Hoon Chi, Soon-Ja Kim, Ho Kyung Seo, Hye-Hyun Seo, Sang-Jin Lee, Jong Kyou Kwon, Tae-Jin Lee, In Ho Chang
We investigated how the dual inhibition of the molecular mechanism of the mammalian target of the rapamycin (mTOR) downstreams, P70S6 kinase (P70S6K) and eukaryotic initiation factor 4E (eIF4E), can lead to a suppression of the proliferation and progression of urothelial carcinoma (UC) in an orthotopic mouse non-muscle invasive bladder tumor (NMIBT) model. A KU-7-luc cell intravesically instilled orthotopic mouse NMIBC model was monitored using bioluminescence imaging (BLI) in vivo by interfering with different molecular components using rapamycin and siRNA technology...
March 2015: Journal of Korean Medical Science
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