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"Essential gene"

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https://www.readbyqxmd.com/read/29038160/a-high-resolution-genome-wide-crispr-cas9-viability-screen-reveals-structural-features-and-contextual-diversity-of-the-human-cell-essential-proteome
#1
Thierry Bertomeu, Jasmin Coulombe-Huntington, Andrew Chatr-Aryamontri, Karine Bourdages, Etienne Coyaud, Brian Raught, Yu Xia, Mike Tyers
To interrogate genes essential for cell growth, proliferation and survival in human cells, we carried out a genome-wide CRISPR/Cas9 screen in a B-cell lymphoma line using a custom extended knockout (EKO) library of 278,754 sgRNAs that targeted 19,084 RefSeq genes, 20,852 alternatively-spliced exons and 3,872 hypothetical genes. A new statistical analysis tool called RANKS identified 2,280 essential genes, 234 of which were unique. Individual essential genes were validated experimentally and linked to ribosome biogenesis and stress responses...
October 16, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/29033457/emerging-and-evolving-concepts-in-gene-essentiality
#2
REVIEW
Giulia Rancati, Jason Moffat, Athanasios Typas, Norman Pavelka
Gene essentiality is a founding concept of genetics with important implications in both fundamental and applied research. Multiple screens have been performed over the years in bacteria, yeasts, animals and more recently in human cells to identify essential genes. A mounting body of evidence suggests that gene essentiality, rather than being a static and binary property, is both context dependent and evolvable in all kingdoms of life. This concept of a non-absolute nature of gene essentiality changes our fundamental understanding of essential biological processes and could directly affect future treatment strategies for cancer and infectious diseases...
October 16, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29032659/in-silico-analysis-of-putative-drug-and-vaccine-target-of-the-metabolic-pathways-of-actinobacillus-pleuropneumoniae-using-subtractive-comparative-genomics-approach
#3
Biruk Tesfaye Birhanu, Seung-Jin Lee, Na-Hye Park, Ju-Beom Song, Seung-Chun Park
Actinobacillus pleuropneumoniae is a gram-negative bacterium residing in the respiratory tract of pigs that causes porcine respiratory disease complex, which leads to significant losses in the pig industry worldwide. The incidence of drug resistance in this bacterium is increasing; thus, identifying new protein/gene targets for drug and vaccine development is critical. In this study, we used an in silico approach, utilizing several databases, including Kyoto Encyclopedia of Genes and Genomes (KEGG), the database of essential genes (DEG), DrugBank, and Swiss-Prot, to identify non-homologous essential genes and prioritize these proteins for their druggability...
October 13, 2017: Journal of Veterinary Science
https://www.readbyqxmd.com/read/29017819/jasmonates-are-signals-in-the-biosynthesis-of-secondary-metabolites-pathways-transcription-factors-and-applied-aspects-a-brief-review
#4
REVIEW
Claus Wasternack, Miroslav Strnad
Jasmonates (JAs) are signals in plant stress responses and development. One of the first observed and prominent responses to JAs is the induction of biosynthesis of different groups of secondary compounds. Among them are nicotine, isoquinolines, glucosinolates, anthocyanins, benzophenanthridine alkaloids, artemisinin, and terpenoid indole alkaloids (TIAs), such as vinblastine. This brief review describes modes of action of JAs in the biosynthesis of anthocyanins, nicotine, TIAs, glucosinolates and artemisinin...
October 7, 2017: New Biotechnology
https://www.readbyqxmd.com/read/28994778/creation-of-a-dense-transposon-insertion-library-using-bacterial-conjugation-in-enterobacterial-strains-such-as-escherichia-coli-or-shigella-flexneri
#5
Nikki E Freed
Transposon mutagenesis is a method that allows gene disruption via the random genomic insertion of a piece of DNA called a transposon. The protocol below outlines a method for high efficiency transfer between bacterial strains of a plasmid harboring a transposon containing a kanamycin resistance marker. The plasmid-borne transposase is encoded by a variant tnp gene that inserts the transposon into the genome of the recipient strain with very low insertional bias. This method thus allows the creation of large mutant libraries in which transposons have been inserted into unique genomic positions in a recipient strain of either Escherichia coli or Shigella flexneri bacteria...
