keyword
MENU ▼
Read by QxMD icon Read
search

interactome

keyword
https://www.readbyqxmd.com/read/28102760/phf13-a-new-player-involved-in-rna-polymerase-ii-transcriptional-regulation-and-co-transcriptional-splicing
#1
Alisa Fuchs, Marcos Torroba, Sarah Kinkley
We recently identified PHF13 as an H3K4me2/3 chromatin reader and transcriptional co-regulator. We found that PHF13 interacts with RNAPIIS5P and PRC2 stabilizing their association with active and bivalent promoters. Furthermore, mass spectrometry analysis identified ∼50 spliceosomal proteins in PHF13's interactome. Here we will discuss the potential role of PHF13 in RNAPII pausing and co-transcriptional splicing.
January 19, 2017: Transcription
https://www.readbyqxmd.com/read/28099817/applying-proteomics-to-tick-vaccine-development-where-are-we
#2
Margarita Villar, Anabel Marina, José de la Fuente
Ticks are second to mosquitoes as a vector of human diseases and are the first vector of animal diseases with a great impact on livestock farming. Tick vaccines represent a sustainable and effective alternative to chemical acaricides for the control of tick infestations and transmitted pathogens. The application of proteomics to tick vaccine development is a fairly recent area, which has resulted in the characterization of some tick-host-pathogen interactions and the identification of candidate protective antigens...
January 18, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28099032/pathogenicity-genes-in-ustilaginoidea-virens-revealed-by-a-predicted-protein-protein-interaction-network
#3
Kang Zhang, Yuejiao Li, Tengjiao Li, Zhi-Gang Li, Tom Hsiang, Ziding Zhang, Wenxian Sun
Rice false smut, caused by Ustilaginoidea virens, produces significant loss in rice yield and grain quality, and has recently emerged as one of the most important rice diseases worldwide. Despite its importance in rice production, relatively few studies have been conducted to illustrate the complex interactome and the pathogenicity gene interactions. Here, a protein-protein interaction (PPI) network of U. virens was built through two well-recognized approaches, interolog and domain-domain interaction-based methods...
January 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28098450/the-serum-amyloid-p-component-sap-interactome-in-human-plasma-containing-physiological-calcium-levels
#4
Ebbe Toftgaard Poulsen, Kata Wolff Pedersen, Anna Maria Marzeda, Jan Johannes Enghild
The pentraxin serum amyloid p component (SAP) is secreted by the liver and found in plasma at a concentration of approximately 30 mg/L. SAP is a 25 kDa homo-pentamer known to bind both protein and non-protein ligands, all in a calcium-dependent manner. The function of SAP is unclear, but likely involves the humoral innate immune system spanning the complement system, inflammation, and coagulation. Also, SAP is known to binding to the generic structure of amyloid deposits and possibly to protect these against proteolysis...
January 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28097092/comparative-interactomics-for-virus-human-protein-protein-interactions-dna-viruses-versus-rna-viruses
#5
Saliha Durmuş, Kutlu Ö Ülgen
Viruses are obligatory intracellular pathogens and completely depend on their hosts for survival and reproduction. The strategies adopted by viruses to exploit host cell processes and to evade host immune systems during infections may differ largely with the type of the viral genetic material. An improved understanding of these viral infection mechanisms is only possible through a better understanding of the pathogen-host interactions (PHIs) that enable viruses to enter into the host cells and manipulate the cellular mechanisms to their own advantage...
January 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28090086/centrality-in-the-host-pathogen-interactome-is-associated-with-pathogen-fitness-during-infection
#6
Núria Crua Asensio, Elisabet Muñoz Giner, Natalia Sánchez de Groot, Marc Torrent Burgas
To perform their functions proteins must interact with each other, but how these interactions influence bacterial infection remains elusive. Here we demonstrate that connectivity in the host-pathogen interactome is directly related to pathogen fitness during infection. Using Y. pestis as a model organism, we show that the centrality-lethality rule holds for pathogen fitness during infection but only when the host-pathogen interactome is considered. Our results suggest that the importance of pathogen proteins during infection is directly related to their number of interactions with the host...
