Improved discovery of genetic interactions using CRISPRiSeq across multiple environments.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
04 2019
04 2019
Historique:
received:
19
11
2018
accepted:
13
02
2019
pubmed:
21
2
2019
medline:
14
6
2019
entrez:
21
2
2019
Statut:
ppublish
Résumé
Large-scale genetic interaction (GI) screens in yeast have been invaluable for our understanding of molecular systems biology and for characterizing novel gene function. Owing in part to the high costs and long experiment times required, a preponderance of GI data has been generated in a single environmental condition. However, an unknown fraction of GIs may be specific to other conditions. Here, we developed a pooled-growth CRISPRi-based sequencing assay for GIs, CRISPRiSeq, which increases throughput such that GIs can be easily assayed across multiple growth conditions. We assayed the fitness of approximately 17,000 strains encompassing approximately 7700 pairwise interactions in five conditions and found that the additional conditions increased the number of GIs detected nearly threefold over the number detected in rich media alone. In addition, we found that condition-specific GIs are prevalent and improved the power to functionally classify genes. Finally, we found new links during respiratory growth between members of the Ras nutrient-sensing pathway and both the COG complex and a gene of unknown function. Our results highlight the potential of conditional GI screens to improve our understanding of cellular genetic networks.
Identifiants
pubmed: 30782640
pii: gr.246603.118
doi: 10.1101/gr.246603.118
pmc: PMC6442382
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
668-681Subventions
Organisme : NHGRI NIH HHS
ID : R01 HG008354
Pays : United States
Organisme : NHGRI NIH HHS
ID : P01 HG000205
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM110275
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG000044
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA124435
Pays : United States
Organisme : NHGRI NIH HHS
ID : R21 HG009255
Pays : United States
Organisme : NIGMS NIH HHS
ID : U01 GM110706
Pays : United States
Informations de copyright
© 2019 Jaffe et al.; Published by Cold Spring Harbor Laboratory Press.
Références
EMBO J. 2000 Apr 3;19(7):1661-71
pubmed: 10747033
Mol Biol Cell. 2000 Dec;11(12):4241-57
pubmed: 11102521
Science. 2001 Dec 14;294(5550):2364-8
pubmed: 11743205
Nature. 2003 Oct 16;425(6959):686-91
pubmed: 14562095
Mol Cell Biol. 2004 Jan;24(1):338-51
pubmed: 14673167
J Biol Chem. 2004 May 14;279(20):20663-71
pubmed: 15016820
Mol Cell. 2004 Nov 5;16(3):487-96
pubmed: 15525520
Cell. 2005 Nov 4;123(3):507-19
pubmed: 16269340
Cell. 2006 Mar 10;124(5):1069-81
pubmed: 16487579
Nature. 2006 Jun 15;441(7095):840-6
pubmed: 16699522
Nat Genet. 2007 Feb;39(2):199-206
pubmed: 17206143
Nature. 2007 Apr 12;446(7137):806-10
pubmed: 17314980
Nat Genet. 2007 Apr;39(4):550-4
pubmed: 17322879
Nat Protoc. 2007;2(1):31-4
pubmed: 17401334
Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81
pubmed: 17982175
Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5821-6
pubmed: 18408161
Science. 2008 Apr 18;320(5874):362-5
pubmed: 18420932
Genome Res. 2008 Jul;18(7):1092-9
pubmed: 18463300
Nat Methods. 2008 Aug;5(8):711-8
pubmed: 18622397
Comp Funct Genomics. 2005;6(1-2):2-16
pubmed: 18629296
Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16653-8
pubmed: 18931302
Nat Genet. 2008 Dec;40(12):1499-504
pubmed: 19029899
PLoS Genet. 2009 Jul;5(7):e1000578
pubmed: 19629166
J Cell Biol. 2010 Jan 11;188(1):101-14
pubmed: 20065092
Science. 2010 Jan 22;327(5964):425-31
pubmed: 20093466
Science. 2010 Dec 3;330(6009):1385-9
pubmed: 21127252
Mol Biol Cell. 2011 Apr;22(7):911-20
pubmed: 21289098
Mol Cell Biol. 1990 Jul;10(7):3405-14
pubmed: 2192256
Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10420-5
pubmed: 22689976
Genetics. 2012 Sep;192(1):73-105
pubmed: 22964838
Mol Cell. 2013 Jan 24;49(2):346-58
pubmed: 23273983
Cell. 2013 Feb 14;152(4):909-22
pubmed: 23394947
Cell. 2013 Feb 28;152(5):1173-83
pubmed: 23452860
Nature. 2013 May 2;497(7447):127-31
pubmed: 23615609
Cell. 2013 Jul 18;154(2):442-51
pubmed: 23849981
Genome Biol. 2013 Jul 26;14(7):R76
pubmed: 23889884
Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):14024-9
pubmed: 23924614
Genome Med. 2014 Sep 17;6(9):68
pubmed: 25302077
Nat Rev Mol Cell Biol. 2015 Apr;16(4):258-64
pubmed: 25549891
PLoS One. 2015 Jan 27;10(1):e0114911
pubmed: 25625594
Nature. 2015 Mar 12;519(7542):181-6
pubmed: 25731169
Elife. 2015 Mar 06;4:null
pubmed: 25748138
Mol Syst Biol. 2015 Apr 17;11(4):800
pubmed: 25888283
Cell Rep. 2016 Jan 26;14(3):648-661
pubmed: 26774489
Genetics. 2016 Apr;202(4):1395-409
pubmed: 26837754
Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):2544-9
pubmed: 26864203
Genome Biol. 2016 Mar 08;17:45
pubmed: 26956608
Cell. 2016 Jun 2;165(6):1493-1506
pubmed: 27238023
J Bacteriol. 2016 Oct 7;198(21):2925-2935
pubmed: 27528508
Science. 2016 Sep 23;353(6306):
pubmed: 27708008
Science. 2016 Nov 4;354(6312):
pubmed: 27811238
G3 (Bethesda). 2017 Jan 5;7(1):143-153
pubmed: 27821633
Cell. 2016 Dec 15;167(7):1853-1866.e17
pubmed: 27984732
Microb Cell Fact. 2017 Feb 8;16(1):25
pubmed: 28179021
Mol Syst Biol. 2017 Feb 13;13(2):913
pubmed: 28193641
Metab Eng. 2017 Mar;40:14-22
pubmed: 28212815
Nat Biotechnol. 2017 May;35(5):463-474
pubmed: 28319085
Nat Methods. 2017 Jun;14(6):577-580
pubmed: 28481362
Mol Syst Biol. 2017 May 10;13(5):931
pubmed: 28490437
Nat Commun. 2017 May 25;8:15586
pubmed: 28541284
Science. 2017 Sep 29;357(6358):1420-1424
pubmed: 28963258
Nat Microbiol. 2018 Jan;3(1):73-82
pubmed: 29062088
Science. 2018 Apr 20;360(6386):null
pubmed: 29674565
Mol Syst Biol. 2018 May 28;14(5):e7985
pubmed: 29807908
J Biol Chem. 1997 Jul 4;272(27):17134-8
pubmed: 9202032