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transcription Cap binding protein

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https://www.readbyqxmd.com/read/29113272/overexpression-of-calcyphosine-is-associated-with-poor-prognosis-in-esophageal-squamous-cell-carcinoma
#1
Feng Li, Dengyan Zhu, Yang Yang, Kai Wu, Song Zhao
Calcyphosine (CAPS), a calcium-binding protein, has been identified as a potential diagnostic and prognostic biomarker in several human carcinomas. However, little is known about CAPS in esophageal squamous cell carcinoma (ESCC). The present study aimed to investigate the expression levels of CAPS in ESCC tissues and evaluate its clinicopathological significance. Reverse transcription-quantitative polymerase chain reaction and immunohistochemical staining were conducted to detect the expression of CAPS in ESCC tissues and adjacent non-cancerous tissues...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29107534/m-6-a-facilitates-eif4f-independent-mrna-translation
#2
Ryan A Coots, Xiao-Min Liu, Yuanhui Mao, Leiming Dong, Jun Zhou, Ji Wan, Xingqian Zhang, Shu-Bing Qian
In eukaryotic cells, protein synthesis typically begins with the binding of eIF4F to the 7-methylguanylate (m(7)G) cap found on the 5' end of the majority of mRNAs. Surprisingly, overall translational output remains robust under eIF4F inhibition. The broad spectrum of eIF4F-resistant translatomes is incompatible with cap-independent translation mediated by internal ribosome entry sites (IRESs). Here, we report that N(6)-methyladenosine (m(6)A) facilitates mRNA translation that is resistant to eIF4F inactivation...
October 23, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29101316/structural-basis-for-mutually-exclusive-co-transcriptional-nuclear-cap-binding-complexes-with-either-nelf-e-or-ars2
#3
Wiebke Manuela Schulze, Stephen Cusack
Pol II transcribes diverse classes of RNAs that need to be directed into the appropriate nuclear maturation pathway. All nascent Pol II transcripts are 5'-capped and the cap is immediately sequestered by the nuclear cap-binding complex (CBC). Mutually exclusive interactions of CBC with different partner proteins have been implicated in transcript fate determination. Here, we characterise the direct interactions between CBC and NELF-E, a subunit of the negative elongation factor complex, ARS2 and PHAX. Our biochemical and crystal structure results show that the homologous C-terminal peptides of NELF-E and ARS2 bind identically to CBC and in each case the affinity is enhanced when CBC is bound to a cap analogue...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29093101/vp1-and-vp3-are-required-and-sufficient-for-translation-initiation-of-uncapped-ibdv-genomic-dsrna
#4
Chengjin Ye, Yu Wang, Enli Zhang, Xinpeng Han, Zhaoli Yu, Hebin Liu
Infectious bursal disease virus (IBDV) is a bi-segmented double-strand RNA (dsRNA) virus of the Birnaviridae family. While IBDV genomic dsRNA lacks a 5' cap, the means by which the uncapped IBDV genomic RNA is translated effectively is unknown. In this study, we describe a cap-independent pathway of translation initiation of IBDV uncapped RNA that relies on VP1 and VP3. We show that neither purified IBDV genomic dsRNA nor the uncapped viral plus-sense RNA transcripts was directly translated and rescued into infectious viruses in host cells...
November 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29077018/the-role-of-cytoplasmic-mrna-cap-binding-protein-complexes-in-trypanosoma-brucei-and-other-trypanosomatids
#5
REVIEW
Eden R Freire, Nancy R Sturm, David A Campbell, Osvaldo P de Melo Neto
Trypanosomatid protozoa are unusual eukaryotes that are well known for having unusual ways of controlling their gene expression. The lack of a refined mode of transcriptional control in these organisms is compensated by several post-transcriptional control mechanisms, such as control of mRNA turnover and selection of mRNA for translation, that may modulate protein synthesis in response to several environmental conditions found in different hosts. In other eukaryotes, selection of mRNA for translation is mediated by the complex eIF4F, a heterotrimeric protein complex composed by the subunits eIF4E, eIF4G, and eIF4A, where the eIF4E binds to the 5'-cap structure of mature mRNAs...