September 23, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28993509/a-large-scale-rnai-screen-identifies-sgk1-as-a-key-survival-kinase-for-gbm-stem-cells
#6
Shreya Kulkarni, Surbhi Goel, Sejuti Sengupta, Brent H Cochran
Glioblastoma Multiforme (GBM) is the most common type of primary malignant brain cancer and has a very poor prognosis. A subpopulation of cells known as GBM stem-like cells (GBM-SCs) have the capacity to initiate and sustain tumor growth and possess molecular characteristics similar to the parental tumor. GBM-SCs are known to be enriched in hypoxic niches and may contribute to therapeutic resistance. Therefore, to identify genetic determinants important for the proliferation and survival of GBM stem cells, an unbiased pooled shRNA screen of 10,000 genes was conducted under normoxic as well as hypoxic conditions...
October 9, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28984184/using-machine-learning-algorithms-to-identify-genes-essential-for-cell-survival
#7
Santosh Philips, Heng-Yi Wu, Lang Li
BACKGROUND: With the explosion of data comes a proportional opportunity to identify novel knowledge with the potential for application in targeted therapies. In spite of this huge amounts of data, the solutions to treating complex disease is elusive. One reason being that these diseases are driven by a network of genes that need to be targeted in order to understand and treat them effectively. Part of the solution lies in mining and integrating information from various disciplines. Here we propose a machine learning method to mining through publicly available literature on RNA interference with the goal of identifying genes essential for cell survival...
October 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28981838/an-efficient-method-for-generation-of-bi-allelic-null-mutant-mouse-embryonic-stem-cells-and-its-application-for-investigating-epigenetic-modifiers
#8
Cynthia L Fisher, Hendrik Marks, Lily Ting-Yin Cho, Robert Andrews, Sam Wormald, Thomas Carroll, Vivek Iyer, Peri Tate, Barry Rosen, Hendrik G Stunnenberg, Amanda G Fisher, William C Skarnes
Mouse embryonic stem (ES) cells are a popular model system to study biological processes, though uncovering recessive phenotypes requires inactivating both alleles. Building upon resources from the International Knockout Mouse Consortium (IKMC), we developed a targeting vector for second allele inactivation in conditional-ready IKMC 'knockout-first' ES cell lines. We applied our technology to several epigenetic regulators, recovering bi-allelic targeted clones with a high efficiency of 60% and used Flp recombinase to restore expression in two null cell lines to demonstrate how our system confirms causality through mutant phenotype reversion...
September 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28981713/crispr-cas9-based-genome-editing-for-simultaneous-interference-with-gene-expression-and-protein-stability
#9
Virginia Martínez, Ida Lauritsen, Tonja Hobel, Songyuan Li, Alex Toftgaard Nielsen, Morten H H Nørholm
Interference with genes is the foundation of reverse genetics and is key to manipulation of living cells for biomedical and biotechnological applications. However, classical genetic knockout and transcriptional knockdown technologies have different drawbacks and offer no control over existing protein levels. Here, we describe an efficient genome editing approach that affects specific protein abundances by changing the rates of both RNA synthesis and protein degradation, based on the two cross-kingdom control mechanisms CRISPRi and the N-end rule for protein stability...
September 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28974058/network-based-method-for-identifying-co-regeneration-genes-in-bone-dentin-nerve-and-vessel-tissues
#10
Lei Chen, Hongying Pan, Yu-Hang Zhang, Kaiyan Feng, XiangYin Kong, Tao Huang, Yu-Dong Cai
Bone and dental diseases are serious public health problems. Most current clinical treatments for these diseases can produce side effects. Regeneration is a promising therapy for bone and dental diseases, yielding natural tissue recovery with few side effects. Because soft tissues inside the bone and dentin are densely populated with nerves and vessels, the study of bone and dentin regeneration should also consider the co-regeneration of nerves and vessels. In this study, a network-based method to identify co-regeneration genes for bone, dentin, nerve and vessel was constructed based on an extensive network of protein-protein interactions...