January 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28078720/the-intrinsically-disordered-linker-of-e-coli-ssb-is-critical-for-the-release-from-single-stranded-dna
#7
Hui Yin Tan, Luke A Wilczek, Sasheen Pottinger, Maria Manosas, Cong Yu, Trong Nguyenduc, Piero R Bianco
The Escherichia coli single stranded DNA binding protein (SSB) is crucial for DNA replication, recombination and repair. Within each process, it has two seemingly disparate roles: it stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing and, forms complexes with a group of proteins known as the SSB-interactome. Key to both roles is the C-terminal, one-third of the protein, in particular the intrinsically disordered linker (IDL). Previously, we have shown using a series of linker deletion mutants that the IDL links both ssDNA and target protein binding by mediating interactions with the oligosaccharide/oligonucleotide binding fold in the target...
January 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28077445/human-antiviral-protein-ifix-suppresses-viral-gene-expression-during-hsv-1-infection-and-is-counteracted-by-virus-induced-proteasomal-degradation
#8
Marni S Crow, Ileana M Cristea
The interferon inducible protein X (IFIX), a member of the PYHIN family, was recently recognized as an antiviral factor against infection with herpes simplex virus 1 (HSV-1). IFIX binds viral DNA upon infection and promotes antiviral cytokines expression. How IFIX exerts its host defense functions and whether it is inhibited by the virus remains unknown. Here, we integrated live cell microscopy, proteomics, IFIX domain characterization, and molecular virology to investigate IFIX regulation and antiviral functions during HSV-1 infection...
January 11, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28074910/myosin-phosphatase-and-rhoa-activated-kinase-modulate-arginine-methylation-by-the-regulation-of-protein-arginine-methyltransferase-5-in-hepatocellular-carcinoma-cells
#9
Adrienn Sipos, Judit Iván, Bálint Bécsi, Zsuzsanna Darula, István Tamás, Dániel Horváth, Katalin F Medzihradszky, Ferenc Erdődi, Beáta Lontay
Myosin phosphatase (MP) holoenzyme is a protein phosphatase-1 (PP1) type Ser/Thr specific enzyme that consists of a PP1 catalytic (PP1c) and a myosin phosphatase target subunit-1 (MYPT1). MYPT1 is an ubiquitously expressed isoform and it targets PP1c to its substrates. We identified the protein arginine methyltransferase 5 (PRMT5) enzyme of the methylosome complex as a MYPT1-binding protein uncovering the nuclear MYPT1-interactome of hepatocellular carcinoma cells. It is shown that PRMT5 is regulated by phosphorylation at Thr80 by RhoA-associated protein kinase and MP...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28074633/a-computational-interactome-for-prioritizing-genes-associated-with-complex-agronomic-traits-in-rice
#10
Shiwei Liu, Yihui Liu, Jiawei Zhao, Shitao Cai, Hongmei Qian, Kaijing Zuo, Lingxia Zhao, Lida Zhang
Rice is one of the most important staple foods for more than half of the world's population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet/) using machine-learning with structural relationship and functional information...
January 11, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28073302/is-the-average-shortest-path-length-of-gene-set-a-reflection-of-their-biological-relatedness
#11
Varsha Embar, Adam Handen, Madhavi K Ganapathiraju
When a set of genes are identified to be related to a disease, say through gene expression analysis, it is common to examine the average distance among their protein products in the human interactome as a measure of biological relatedness of these genes. The reasoning for this is that, genes associated with a disease would tend to be functionally related, and that functionally related genes would be closely connected to each other in the interactome. Typically, average shortest path length (ASPL) of disease genes (although referred to as genes in the context of disease-associations, the interactions are among protein-products of these genes) is compared to ASPL of randomly selected genes or to ASPL in a randomly permuted network...