October 27, 2017: Pathogens
https://www.readbyqxmd.com/read/29061167/genome-wide-profiling-of-transcribed-enhancers-during-macrophage-activation
#6
Elena Denisenko, Reto Guler, Musa M Mhlanga, Harukazu Suzuki, Frank Brombacher, Sebastian Schmeier
BACKGROUND: Macrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. RESULTS: Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in bone marrow-derived mouse macrophages, their time kinetics, and target protein-coding genes...
October 23, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29028794/condensin-ii-and-gait-complexes-cooperate-to-restrict-line-1-retrotransposition-in-epithelial-cells
#7
Jacqueline R Ward, Kommireddy Vasu, Emily Deutschman, Dalia Halawani, Peter A Larson, Dongmei Zhang, Belinda Willard, Paul L Fox, John V Moran, Michelle S Longworth
LINE-1 (L1) retrotransposons can mobilize (retrotranspose) within the human genome, and mutagenic de novo L1 insertions can lead to human diseases, including cancers. As a result, cells are actively engaged in preventing L1 retrotransposition. This work reveals that the human Condensin II complex restricts L1 retrotransposition in both non-transformed and transformed cell lines through inhibition of L1 transcription and translation. Condensin II subunits, CAP-D3 and CAP-H2, interact with members of the Gamma-Interferon Activated Inhibitor of Translation (GAIT) complex including the glutamyl-prolyl-tRNA synthetase (EPRS), the ribosomal protein L13a, Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and NS1 associated protein 1 (NSAP1)...
October 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29021398/characterization-of-the-african-swine-fever-virus-decapping-enzyme-during-infection
#8
Ana Quintas, Daniel Pérez-Núñez, Elena G Sánchez, Maria L Nogal, Matthias W Hentze, Alfredo Castelló, Yolanda Revilla
African swine fever virus (ASFV) infection is characterized by a progressive decrease in cellular protein synthesis with a concomitant increase in viral protein synthesis, though the mechanism by which the virus achieves this phenomenon is still unknown. Decrease of cellular mRNA is observed during ASFV infection, suggesting that inhibition of cellular proteins is due to an active mRNA degradation process. ASFV carries a gene (Ba71V D250R/Malawi g5R) that encodes a decapping protein (ASFV-DP) which has a Nudix hydrolase motif and decapping activity in vitro Here we show that ASFV-DP was expressed from early times and accumulated throughout the infection with a subcellular localization typical of the endoplasmic reticulum, co-localizing with the cap structure and interacting with the ribosomal protein L23a...
October 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28982715/capturing-the-asc1p-rack1-microenvironment-at-the-head-region-of-the-40s-ribosome-with-quantitative-bioid-in-yeast
#9
Nadine Opitz, Kerstin Schmitt, Verena Hofer-Pretz, Bettina Neumann, Heike Krebber, Gerhard H Braus, Oliver Valerius
The Asc1 protein of Saccharomyces cerevisiae is a scaffold protein at the head region of ribosomal 40S that links mRNA translation to cellular signaling. In this study, proteins that co-localize with Asc1p were identified with proximity-dependent Biotin IDentification (BioID), an in vivo labeling technique described here for the first time for yeast. Biotinylated Asc1p-birA*-proximal proteins were identified and quantitatively verified against controls applying SILAC and mass spectrometry. The mRNA-binding proteins Sro9p and Gis2p appeared together with Scp160p, each providing ribosomes with nuclear transcripts...
October 5, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28981686/the-nuclear-mitotic-apparatus-protein-numa-controls-rdna-transcription-and-mediates-the-nucleolar-stress-response-in-a-p53-independent-manner
#10
Swaathi Jayaraman, Shirisha Chittiboyina, Yunfeng Bai, Patricia C Abad, Pierre-Alexandre Vidi, Cynthia V Stauffacher, Sophie A Lelièvre
The nuclear mitotic apparatus protein, NuMA, is involved in major cellular events such as DNA damage response, apoptosis and p53-mediated growth-arrest, all of which are under the control of the nucleolus upon stress. Proteomic investigation has identified NuMA among hundreds of nucleolar proteins. Yet, the precise link between NuMA and nucleolar function remains undetermined. We confirm that NuMA is present in the nucleolus and reveal redistribution of NuMA upon actinomycin D or doxorubicin-induced nucleolar stress...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28976774/proteomic-analysis-of-extracellular-hmgb1-identifies-binding-partners-and-exposes-its-potential-role-in-airway-epithelial-cell-homeostasis
#11
Sharon L Wong, Joyce To, Jerran Santos, Venkata Sita Rama Raju Allam, John P Dalton, Steven P Djordjevic, Sheila Donnelly, Matthew P Padula, Maria B Sukkar
The release of damage-associated molecular patterns (DAMPs) by airway epithelial cells is believed to play a crucial role in the initiation and development of chronic airway conditions such as asthma and chronic obstructive pulmonary disease (COPD). Intriguingly, the classic DAMP high-mobility group box-1 (HMGB1) is detected in the culture supernatant of airway epithelial cells under basal conditions, indicating a role for HMGB1 in the regulation of epithelial cellular and immune homeostasis. To gain contextual insight into the potential role of HMGB1 in airway epithelial cell homeostasis, we used the orthogonal and complementary methods of high-resolution clear native electrophoresis, immunoprecipitation, and pull-downs coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) to profile HMGB1 and its binding partners in the culture supernatant of unstimulated airway epithelial cells...
