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transcription Cap binding protein

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https://www.readbyqxmd.com/read/29298432/characterizing-zc3h18-a-multi-domain-protein-at-the-interface-of-rna-production-and-destruction-decisions
#1
Kinga Winczura, Manfred Schmid, Claudia Iasillo, Kelly R Molloy, Lea Mørch Harder, Jens S Andersen, John LaCava, Torben Heick Jensen
Nuclear RNA metabolism is influenced by protein complexes connecting to both RNA-productive and -destructive pathways. The ZC3H18 protein binds the cap-binding complex (CBC), universally present on capped RNAs, while also associating with the nuclear exosome targeting (NEXT) complex, linking to RNA decay. To dissect ZC3H18 function, we conducted interaction screening and mutagenesis of the protein, which revealed a phosphorylation-dependent isoform. Surprisingly, the modified region of ZC3H18 associates with core histone proteins...
January 2, 2018: Cell Reports
https://www.readbyqxmd.com/read/29228324/usp9x-controls-translation-efficiency-via-deubiquitination-of-eukaryotic-translation-initiation-factor-4a1
#2
Zengxia Li, Zhao Cheng, Chaerkady Raghothama, Zhaomeng Cui, Kaiyu Liu, Xiaojing Li, Chenxiao Jiang, Wei Jiang, Minjia Tan, Xiaohua Ni, Akhilesh Pandey, Jun O Liu, Yongjun Dang
Controlling translation initiation is an efficient way to regulate gene expression at the post-transcriptional level. However, current knowledge regarding regulatory proteins and their modes of controlling translation initiation is still limited. In this study, we employed tandem affinity purification and mass spectrometry to screen for unknown proteins associated with the translation initiation machinery. Ubiquitin specific peptidase 9, X-linked (USP9X), was identified as a novel binding partner, that interacts with the eukaryotic translation initiation factor 4B (eIF4B) in a mRNA-independent manner...
December 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29209637/a-role-for-p53-in-telomere-protection
#3
Stephen Tutton, Paul M Lieberman
Telomeres cap the ends of chromosomes and are crucial for genome stability. The p53 protein (TP53) is a vital tumor suppressor, activating the transcription of numerous genes in response to cell stress. We reported that direct binding of p53 at human subtelomeres corresponds with local transcription activation and enhanced telomere stability in the presence of DNA damage.
2017: Molecular & Cellular Oncology
https://www.readbyqxmd.com/read/29190286/nucleolar-sub-compartments-in-motion-during-rrna-synthesis-inhibition-contraction-of-nucleolar-condensed-chromatin-and-gathering-of-fibrillar-centers-are-concomitant
#4
Pavel Tchelidze, Aassif Benassarou, Hervé Kaplan, Marie-Françoise O'Donohue, Laurent Lucas, Christine Terryn, Levan Rusishvili, Giorgi Mosidze, Nathalie Lalun, Dominique Ploton
The nucleolus produces the large polycistronic transcript (47S precursor) containing the 18S, 5.8S and 28S rRNA sequences and hosts most of the nuclear steps of pre-rRNA processing. Among numerous components it contains condensed chromatin and active rRNA genes which adopt a more accessible conformation. For this reason, it is a paradigm of chromosome territory organization. Active rRNA genes are clustered within several fibrillar centers (FCs), in which they are maintained in an open configuration by Upstream Binding Factor (UBF) molecules...
2017: PloS One
https://www.readbyqxmd.com/read/29174799/the-emerging-functions-and-roles-of-circular-rnas-in-cancer
#5
Shibin Qu, Zhengcai Liu, Xisheng Yang, Jingshi Zhou, Hengchao Yu, Rui Zhang, Haimin Li
Circular RNAs (circRNAs) are a class of single-stranded closed RNA molecules that undergo a specific backsplicing from pre-mRNA. With the application of high-throughput sequencing and bioinformatics, circRNAs are found to be widely expressed across species. Some functionally characterized circRNAs have critical roles in gene regulation through various actions, including sponging microRNAs and proteins as well as regulating transcription and splicing. Moreover, most circRNAs are aberrantly expressed in different cancer types, and some of them have been reported to play important roles in the development and progression of cancer...
November 21, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29168419/truncated-forms-of-u2-snrna-u2-tfs-are-shunted-toward-a-novel-uridylylation-pathway-that-differs-from-the-degradation-pathway-for-u1-tfs
#6
Hideaki Ishikawa, Yuko Nobe, Keiichi Izumikawa, Masato Taoka, Yoshio Yamauchi, Hiroshi Nakayama, Richard J Simpson, Toshiaki Isobe, Nobuhiro Takahash
During the biogenesis of U1 small nuclear ribonucleoprotein, a small population of U1 snRNA molecules receives an extra methylation at the first transcribed nucleotide and nucleolytic cleavage to remove the 3' structured region including the Sm protein-binding site and stem-loop 4. These modifications occur before hypermethylation of the monomethylated 5' cap, and produce truncated forms of U1 snRNA (U1-tfs) that are diverted from the normal pathway to a processing body-associated degradation pathway. Here, we demonstrate that a small population of U2 snRNA molecules receives post-transcriptional modifications similar to those of U1 to yield U2-tfs...
November 23, 2017: RNA Biology
https://www.readbyqxmd.com/read/29166596/the-gcn2-atf4-signaling-pathway-induces-4e-bp-to-bias-translation-and-boost-antimicrobial-peptide-synthesis-in-response-to-bacterial-infection
#7
Deepika Vasudevan, Nicholas K Clark, Jessica Sam, Victoria C Cotham, Beatrix Ueberheide, Michael T Marr, Hyung Don Ryoo
Bacterial infection often leads to suppression of mRNA translation, but hosts are nonetheless able to express immune response genes through as yet unknown mechanisms. Here, we use a Drosophila model to demonstrate that antimicrobial peptide (AMP) production during infection is paradoxically stimulated by the inhibitor of cap-dependent translation, 4E-BP (eIF4E-binding protein; encoded by the Thor gene). We found that 4E-BP is induced upon infection with pathogenic bacteria by the stress-response transcription factor ATF4 and its upstream kinase, GCN2...
November 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/29113272/overexpression-of-calcyphosine-is-associated-with-poor-prognosis-in-esophageal-squamous-cell-carcinoma
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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