High-throughput functional characterization of combinations of transcriptional activators and repressors.
eukaryotic gene regulation
high-throughput screening
mammalian synthetic biology
systems biology
transcriptional effector domains
Journal
Cell systems
ISSN: 2405-4720
Titre abrégé: Cell Syst
Pays: United States
ID NLM: 101656080
Informations de publication
Date de publication:
20 09 2023
20 09 2023
Historique:
received:
20
12
2022
revised:
26
06
2023
accepted:
06
07
2023
pmc-release:
20
09
2024
medline:
25
9
2023
pubmed:
6
8
2023
entrez:
5
8
2023
Statut:
ppublish
Résumé
Despite growing knowledge of the functions of individual human transcriptional effector domains, much less is understood about how multiple effector domains within the same protein combine to regulate gene expression. Here, we measure transcriptional activity for 8,400 effector domain combinations by recruiting them to reporter genes in human cells. In our assay, weak and moderate activation domains synergize to drive strong gene expression, whereas combining strong activators often results in weaker activation. In contrast, repressors combine linearly and produce full gene silencing, and repressor domains often overpower activation domains. We use this information to build a synthetic transcription factor whose function can be tuned between repression and activation independent of recruitment to target genes by using a small-molecule drug. Altogether, we outline the basic principles of how effector domains combine to regulate gene expression and demonstrate their value in building precise and flexible synthetic biology tools. A record of this paper's transparent peer review process is included in the supplemental information.
Identifiants
pubmed: 37543039
pii: S2405-4712(23)00186-2
doi: 10.1016/j.cels.2023.07.001
pmc: PMC10642976
mid: NIHMS1923680
pii:
doi:
Substances chimiques
Repressor Proteins
0
Transcription Factors
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
746-763.e5Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM007365
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM145402
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM113854
Pays : United States
Organisme : NIDDK NIH HHS
ID : F99 DK126120
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG011866
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM128947
Pays : United States
Organisme : NIDDK NIH HHS
ID : K00 DK126120
Pays : United States
Informations de copyright
Copyright © 2023 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests L.B., M.C.B., and J.T. acknowledge outside interest in Stylus Medicine.
Références
Life (Basel). 2021 Nov 19;11(11):
pubmed: 34833139
Curr Opin Genet Dev. 1998 Oct;8(5):552-9
pubmed: 9794820
Cell. 1990 Sep 21;62(6):1217-26
pubmed: 2169353
Cell Syst. 2022 Nov 16;13(11):864-873
pubmed: 36395726
Science. 2019 May 10;364(6440):593-597
pubmed: 31000590
Nat Rev Mol Cell Biol. 2016 Nov;17(11):722-735
pubmed: 27507209
Immunity. 1996 May;4(5):515-25
pubmed: 8630736
Bioinformatics. 2020 Aug 15;36(16):4508-4509
pubmed: 32647895
Cell Syst. 2018 Apr 25;6(4):444-455.e6
pubmed: 29525204
Biochemistry. 2011 Sep 27;50(38):8226-40
pubmed: 21851090
Nat Methods. 2015 Apr;12(4):326-8
pubmed: 25730490
Subcell Biochem. 2011;52:261-77
pubmed: 21557087
Curr Opin Syst Biol. 2020 Oct;23:22-31
pubmed: 33134611
Nature. 2015 Jan 29;517(7536):583-8
pubmed: 25494202
J Biol Chem. 2010 Jul 16;285(29):21951-60
pubmed: 20460684
Nature. 2023 Apr;616(7956):365-372
pubmed: 37020022
Nat Commun. 2016 Aug 10;7:12284
pubmed: 27506838
J Biochem. 2017 Jul 1;162(1):17-25
pubmed: 28057797