November 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28971096/protein-translation-and-signaling-in-human-eosinophils
#12
REVIEW
Stephane Esnault, Zhong-Jian Shen, James S Malter
We have recently reported that, unlike IL-5 and GM-CSF, IL-3 induces increased translation of a subset of mRNAs. In addition, we have demonstrated that Pin1 controls the activity of mRNA binding proteins, leading to enhanced mRNA stability, GM-CSF protein production and prolonged eosinophil (EOS) survival. In this review, discussion will include an overview of cap-dependent protein translation and its regulation by intracellular signaling pathways. We will address the more general process of mRNA post-transcriptional regulation, especially regarding mRNA binding proteins, which are critical effectors of protein translation...
2017: Frontiers in Medicine
https://www.readbyqxmd.com/read/28928453/molecular-characterization-of-emaraviruses-associated-with-pigeonpea-sterility-mosaic-disease
#13
Surender Kumar, B L Subbarao, Vipin Hallan
Sterility Mosaic Disease (SMD) of pigeonpea (Cajanus cajan (L.) Millspaugh) is a complex disease due to various factors including the presence of a mixed infection. Comparison of dsRNA profile and small RNA (sRNA) deep sequencing analysis of samples from three locations revealed the presence of Pigeonpea sterility mosaic virus-I and II (PPSMV-I and II) from Chevella and only PPSMV-II from Bengaluru and Coimbatore. PPSMV-I genome consisted of four while PPSMV-II encompassed six RNAs. The two viruses have modest sequence homology between their corresponding RNA 1-4 encoding RdRp, glycoprotein precursor, nucleocapsid and movement proteins and the corresponding orthologs of other emaraviruses...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28904350/tia1-dependent-regulation-of-mrna-subcellular-location-and-translation-controls-p53-expression-in-b-cells
#14
Manuel D Díaz-Muñoz, Vladimir Yu Kiselev, Nicolas Le Novère, Tomaz Curk, Jernej Ule, Martin Turner
Post-transcriptional regulation of cellular mRNA is essential for protein synthesis. Here we describe the importance of mRNA translational repression and mRNA subcellular location for protein expression during B lymphocyte activation and the DNA damage response. Cytoplasmic RNA granules are formed upon cell activation with mitogens, including stress granules that contain the RNA binding protein Tia1. Tia1 binds to a subset of transcripts involved in cell stress, including p53 mRNA, and controls translational silencing and RNA granule localization...
September 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28839261/structural-basis-for-therapeutic-inhibition-of-influenza-a-polymerase-pb2-subunit
#15
Xiaolei Ma, Lili Xie, Charles Wartchow, Robert Warne, Yongjin Xu, Alexey Rivkin, David Tully, Steven Shia, Kyoko Uehara, Dianna M Baldwin, Gladys Muiru, Weidong Zhong, Isabel Zaror, Dirksen E Bussiere, Vincent H J Leonard
Influenza virus uses a unique mechanism to initiate viral transcription named cap-snatching. The PB2 subunit of the viral heterotrimeric RNA polymerase binds the cap structure of cellular pre-mRNA to promote its cleavage by the PA subunit. The resulting 11-13 capped oligomer is used by the PB1 polymerase subunit to initiate transcription of viral proteins. VX-787 is an inhibitor of the influenza A virus pre-mRNA cap-binding protein PB2. This clinical stage compound was shown to bind the minimal cap-binding domain of PB2 to inhibit the cap-snatching machinery...
