Genome-wide CRISPR screening identifies new regulators of glycoprotein secretion

Background: The fundamental process of protein secretion from eukaryotic cells has been well described for many years, yet gaps in our understanding of how this process is regulated remain. Methods: With the aim of identifying novel genes involved in the secretion of glycoproteins, we used a screening pipeline consisting of a pooled genome-wide CRISPR screen, followed by secondary siRNA screening of the hits to identify and validate several novel regulators of protein secretion. Results: We present approximately 50 novel genes not previously associated with protein secretion, many of which also had an effect on the structure of the Golgi apparatus. We further studied a small selection of hits to investigate their subcellular localisation. One of these, GPR161, is a novel Golgi-resident protein that we propose maintains Golgi structure via an interaction with golgin A5. Conclusions: This study has identified new factors for protein secretion involved in Golgi homeostasis.

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Genome-wide CRISPR screening identifies new regulators of glycoprotein secretion

Wellcome Open Research ◽

10.12688/wellcomeopenres.15232.2 ◽

2020 ◽

Vol 4 ◽

pp. 119

Author(s):

Stephanie Popa ◽

Julien Villeneuve ◽

Sarah Stewart ◽

Esther Perez Garcia ◽

Anna Petrunkina Harrison ◽

...

Keyword(s):

Protein Secretion ◽

Subcellular Localisation ◽

Novel Genes ◽

Genome Wide ◽

Fundamental Process ◽

Crispr Screen ◽

Secondary Sirna ◽

Golgi Structure ◽

Glycoprotein Secretion ◽

Selection Of

Background: The fundamental process of protein secretion from eukaryotic cells has been well described for many years, yet gaps in our understanding of how this process is regulated remain. Methods: With the aim of identifying novel genes involved in the secretion of glycoproteins, we used a screening pipeline consisting of a pooled genome-wide CRISPR screen, followed by secondary siRNA screening of the hits to identify and validate several novel regulators of protein secretion. Results: We present approximately 50 novel genes not previously associated with protein secretion, many of which also had an effect on the structure of the Golgi apparatus. We further studied a small selection of hits to investigate their subcellular localisation. One of these, GPR161, is a novel Golgi-resident protein that we propose maintains Golgi structure via an interaction with golgin A5. Conclusions: This study has identified new factors for protein secretion involved in Golgi homeostasis.

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Establishment of a genome-wide RNAi screen; Identification of novel genes involved in clonal maintenance of ALL

Klinische Pädiatrie ◽

10.1055/s-0034-1374830 ◽

2014 ◽

Vol 226 (03) ◽

Author(s):

F Ponthan ◽

D Pal ◽

J Vormoor ◽

O Heidenreich

Keyword(s):

Rnai Screen ◽

Novel Genes ◽

Genome Wide ◽

A Genome

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Genome-wide diversity analysis for signatures of selection of Bos indicus adaptability under extreme agro-climatic conditions of temperate and tropical ecosystems

Animal Gene ◽

10.1016/j.angen.2021.200115 ◽

2021 ◽

pp. 200115

Author(s):

Shivam Bhardwaj ◽

Sanjeev Singh ◽

Indrajit Ganguly ◽

A.K. Bhatia ◽

Vijay K. Bharti ◽

...

Keyword(s):

Bos Indicus ◽

Climatic Conditions ◽

Diversity Analysis ◽

Tropical Ecosystems ◽

Genome Wide ◽

Signatures Of Selection ◽

Selection Of

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A genome-wide CRISPR screen identifies UFMylation and TRAMP-like complexes as host factors required for hepatitis A virus infection

Cell Reports ◽

10.1016/j.celrep.2021.108859 ◽

2021 ◽

Vol 34 (11) ◽

pp. 108859

Author(s):

Jessie Kulsuptrakul ◽

Ruofan Wang ◽

Nathan L. Meyers ◽

Melanie Ott ◽

Andreas S. Puschnik

Keyword(s):

Virus Infection ◽

Hepatitis A ◽

Hepatitis A Virus ◽

Host Factors ◽

Genome Wide ◽

A Genome ◽

Crispr Screen

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A Genome-wide CRISPR Screen Identifies CDC25A as a Determinant of Sensitivity to ATR Inhibitors

Molecular Cell ◽

10.1016/j.molcel.2016.03.006 ◽

2016 ◽

Vol 62 (2) ◽

pp. 307-313 ◽

Cited By ~ 87

Author(s):

Sergio Ruiz ◽

Cristina Mayor-Ruiz ◽

Vanesa Lafarga ◽

Matilde Murga ◽

Maria Vega-Sendino ◽

...