Phys Rev Lett. 2006 Oct 20;97(16):168302
pubmed: 17155441
Cell Rep. 2016 Oct 25;17(5):1247-1254
pubmed: 27783940
Curr Opin Genet Dev. 2017 Apr;43:73-81
pubmed: 28110180
J Biol Chem. 2000 Dec 22;275(51):40614-9
pubmed: 11016936
Nature. 1988 Aug 25;334(6184):721-4
pubmed: 3412449
Nat Protoc. 2013 Nov;8(11):2180-96
pubmed: 24136345
EMBO J. 2018 Aug 15;37(16):
pubmed: 30006452
Science. 2023 Jul 14;381(6654):198-204
pubmed: 37440660
Mol Cell. 2022 Feb 3;82(3):677-695.e7
pubmed: 35016035
Nat Commun. 2021 May 19;12(1):2953
pubmed: 34012049
Cell Syst. 2021 Nov 17;12(11):1079-1093.e6
pubmed: 34469745
J Biol Chem. 2011 Mar 11;286(10):7788-7796
pubmed: 21233212
Science. 2022 Nov 25;378(6622):848-852
pubmed: 36423287
Nat Biotechnol. 2017 Aug 8;35(8):732-746
pubmed: 28787426
Dev Cell. 2018 Apr 23;45(2):262-275.e8
pubmed: 29689199
Mol Cell. 2022 Feb 3;82(3):514-526
pubmed: 34863368
Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17454-9
pubmed: 23064634
Nat Methods. 2016 Dec;13(12):1043-1049
pubmed: 27776111
Nat Struct Mol Biol. 2007 Apr;14(4):295-300
pubmed: 17401372
Biochemistry. 2006 Jun 6;45(22):6873-88
pubmed: 16734424
J Theor Biol. 2022 Feb 21;535:110977
pubmed: 34919934
Cell. 2010 Mar 5;140(5):744-52
pubmed: 20211142
Mol Cell. 2020 Sep 17;79(6):1066
pubmed: 32946759
Genome Res. 2022 Jan;32(1):85-96
pubmed: 34961747
Cell. 2016 Feb 11;164(4):770-9
pubmed: 26830879
Cell Syst. 2022 Apr 20;13(4):334-345.e5
pubmed: 35120642
Cell Mol Life Sci. 2000 Aug;57(8-9):1207-19
pubmed: 11028913
Mol Cell Biol. 1989 Nov;9(11):4746-9
pubmed: 2557540
Nat Struct Mol Biol. 2011 Dec 18;19(1):31-9
pubmed: 22179789
Mol Cell. 2022 May 19;82(10):1878-1893.e10
pubmed: 35537448
Development. 2017 Aug 1;144(15):2719-2729
pubmed: 28765213
Cell. 2022 Apr 14;185(8):1431-1443.e16
pubmed: 35427499
EMBO J. 2002 Aug 1;21(15):4183-95
pubmed: 12145218
Cell. 2021 Apr 29;184(9):2503-2519.e17
pubmed: 33838111
Nucleic Acids Res. 2017 Sep 29;45(17):9901-9916
pubmed: 28973434
Nat Genet. 2023 Feb;55(2):346-354
pubmed: 36635387
Biochim Biophys Acta. 2010 May-Jun;1799(5-6):463-8
pubmed: 20176155
Cell Syst. 2021 Jun 16;12(6):561-592
pubmed: 34139166
Nat Methods. 2018 Jul;15(7):523-526
pubmed: 29967496
Cell. 2020 Dec 23;183(7):2020-2035.e16
pubmed: 33326746
Cell Syst. 2023 Apr 19;14(4):324-339.e7
pubmed: 37080164
Genome Inform. 2004;15(2):276-86
pubmed: 15706513
Nat Methods. 2016 Feb;13(2):127-37
pubmed: 26820547
Dev Cell. 2020 Nov 23;55(4):483-499.e7
pubmed: 33002421
Nature. 1991 Oct 24;353(6346):715-9
pubmed: 1944532
Elife. 2021 Apr 27;10:
pubmed: 33904398
Annu Rev Genomics Hum Genet. 2018 Aug 31;19:43-71
pubmed: 29852072
Mol Syst Biol. 2018 May 14;14(5):e8190
pubmed: 29759983
Biochem Biophys Res Commun. 2003 Jan 24;300(4):862-7
pubmed: 12559952
Epigenetics Chromatin. 2015 Mar 18;8:12
pubmed: 25901185
Curr Opin Genet Dev. 2022 Apr;73:101899
pubmed: 35091256
Cell. 2014 Jul 3;158(1):110-20
pubmed: 24995982
Curr Opin Genet Dev. 2018 Oct;52:13-21
pubmed: 29803990
Science. 2016 Feb 12;351(6274):720-4
pubmed: 26912859
Nucleic Acids Res. 2022 Apr 8;50(6):3239-3253
pubmed: 35234927
PLoS Biol. 2006 Oct;4(10):e309
pubmed: 17048983
Nat Struct Mol Biol. 2004 Sep;11(9):812-5
pubmed: 15332082
Cell. 2012 Jun 22;149(7):1447-60
pubmed: 22704655
J Biol Chem. 1997 Feb 14;272(7):4021-6
pubmed: 9020109
PLoS Comput Biol. 2019 Feb 19;15(2):e1006784
pubmed: 30779734
Cell. 2016 Sep 22;167(1):219-232.e14
pubmed: 27662090
Cell. 2018 Feb 8;172(4):650-665
pubmed: 29425488
Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14628-33
pubmed: 9843940
ACS Synth Biol. 2020 Nov 20;9(11):2917-2926
pubmed: 33166452