August 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821580/cap-independent-translation-ensures-mtor-expression-and-function-upon-protein-synthesis-inhibition
#16
Ana Marques-Ramos, Marco M Candeias, Juliane Menezes, Rafaela Lacerda, Margaret Willcocks, Alexandre Teixeira, Nicolas Locker, Luísa Romão
The mechanistic/mammalian target of rapamycin (mTOR) is a conserved serine/threonine kinase that integrates cellular signals from the nutrient and energy status to act, namely, on the protein synthesis machinery. While major advances have emerged regarding the regulators and effects of the mTOR signaling pathway, little is known about the regulation of mTOR gene expression. Here, we show that the human mTOR transcript can be translated in a cap-independent manner, and that its 5' untranslated region (UTR) is a highly folded RNA scaffold capable of binding directly to the 40S ribosomal subunit...
November 2017: RNA
https://www.readbyqxmd.com/read/28791367/molecular-mechanisms-of-breast-cancer-metastasis-by-gene-expression-profile-analysis
#17
Tianying Zheng, Aijun Wang, Dongyan Hu, Yonggang Wang
Metastasis is the main cause of breast cancer‑related mortalities. The present study aimed to uncover the relevant molecular mechanisms of breast cancer metastasis and to explore potential biomarkers that may be used for prognosis. Expression profile microarray data GSE8977, which contained 22 stroma samples (15 were from normal breast and 7 were from invasive ductal carcinoma tumor samples), were obtained from the Gene Expression Omnibus database. Following data preprocessing, differentially expressed genes (DEGs) were selected based on analyses conducted using the linear models for microarray analysis package from R and Bioconductor software...
October 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28771520/variations-of-five-eif4e-genes-across-cassava-accessions-exhibiting-tolerant-and-susceptible-responses-to-cassava-brown-streak-disease
#18
Shanshan Shi, Xiuchun Zhang, M Alejandra Mandel, Peng Zhang, Yuliang Zhang, Morag Ferguson, Teddy Amuge, Steve Rounsley, Zhixin Liu, Zhongguo Xiong
Cassava (Manihot esculenta) is an important tropical subsistence crop that is severely affected by cassava brown streak disease (CBSD) in East Africa. The disease is caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Both have a (+)-sense single-stranded RNA genome with a 5' covalently-linked viral protein, which functionally resembles the cap structure of mRNA, binds to eukaryotic translation initiation factor 4E (eIF4E) or its analogues, and then enable the translation of viral genomic RNA in host cells...
2017: PloS One
https://www.readbyqxmd.com/read/28747503/identification-of-vaccinia-virus-replisome-and-transcriptome-proteins-by-isolation-of-proteins-on-nascent-dna-coupled-with-mass-spectrometry
#19
Tatiana G Senkevich, George C Katsafanas, Andrea Weisberg, Lisa R Olano, Bernard Moss
Poxviruses replicate within the cytoplasm and encode proteins for DNA and mRNA synthesis. To investigate poxvirus replication and transcription from a new perspective, we incorporated 5-ethynyl-2'-deoxyuridine (EdU) into nascent DNA in cells infected with vaccinia virus (VACV). The EdU-labeled DNA was conjugated to fluor- or biotin-azide and visualized by confocal, superresolution, and transmission electron microscopy. Nuclear labeling decreased dramatically after infection, accompanied by intense labeling of cytoplasmic foci...
October 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28746365/cbp80-is-needed-for-the-expression-of-pirna-components-and-pirnas
#20
Ravish Rashpa, Paula Vazquez-Pianzola, Martino Colombo, Greco Hernandez, Dirk Beuchle, Fabienne Berger, Stephan Peischl, Rémy Bruggmann, Beat Suter
Cap binding protein 80 (Cbp80) is the larger subunit of the nuclear cap-binding complex (nCBC), which is known to play important roles in nuclear mRNA processing, export, stability and quality control events. Reducing Cbp80 mRNA levels in the female germline revealed that Cbp80 is also involved in defending the germline against transposable elements. Combining such knockdown experiments with large scale sequencing of small RNAs further showed that Cbp80 is involved in the initial biogenesis of piRNAs as well as in the secondary biogenesis pathway, the ping-pong amplification cycle...
2017: PloS One
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