December 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28071740/elucidating-the-modes-of-action-for-bioactive-compounds-in-a-cell-specific-manner-by-large-scale-chemically-induced-transcriptomics
#12
Michio Iwata, Ryusuke Sawada, Hiroaki Iwata, Masaaki Kotera, Yoshihiro Yamanishi
The identification of the modes of action of bioactive compounds is a major challenge in chemical systems biology of diseases. Genome-wide expression profiling of transcriptional responses to compound treatment for human cell lines is a promising unbiased approach for the mode-of-action analysis. Here we developed a novel approach to elucidate the modes of action of bioactive compounds in a cell-specific manner using large-scale chemically-induced transcriptome data acquired from the Library of Integrated Network-based Cellular Signatures (LINCS), and analyzed 16,268 compounds and 68 human cell lines...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28068325/trim28-interacts-with-ezh2-and-swi-snf-to-activate-genes-that-promote-mammosphere-formation
#13
J Li, Y Xi, W Li, R L McCarthy, S A Stratton, W Zou, W Li, S Y Dent, A K Jain, M C Barton
Histone methyl transferase EZH2 (Enhancer of Zeste Homolog 2) is generally associated with H3K27 methylation and gene silencing, as a member of the polycomb repressor 2 (PRC2) complex. Immunoprecipitation and mass spectrometry of the EZH2-protein interactome in estrogen receptor positive, breast cancer-derived MCF7 cells revealed EZH2 interactions with subunits of chromatin remodeler SWI/SNF complex and TRIM28, which formed a complex with EZH2 distinct from PRC2. Unexpectedly, transcriptome profiling showed that EZH2 primarily activates, rather than represses, transcription in MCF7 cells and with TRIM28 co-regulates a set of genes associated with stem cell maintenance and poor survival of breast cancer patients...
January 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28065597/a-global-analysis-of-the-receptor-tyrosine-kinase-protein-phosphatase-interactome
#14
Zhong Yao, Katelyn Darowski, Nicole St-Denis, Victoria Wong, Fabian Offensperger, Annabel Villedieu, Shahreen Amin, Ramy Malty, Hiroyuki Aoki, Hongbo Guo, Yang Xu, Caterina Iorio, Max Kotlyar, Andrew Emili, Igor Jurisica, Benjamin G Neel, Mohan Babu, Anne-Claude Gingras, Igor Stagljar
Receptor tyrosine kinases (RTKs) and protein phosphatases comprise protein families that play crucial roles in cell signaling. We used two protein-protein interaction (PPI) approaches, the membrane yeast two-hybrid (MYTH) and the mammalian membrane two-hybrid (MaMTH), to map the PPIs between human RTKs and phosphatases. The resulting RTK-phosphatase interactome reveals a considerable number of previously unidentified interactions and suggests specific roles for different phosphatase families. Additionally, the differential PPIs of some protein tyrosine phosphatases (PTPs) and their mutants suggest diverse mechanisms of these PTPs in the regulation of RTK signaling...
January 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28060343/protein-complex-affinity-capture-from-cryomilled-mammalian-cells
#15
John LaCava, Hua Jiang, Michael P Rout
Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this technique is also frequently referred to as immunoprecipitation. Affinity capture can be applied in a bench-scale and in a high-throughput context. When coupled with protein mass spectrometry, affinity capture has proven to be a workhorse of interactome analysis. Although there are potentially many ways to execute the numerous steps involved, the following protocols implement our favored methods...
