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Literature DB >> 30954477

iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast.

Xianan Liu¹, Zhimin Liu¹, Adam K Dziulko¹, Fangfei Li², Darach Miller³, Robert D Morabito¹, Danielle Francois¹, Sasha F Levy⁴.

Abstract

We developed a flexible toolkit for combinatorial screening in Saccharomyces cerevisiae, which generates large libraries of cells, each uniquely barcoded to mark a combination of DNA elements. This interaction sequencing platform (iSeq 2.0) includes genomic landing pads that assemble combinations through sequential integration of plasmids or yeast mating, 15 barcoded plasmid libraries containing split selectable markers (URA3AI, KanMXAI, HphMXAI, and NatMXAI), and an array of ∼24,000 "double-barcoder" strains that can make existing yeast libraries iSeq compatible. Various DNA elements are compatible with iSeq: DNA introduced on integrating plasmids, engineered genomic modifications, or entire genetic backgrounds. DNA element libraries are modular and interchangeable, and any two libraries can be combined, making iSeq capable of performing many new combinatorial screens by short-read sequencing.

Entities: Chemical Disease Gene Mutation Species

Keywords: Cre; Saccharomyces cerevisiae, barcode sequencing; combinatorial screening; fitness; iSeq; interaction screening; landing pad; loxP; yeast

Mesh：

Substances：

Year: 2019 PMID： 30954477 PMCID： PMC6483859 DOI： 10.1016/j.cels.2019.03.005

Source DB: PubMed Journal: Cell Syst ISSN： 2405-4712 Impact factor: 10.304

69 in total

1. Global analysis of protein localization in budding yeast.

Authors: Won-Ki Huh; James V Falvo; Luke C Gerke; Adam S Carroll; Russell W Howson; Jonathan S Weissman; Erin K O'Shea
Journal: Nature Date: 2003-10-16 Impact factor: 49.962

2. Global mapping of the yeast genetic interaction network.

Authors: Amy Hin Yan Tong; Guillaume Lesage; Gary D Bader; Huiming Ding; Hong Xu; Xiaofeng Xin; James Young; Gabriel F Berriz; Renee L Brost; Michael Chang; YiQun Chen; Xin Cheng; Gordon Chua; Helena Friesen; Debra S Goldberg; Jennifer Haynes; Christine Humphries; Grace He; Shamiza Hussein; Lizhu Ke; Nevan Krogan; Zhijian Li; Joshua N Levinson; Hong Lu; Patrice Ménard; Christella Munyana; Ainslie B Parsons; Owen Ryan; Raffi Tonikian; Tania Roberts; Anne-Marie Sdicu; Jesse Shapiro; Bilal Sheikh; Bernhard Suter; Sharyl L Wong; Lan V Zhang; Hongwei Zhu; Christopher G Burd; Sean Munro; Chris Sander; Jasper Rine; Jack Greenblatt; Matthias Peter; Anthony Bretscher; Graham Bell; Frederick P Roth; Grant W Brown; Brenda Andrews; Howard Bussey; Charles Boone
Journal: Science Date: 2004-02-06 Impact factor: 47.728

3. Massively parallel high-order combinatorial genetics in human cells.

Authors: Alan S L Wong; Gigi C G Choi; Allen A Cheng; Oliver Purcell; Timothy K Lu
Journal: Nat Biotechnol Date: 2015-08-17 Impact factor: 54.908

4. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method.

Authors: R Daniel Gietz; Robert H Schiestl
Journal: Nat Protoc Date: 2007 Impact factor: 13.491

5. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.

Authors: Ryan D Morin; Elbert Chang; Anca Petrescu; Nancy Liao; Malachi Griffith; William Chow; Robert Kirkpatrick; Yaron S Butterfield; Alice C Young; Jeffrey Stott; Sarah Barber; Ryan Babakaiff; Mark C Dickson; Corey Matsuo; David Wong; George S Yang; Duane E Smailus; Keith D Wetherby; Peggy N Kwong; Jane Grimwood; Charles P Brinkley; Mabel Brown-John; Natalie D Reddix-Dugue; Michael Mayo; Jeremy Schmutz; Jaclyn Beland; Morgan Park; Susan Gibson; Teika Olson; Gerard G Bouffard; Miranda Tsai; Ruth Featherstone; Steve Chand; Asim S Siddiqui; Wonhee Jang; Ed Lee; Steven L Klein; Robert W Blakesley; Barry R Zeeberg; Sudarshan Narasimhan; John N Weinstein; Christa Prange Pennacchio; Richard M Myers; Eric D Green; Lukas Wagner; Daniela S Gerhard; Marco A Marra; Steven J M Jones; Robert A Holt
Journal: Genome Res Date: 2006-05-03 Impact factor: 9.043