Keyword(s):

Genome Wide ◽

A Genome ◽

Crispr Screen

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Analysis of yield and oil from a series of canola breeding trials. Part II. Exploring variety by environment interaction using factor analysisThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽

10.1139/g10-080 ◽

2010 ◽

Vol 53 (11) ◽

pp. 1002-1016 ◽

Cited By ~ 59

Author(s):

B.R. Cullis ◽

A.B. Smith ◽

C.P. Beeck ◽

W.A. Cowling

Keyword(s):

Pedigree Information ◽

Environment Interaction ◽

Correlation Matrices ◽

New Approach ◽

Genome Wide ◽

Selection Indices ◽

New Varieties ◽

Oilseed Brassicas ◽

Analytic Models ◽

Selection Of

Exploring and exploiting variety by environment (V × E) interaction is one of the major challenges facing plant breeders. In paper I of this series, we presented an approach to modelling V × E interaction in the analysis of complex multi-environment trials using factor analytic models. In this paper, we develop a range of statistical tools which explore V × E interaction in this context. These tools include graphical displays such as heat-maps of genetic correlation matrices as well as so-called E-scaled uniplots that are a more informative alternative to the classical biplot for large plant breeding multi-environment trials. We also present a new approach to prediction for multi-environment trials that include pedigree information. This approach allows meaningful selection indices to be formed either for potential new varieties or potential parents.

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Novel genes identified in a high-density genome wide association study for nicotine dependence

Human Molecular Genetics ◽

10.1093/hmg/ddl441 ◽

2006 ◽

Vol 16 (1) ◽

pp. 24-35 ◽

Cited By ~ 437

Author(s):

Laura Jean Bierut ◽

Pamela A.F. Madden ◽

Naomi Breslau ◽

Eric O. Johnson ◽

Dorothy Hatsukami ◽

...

Keyword(s):

Association Study ◽

Nicotine Dependence ◽

Genome Wide Association Study ◽

High Density ◽

Genome Wide Association ◽

Novel Genes ◽

Genome Wide

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A Robust Rerank Approach for Feature Selection and Its Application to Pooling-Based GWA Studies

Computational and Mathematical Methods in Medicine ◽

10.1155/2013/860673 ◽

2013 ◽

Vol 2013 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Jia-Rou Liu ◽

Po-Hsiu Kuo ◽

Hung Hung

Keyword(s):

Characteristic Curve ◽

Real Data ◽

Tuning Parameter ◽

Practical Implementation ◽

Tuning Parameters ◽

Genome Wide ◽

Feature Based ◽

The Difference ◽

Gwa Studies ◽

Selection Of

Large-p-small-ndatasets are commonly encountered in modern biomedical studies. To detect the difference between two groups, conventional methods would fail to apply due to the instability in estimating variances int-test and a high proportion of tied values in AUC (area under the receiver operating characteristic curve) estimates. The significance analysis of microarrays (SAM) may also not be satisfactory, since its performance is sensitive to the tuning parameter, and its selection is not straightforward. In this work, we propose a robust rerank approach to overcome the above-mentioned diffculties. In particular, we obtain a rank-based statistic for each feature based on the concept of “rank-over-variable.” Techniques of “random subset” and “rerank” are then iteratively applied to rank features, and the leading features will be selected for further studies. The proposed re-rank approach is especially applicable for large-p-small-ndatasets. Moreover, it is insensitive to the selection of tuning parameters, which is an appealing property for practical implementation. Simulation studies and real data analysis of pooling-based genome wide association (GWA) studies demonstrate the usefulness of our method.

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Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62

eLife ◽

10.7554/elife.17290 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 78

Author(s):

Rowena DeJesus ◽

Francesca Moretti ◽

Gregory McAllister ◽

Zuncai Wang ◽

Phil Bergman ◽

...

Keyword(s):

Adaptor Protein ◽

Er Stress Response ◽

Genome Wide ◽

A Genome ◽

Crispr Screen ◽

Selection Step ◽

A Cell ◽

Cell Type Specific ◽

Cellular Pathways ◽

Mtor Signalling

SQSTM1 is an adaptor protein that integrates multiple cellular signaling pathways and whose expression is tightly regulated at the transcriptional and post-translational level. Here, we describe a forward genetic screening paradigm exploiting CRISPR-mediated genome editing coupled to a cell selection step by FACS to identify regulators of SQSTM1. Through systematic comparison of pooled libraries, we show that CRISPR is superior to RNAi in identifying known SQSTM1 modulators. A genome-wide CRISPR screen exposed MTOR signalling and the entire macroautophagy machinery as key regulators of SQSTM1 and identified several novel modulators including HNRNPM, SLC39A14, SRRD, PGK1 and the ufmylation cascade. We show that ufmylation regulates SQSTM1 by eliciting a cell type-specific ER stress response which induces SQSTM1 expression and results in its accumulation in the cytosol. This study validates pooled CRISPR screening as a powerful method to map the repertoire of cellular pathways that regulate the fate of an individual target protein.

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