December 9, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28056051/mapping-the-interactome-of-a-major-mammalian-endoplasmic-reticulum-heat-shock-protein-90
#16
Feng Hong, Saleh Mohammad Rachidi, Debbie Lundgren, David Han, Xiu Huang, Hongyu Zhao, Yayoi Kimura, Hisashi Hirano, Osamu Ohara, Heichiiro Udono, Songdong Meng, Bei Liu, Zihai Li
Up to 10% of cytosolic proteins are dependent on the mammalian heat shock protein 90 (HSP90) for folding. However, the interactors of its endoplasmic reticulum (ER) paralogue (gp96, Grp94 and HSP90b1) has not been systematically identified. By combining genetic and biochemical approaches, we have comprehensively mapped the interactome of gp96 in macrophages and B cells. A total of 511 proteins were reduced in gp96 knockdown cells, compared to levels observed in wild type cells. By immunoprecipitation, we found that 201 proteins associated with gp96...
2017: PloS One
https://www.readbyqxmd.com/read/28054643/network-based-approach-to-identify-potential-targets-and-drugs-that-promote-neuroprotection-and-neurorepair-in-acute-ischemic-stroke
#17
Yiwei Wang, Hailong Liu, Yongzhong Lin, Guangming Liu, Hongwei Chu, Pengyao Zhao, Xiaohan Yang, Tiezheng Zheng, Ming Fan, Xuezhong Zhou, Jun Meng, Changkai Sun
Acute ischemic stroke (AIS) accounts for more than 80% of the approximately 610,000 new stroke cases worldwide every year. Both ischemia and reperfusion can cause death, damage, and functional changes of affected nerve cells, and these alterations can result in high rates of disability and mortality. Therefore, therapies aimed at increasing neuroprotection and neurorepair would make significant contributions to AIS management. However, with regard to AIS therapies, there is currently a large gap between experimental achievements and practical clinical solutions (EC-GAP-AIS)...
January 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28049721/pex35-is-a-regulator-of-peroxisome-abundance
#18
Ido Yofe, Kareem Soliman, Silvia G Chuartzman, Bruce Morgan, Uri Weill, Eden Yifrach, Tobias P Dick, Sara J Cooper, Christer S Ejsing, Maya Schuldiner, Einat Zalckvar, Sven Thoms
Peroxisomes are cellular organelles with vital functions in lipid, amino acid, and redox metabolism. The cellular formation and dynamics of peroxisomes are governed by PEX genes, however, the regulation of peroxisome abundance is yet poorly understood. Here we use a high-content microscopy screen to identify novel regulators of peroxisome size and abundance. Our screen led to the identification of a previously uncharacterized gene, which we term PEX35, which affects peroxisome abundance. PEX35 encodes a peroxisomal membrane protein, a remote homolog to several curvature generating human proteins...
January 3, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28045121/interactome-of-e-piscicida-and-grouper-liver-proteins-reveals-strategies-of-bacterial-infection-and-host-immune-response
#19
Hui Li, Qing-Feng Zhu, Xuan-Xian Peng, Bo Peng
The occurrence of infectious diseases is related to heterogeneous protein interactions between a host and a microbe. Therefore, elucidating the host-pathogen interplay is essential. We previously revealed the protein interactome between Edwardsiella piscicida and fish gill cells, and the present study identified the protein interactome between E. piscicida and E. drummondhayi liver cells. E. drummondhayi liver cells and bacterial pull-down approaches were used to identify E. piscicida outer membrane proteins that bind to liver cells and fish liver cell proteins that interact with bacterial cells, respectively...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043953/subgenic-pol-ii-interactomes-identify-region-specific-transcription-elongation-regulators
#20
Kevin M Harlen, L Stirling Churchman
Transcription, RNA processing, and chromatin-related factors all interact with RNA polymerase II (Pol II) to ensure proper timing and coordination of transcription and co-transcriptional processes. Many transcription elongation regulators must function simultaneously to coordinate these processes, yet few strategies exist to explore the complement of factors regulating specific stages of transcription. To this end, we developed a strategy to purify Pol II elongation complexes from subgenic regions of a single gene, namely the 5' and 3' regions, using sequences in the nascent RNA...
January 2, 2017: Molecular Systems Biology
keyword
keyword
2225
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"