October 2, 2017: Genes
https://www.readbyqxmd.com/read/28973457/direct-modulation-of-t-box-riboswitch-controlled-transcription-by-protein-synthesis-inhibitors
#11
Vassiliki Stamatopoulou, Maria Apostolidi, Shuang Li, Katerina Lamprinou, Athanasios Papakyriakou, Jinwei Zhang, Constantinos Stathopoulos
Recently, it was discovered that exposure to mainstream antibiotics activate numerous bacterial riboregulators that control antibiotic resistance genes including metabolite-binding riboswitches and other transcription attenuators. However, the effects of commonly used antibiotics, many of which exhibit RNA-binding properties, on the widespread T-box riboswitches, remain unknown. In Staphylococcus aureus, a species-specific glyS T-box controls the supply of glycine for both ribosomal translation and cell wall synthesis, making it a promising target for next-generation antimicrobials...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28972570/high-throughput-rnai-screen-for-essential-genes-and-drug-synergistic-combinations-in-colorectal-cancer
#12
Steven P Williams, Andrew S Barthorpe, Howard Lightfoot, Mathew J Garnett, Ultan McDermott
Metastatic colorectal cancer is a leading cause of cancer death. However, current therapy options are limited to chemotherapy, with the addition of anti-EGFR antibodies for patients with RAS wild-type tumours. Novel drug targets, or drug combinations that induce a synergistic response, would be of great benefit to patients. The identification of genes that are essential for cell survival can be undertaken using functional genomics screens. Furthermore, performing such screens in the presence of a targeted agent would allow the identification of combinations that result in a synthetic lethal interaction...
October 3, 2017: Scientific Data
https://www.readbyqxmd.com/read/28971869/abci3-a-new-mitochondrial-abc-transporter-from-leishmania-major-involved-in-susceptibility-to-antimonials-and-infectivity
#13
Talia Arcari, José Ignacio Manzano, Francisco Gamarro
We have identified and characterized ABCI3 as a new mitochondrial ABC transporter from Leishmania major. Localization studies using confocal microscope, surface biotinylation assay and trypsin digestion after digitonin permeabilization suggested that ABCI3 presents a dual localization in both mitochondria and plasma membrane. Using single-knock out parasites for ABCI3 (ABCI3(+/-) ), we provided evidence that ABCI3 is directly involved in Sb(III) and metal ions susceptibility. Attempts to obtain double knock-out parasites for ABCI3 were unsuccessful, suggesting that ABCI3 could be an essential gene in L...
October 2, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28969074/mir-19b-promotes-breast-cancer-metastasis-through-targeting-mylip-and-its-related-cell-adhesion-molecules
#14
Luqing Zhao, Yuelong Zhao, Yanong He, Yitao Mao
miR-19b is a key molecule for cancer development, however its crucial roles in breast cancer metastasis are rarely studied right now. In this study, using several bioinformatics databases to predict the downstream targets for miR-19b, we verified that a novel target gene, myosin regulatory light chain interacting protein (MYLIP), could be directly down-regulated by miR-19b through its 3'-UTR region. MYLIP belongs to the cytoskeletal protein clusters and is involved in the regulation of cell movement and migration...
September 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28967614/tissue-specific-genome-editing-of-lamina-c-in-the-posterior-silk-glands-of-bombyx-mori
#15
Yuanyuan Liu, Sanyuan Ma, Jiasong Chang, Tong Zhang, Xiaogang Wang, Run Shi, Jianduo Zhang, Wei Lu, Yue Liu, Qingyou Xia
The RNA-guided CRISPR/Cas9 system has been shown to be a powerful tool for genome editing in various organisms. A comprehensive toolbox for multiplex genome editing has been developed for the silkworm, Bombyx mori, a lepidopteran model insect of economic importance. However, as previous methods mainly relied on delivery of transient Cas9/guide RNA (gRNA), they could not be used in loss-of-function studies of essential genes. Here, we report a simple and versatile tissue-specific genome editing strategy. We perform a proof-of-principle demonstration by establishing and crossing two transgenic B...
September 14, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28961729/identification-of-a-fabz-gene-essential-for-flexirubin-synthesis-in-cytophaga-hutchinsonii
#16
Xinfeng Bai, Shibo Zhu, Xifeng Wang, Weican Zhang, Changheng Liu, Xuemei Lu
Cytophaga hutchinsonii, an aerobic soil bacterium which could degrade cellulose, produces yellow flexirubin pigments. In this study, fabZ, annotated as a putative β-hydroxyacyl-(acyl carrier protein) (ACP) dehydratase gene, was identified by insertional mutation and gene deletion as an essential gene for flexirubin pigment synthesis. The availability of a FabZ-mutant that fails to produce flexirubin allowed us to investigate the biological role of the pigment in C. hutchinsonii. Loss of flexirubin made the FabZ-mutant more sensitive to UV radiation, oxidative stress and alkaline stress than the wild-type...
