Faculty Opinions recommendation of A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

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A genome-wide screen in the mouse liver reveals sex-specific and cell non-autonomous regulation of cell fitness

10.1101/2021.01.30.428976 ◽

2021 ◽

Author(s):

Heather R. Keys ◽

Kristin A. Knouse

Keyword(s):

Functional Genomics ◽

High Throughput ◽

Mouse Liver ◽

Ex Vivo ◽

Screening Method ◽

Living Organism ◽

Cellular Processes ◽

Autonomous Regulation ◽

Genome Wide ◽

A Genome

ABSTRACTOur ability to understand and modulate mammalian physiology and disease requires knowing how all genes contribute to any given phenotype in the organism. Genome-wide screening using CRISPR-Cas9 has emerged as a powerful method for the genetic dissection of cellular processes1,2, but the need to stably deliver single guide RNAs to millions of cells has restricted its implementation to ex vivo systems. These ex vivo systems cannot reproduce all of the cellular phenotypes observed in vivo nor can they recapitulate all of the factors that influence these phenotypes. There thus remains a pressing need for high-throughput functional genomics in a living organism. Here, we establish accessible genome-wide screening in the mouse liver and use this approach to uncover the complete regulation of cellular fitness in a living organism. We discover novel sex-specific and cell non-autonomous regulation of cell growth and viability. In particular, we find that the class I major histocompatibility complex is essential for preventing immune-mediated clearance of hepatocytes. Our approach provides the first comprehensive picture of cell fitness in a living organism and highlights the importance of investigating cellular phenomena in their native context. Our screening method is robust, scalable, and easily adapted to examine diverse cellular processes using any CRISPR application. We have hereby established a foundation for high-throughput functional genomics in a living mammal, enabling unprecedented insight into mammalian physiology and disease.

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A Genome-wide siRNA Screen Identifies Proteasome Addiction as a Vulnerability of Basal-like Triple-Negative Breast Cancer Cells

Cancer Cell ◽

10.1016/j.ccr.2013.07.008 ◽

2013 ◽

Vol 24 (2) ◽

pp. 182-196 ◽

Cited By ~ 99

Author(s):

Fabio Petrocca ◽

Gabriel Altschuler ◽

Shen Mynn Tan ◽

Marc L. Mendillo ◽

Haoheng Yan ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Cells ◽

Triple Negative Breast Cancer ◽

Breast Cancer Cells ◽

Triple Negative ◽

Sirna Screen ◽

Genome Wide ◽

A Genome

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An inducible CRISPR interference library for genetic interrogation of Saccharomyces cerevisiae biology

Communications Biology ◽

10.1038/s42003-020-01452-9 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Amir Momen-Roknabadi ◽

Panos Oikonomou ◽

Maxwell Zegans ◽

Saeed Tavazoie

Keyword(s):

Saccharomyces Cerevisiae ◽

Transcriptional Repression ◽

Nucleosome Occupancy ◽

Design Parameters ◽

Experimental Conditions ◽

Crispr Interference ◽

Cellular Processes ◽

Genome Wide ◽

Reliable Assessment ◽

A Genome

AbstractGenome-scale CRISPR interference (CRISPRi) is widely utilized to study cellular processes in a variety of organisms. Despite the dominance of Saccharomyces cerevisiae as a model eukaryote, an inducible genome-wide CRISPRi library in yeast has not yet been presented. Here, we present a genome-wide, inducible CRISPRi library, based on spacer design rules optimized for S. cerevisiae. We have validated this library for genome-wide interrogation of gene function across a variety of applications, including accurate discovery of haploinsufficient genes and identification of enzymatic and regulatory genes involved in adenine and arginine biosynthesis. The comprehensive nature of the library also revealed refined spacer design parameters for transcriptional repression, including location, nucleosome occupancy and nucleotide features. CRISPRi screens using this library can identify genes and pathways with high precision and a low false discovery rate across a variety of experimental conditions, enabling rapid and reliable assessment of genetic function and interactions in S. cerevisiae.

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A Genome-Wide siRNA Screen Reveals Multiple mTORC1 Independent Signaling Pathways Regulating Autophagy under Normal Nutritional Conditions

Developmental Cell ◽

10.1016/j.devcel.2010.05.005 ◽

2010 ◽

Vol 18 (6) ◽

pp. 1041-1052 ◽

Cited By ~ 154

Author(s):

Marta M. Lipinski ◽

Greg Hoffman ◽

Aylwin Ng ◽

Wen Zhou ◽

Bénédicte F. Py ◽

...

Keyword(s):

Signaling Pathways ◽

Sirna Screen ◽

Nutritional Conditions ◽

Genome Wide ◽

A Genome

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Study strategies for long non-coding RNAs and their roles in regulating gene expression

Cellular & Molecular Biology Letters ◽

10.1515/cmble-2015-0021 ◽

2015 ◽

Vol 20 (2) ◽

Cited By ~ 3

Author(s):

Dan Qin ◽

Cunshuan Xu

Keyword(s):

Gene Expression ◽

Regulatory Network ◽

Experimental Methods ◽

Study Strategies ◽

Mechanisms Of Action ◽

Cellular Processes ◽

Genome Wide ◽

A Genome ◽

Wide Scale ◽

Non Coding Rnas

AbstractLong non-coding RNAs (lncRNAs) have attracted considerable attention recently due to their involvement in numerous key cellular processes and in the development of various disorders. New high-throughput methods enable their study on a genome-wide scale. Numerous lncRNAs have been identified and characterized as important members of the biological regulatory network, with significant roles in regulating gene expression at the epigenetic, transcriptional and post-transcriptional levels. This paper summarizes the diverse mechanisms of action of these lncRNAs and looks at the study strategies in this field. A major challenge in future study is to establish more effective bioinformatics and experimental methods to explore the functions, detailed mechanisms of action and structures deciding the functional diversity of lncRNAs, since the vast majority remain unresolved.

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