6. The next frontier of systems biology: higher-order and interspecies interactions.

Authors: Michael A Fischbach; Nevan J Krogan
Journal: Genome Biol Date: 2010-05-05 Impact factor: 13.583

7. New 'marker swap' plasmids for converting selectable markers on budding yeast gene disruptions and plasmids.

Authors: Warren P Voth; Yi Wei Jiang; David J Stillman
Journal: Yeast Date: 2003-08 Impact factor: 3.239

8. Functional repurposing revealed by comparing S. pombe and S. cerevisiae genetic interactions.

Authors: Adam Frost; Marc G Elgort; Onn Brandman; Clinton Ives; Sean R Collins; Lakshmi Miller-Vedam; Jimena Weibezahn; Marco Y Hein; Ina Poser; Matthias Mann; Anthony A Hyman; Jonathan S Weissman
Journal: Cell Date: 2012-06-08 Impact factor: 41.582

9. A proteome-scale map of the human interactome network.

Authors: Thomas Rolland; Murat Taşan; Benoit Charloteaux; Samuel J Pevzner; Quan Zhong; Nidhi Sahni; Song Yi; Irma Lemmens; Celia Fontanillo; Roberto Mosca; Atanas Kamburov; Susan D Ghiassian; Xinping Yang; Lila Ghamsari; Dawit Balcha; Bridget E Begg; Pascal Braun; Marc Brehme; Martin P Broly; Anne-Ruxandra Carvunis; Dan Convery-Zupan; Roser Corominas; Jasmin Coulombe-Huntington; Elizabeth Dann; Matija Dreze; Amélie Dricot; Changyu Fan; Eric Franzosa; Fana Gebreab; Bryan J Gutierrez; Madeleine F Hardy; Mike Jin; Shuli Kang; Ruth Kiros; Guan Ning Lin; Katja Luck; Andrew MacWilliams; Jörg Menche; Ryan R Murray; Alexandre Palagi; Matthew M Poulin; Xavier Rambout; John Rasla; Patrick Reichert; Viviana Romero; Elien Ruyssinck; Julie M Sahalie; Annemarie Scholz; Akash A Shah; Amitabh Sharma; Yun Shen; Kerstin Spirohn; Stanley Tam; Alexander O Tejeda; Shelly A Trigg; Jean-Claude Twizere; Kerwin Vega; Jennifer Walsh; Michael E Cusick; Yu Xia; Albert-László Barabási; Lilia M Iakoucheva; Patrick Aloy; Javier De Las Rivas; Jan Tavernier; Michael A Calderwood; David E Hill; Tong Hao; Frederick P Roth; Marc Vidal
Journal: Cell Date: 2014-11-20 Impact factor: 41.582

iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast.

1. Global analysis of protein localization in budding yeast.

2. Global mapping of the yeast genetic interaction network.

3. Massively parallel high-order combinatorial genetics in human cells.

4. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method.

5. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.

6. The next frontier of systems biology: higher-order and interspecies interactions.

7. New 'marker swap' plasmids for converting selectable markers on budding yeast gene disruptions and plasmids.

8. Functional repurposing revealed by comparing S. pombe and S. cerevisiae genetic interactions.

9. A proteome-scale map of the human interactome network.

10. bz-rates: A Web Tool to Estimate Mutation Rates from Fluctuation Analysis.

1. Overdominant and partially dominant mutations drive clonal adaptation in diploid Saccharomyces cerevisiae.

2. A large accessory protein interactome is rewired across environments.

3. Emergence and propagation of epistasis in metabolic networks.

4. The interplay of additivity, dominance, and epistasis on fitness in a diploid yeast cross.