September 13, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28955502/systematic-analysis-of-human-telomeric-dysfunction-using-inducible-telosome-shelterin-crispr-cas9-knockout-cells
#17
Hyeung Kim, Feng Li, Quanyuan He, Tingting Deng, Jun Xu, Feng Jin, Cristian Coarfa, Nagireddy Putluri, Dan Liu, Zhou Songyang
CRISPR/Cas9 technology enables efficient loss-of-function analysis of human genes using somatic cells. Studies of essential genes, however, require conditional knockout (KO) cells. Here, we describe the generation of inducible CRISPR KO human cell lines for the subunits of the telosome/shelterin complex, TRF1, TRF2, RAP1, TIN2, TPP1 and POT1, which directly interact with telomeres or can bind to telomeres through association with other subunits. Homozygous inactivation of several subunits is lethal in mice, and most loss-of-function studies of human telomere regulators have relied on RNA interference-mediated gene knockdown, which suffers its own limitations...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28953874/a-reversible-haploid-mouse-embryonic-stem-cell-biobank-resource-for-functional-genomics
#18
Ulrich Elling, Reiner A Wimmer, Andreas Leibbrandt, Thomas Burkard, Georg Michlits, Alexandra Leopoldi, Thomas Micheler, Dana Abdeen, Sergei Zhuk, Irene M Aspalter, Cornelia Handl, Julia Liebergesell, Maria Hubmann, Anna-Maria Husa, Manuela Kinzer, Nicole Schuller, Ellen Wetzel, Nina van de Loo, Jorge Arturo Zepeda Martinez, David Estoppey, Ralph Riedl, Fengtang Yang, Beiyuan Fu, Thomas Dechat, Zoltán Ivics, Chukwuma A Agu, Oliver Bell, Dieter Blaas, Holger Gerhardt, Dominic Hoepfner, Alexander Stark, Josef M Penninger
The ability to directly uncover the contributions of genes to a given phenotype is fundamental for biology research. However, ostensibly homogeneous cell populations exhibit large clonal variance that can confound analyses and undermine reproducibility. Here we used genome-saturated mutagenesis to create a biobank of over 100,000 individual haploid mouse embryonic stem (mES) cell lines targeting 16,970 genes with genetically barcoded, conditional and reversible mutations. This Haplobank is, to our knowledge, the largest resource of hemi/homozygous mutant mES cells to date and is available to all researchers...
October 5, 2017: Nature
https://www.readbyqxmd.com/read/28941315/host-induced-silencing-of-essential-genes-in-puccinia-triticina-through-transgenic-expression-of-rnai-sequences-reduces-severity-of-leaf-rust-infection-in-wheat
#19
Vinay Panwar, Mark Jordan, Brent McCallum, Guus Bakkeren
Leaf rust, caused by the pathogenic fungus Puccinia triticina (Pt), is one of the most serious biotic threats to sustainable wheat production worldwide. This obligate biotrophic pathogen is prevalent worldwide and is known for rapid adaptive evolution to overcome resistant wheat varieties. Novel disease control approaches are therefore required to minimize the yield losses caused by Pt. Having shown previously the potential of host-delivered RNA interference (HD-RNAi) in functional screening of Pt genes involved in pathogenesis, we here evaluated the use of this technology in transgenic wheat plants as a method to achieve protection against wheat leaf rust (WLR) infection...
September 23, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28936208/cas9-nickase-assisted-rna-repression-enables-stable-and-efficient-manipulation-of-essential-metabolic-genes-in-clostridium-cellulolyticum
#20
Tao Xu, Yongchao Li, Zhili He, Joy D Van Nostrand, Jizhong Zhou
Essential gene functions remain largely underexplored in bacteria. Clostridium cellulolyticum is a promising candidate for consolidated bioprocessing; however, its genetic manipulation to reduce the formation of less-valuable acetate is technically challenging due to the essentiality of acetate-producing genes. Here we developed a Cas9 nickase-assisted chromosome-based RNA repression to stably manipulate essential genes in C. cellulolyticum. Our plasmid-based expression of antisense RNA (asRNA) molecules targeting the phosphotransacetylase (pta) gene successfully reduced the enzymatic activity by 35% in cellobiose-grown cells, metabolically decreased the acetate titer by 15 and 52% in wildtype transformants on cellulose and xylan, respectively...
2017: Frontiers in Microbiology
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