Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells.
Animals
Binding Sites
Cell Cycle Proteins
/ metabolism
Cell Line, Tumor
Cerebral Cortex
/ metabolism
Chromatin Immunoprecipitation
DNA Transposable Elements
/ genetics
Gene Expression
Hepatocyte Nuclear Factor 3-beta
/ genetics
Humans
Mice
Protein Binding
Sequence Analysis, RNA
Single-Cell Analysis
/ methods
Sp1 Transcription Factor
/ genetics
Transcription Factors
/ genetics
bromodomains
calling cards
cell state
mouse cortex
single cell
transcription factors
transposons
Journal
Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066
Informations de publication
Date de publication:
20 08 2020
20 08 2020
Historique:
received:
21
02
2019
revised:
14
04
2020
accepted:
23
06
2020
pubmed:
28
7
2020
medline:
2
4
2021
entrez:
26
7
2020
Statut:
ppublish
Résumé
Cellular heterogeneity confounds in situ assays of transcription factor (TF) binding. Single-cell RNA sequencing (scRNA-seq) deconvolves cell types from gene expression, but no technology links cell identity to TF binding sites (TFBS) in those cell types. We present self-reporting transposons (SRTs) and use them in single-cell calling cards (scCC), a novel assay for simultaneously measuring gene expression and mapping TFBS in single cells. The genomic locations of SRTs are recovered from mRNA, and SRTs deposited by exogenous, TF-transposase fusions can be used to map TFBS. We then present scCC, which map SRTs from scRNA-seq libraries, simultaneously identifying cell types and TFBS in those same cells. We benchmark multiple TFs with this technique. Next, we use scCC to discover BRD4-mediated cell-state transitions in K562 cells. Finally, we map BRD4 binding sites in the mouse cortex at single-cell resolution, establishing a new method for studying TF biology in situ.
Identifiants
pubmed: 32710817
pii: S0092-8674(20)30814-X
doi: 10.1016/j.cell.2020.06.037
pmc: PMC7510185
mid: NIHMS1608211
pii:
doi:
Substances chimiques
BRD4 protein, human
0
Cell Cycle Proteins
0
DNA Transposable Elements
0
FOXA2 protein, human
0
Sp1 Transcription Factor
0
Transcription Factors
0
Hepatocyte Nuclear Factor 3-beta
135845-92-0
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
992-1008.e21Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM008151
Pays : United States
Organisme : NIMH NIH HHS
ID : U01 MH109133
Pays : United States
Organisme : NIMH NIH HHS
ID : RF1 MH117070
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007200
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG000045
Pays : United States
Organisme : NINDS NIH HHS
ID : F32 NS105363
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM126112
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007067
Pays : United States
Organisme : NICHD NIH HHS
ID : P50 HD103525
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR002345
Pays : United States
Organisme : NHGRI NIH HHS
ID : F30 HG009986
Pays : United States
Organisme : NIGMS NIH HHS
ID : R25 GM103757
Pays : United States
Organisme : NHGRI NIH HHS
ID : R21 HG009750
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA091842
Pays : United States
Organisme : NHLBI NIH HHS
ID : T32 HL125241
Pays : United States
Informations de copyright
Copyright © 2020 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Interests A.M., M.N.W., Z.Q., and R.D.M. have filed patent applications related to this work.
Références
Biotechniques. 1997 Sep;23(3):456-60
pubmed: 9298216
Nat Genet. 2019 Jun;51(6):1060-1066
pubmed: 31152164
Science. 2012 Sep 21;337(6101):1541-6
pubmed: 22878500
Nature. 2017 Mar 9;543(7644):205-210
pubmed: 28241143
Nucleic Acids Res. 2017 Jan 9;45(1):127-141
pubmed: 27651452
Mol Ther. 2007 Jan;15(1):139-45
pubmed: 17164785
Cell. 2011 Sep 16;146(6):904-17
pubmed: 21889194
Mol Ther. 2011 Sep;19(9):1636-44
pubmed: 21730970
Nature. 2015 Sep 24;525(7570):543-547
pubmed: 26367798
Cell. 2015 May 21;161(5):1202-1214
pubmed: 26000488
BMC Med Genomics. 2018 Nov 06;11(1):97
pubmed: 30400891
Bioinformatics. 2011 Jun 15;27(12):1696-7
pubmed: 21486936
Nat Biotechnol. 2017 Oct;35(10):936-939
pubmed: 28854175
Nat Methods. 2017 Mar;14(3):297-301
pubmed: 28099430
Nature. 1994 Sep 29;371(6496):435-8
pubmed: 8090226
Science. 2016 Nov 11;354(6313):769-773
pubmed: 27708057
J Neurosci. 2014 Sep 3;34(36):11929-47
pubmed: 25186741
Science. 2015 Mar 6;347(6226):1138-42
pubmed: 25700174
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Proc Natl Acad Sci U S A. 2021 Apr 20;118(16):
pubmed: 33850013
Science. 2018 May 25;360(6391):
pubmed: 29674431
Genes Dev. 1994 Oct 1;8(19):2282-92
pubmed: 7958895
Nat Neurosci. 2007 Jul;10(7):819-27
pubmed: 17589506
Cell. 2019 May 16;177(5):1319-1329.e11
pubmed: 30955888
Nucleic Acids Res. 1999 Aug 1;27(15):2991-3000
pubmed: 10454592
Science. 2018 Jul 27;361(6400):
pubmed: 29930091
Nat Rev Cancer. 2013 Mar;13(3):153-9
pubmed: 23550303
Nucleic Acids Res. 2007;35(12):e87
pubmed: 17576687
Cell. 2006 Aug 25;126(4):663-76
pubmed: 16904174
Cell. 2018 Aug 9;174(4):1015-1030.e16
pubmed: 30096299
Neuron. 2001 Sep 13;31(5):757-71
pubmed: 11567615
Nucleic Acids Res. 2017 Jan 4;45(D1):D183-D189
pubmed: 27899595
Cell Res. 2008 Dec;18(12):1177-89
pubmed: 19030024
Cell. 2018 Aug 9;174(4):999-1014.e22
pubmed: 30096314
J Biol Chem. 2007 Dec 21;282(51):37124-33
pubmed: 17940279
Science. 2017 Oct 13;358(6360):194-199
pubmed: 28860209
Cell. 2016 Dec 15;167(7):1853-1866.e17
pubmed: 27984732
Nat Methods. 2017 Sep;14(9):865-868
pubmed: 28759029
Nat Biotechnol. 2019 Jul;37(7):766-772
pubmed: 31209373
Nat Genet. 2015 Jan;47(1):8-12
pubmed: 25547603
Genome Biol. 2017 Jun 28;18(1):122
pubmed: 28655330
Science. 2018 Apr 13;360(6385):176-182
pubmed: 29545511
Genome Res. 2020 Sep;30(9):1317-1331
pubmed: 32887689
Nature. 2014 Oct 16;514(7522):322-7
pubmed: 25296256
Genome Biol. 2018 Feb 6;19(1):15
pubmed: 29409532
J Biol Chem. 1997 Nov 14;272(46):29207-11
pubmed: 9360999
Nat Genet. 2019 Jan;51(1):19-25
pubmed: 30559489
Mol Cell. 2019 Oct 3;76(1):206-216.e7
pubmed: 31471188
Cell. 1987 Dec 24;51(6):987-1000
pubmed: 3690668
Nat Genet. 2014 Apr;46(4):364-70
pubmed: 24584072
Nat Commun. 2019 Aug 20;10(1):3747
pubmed: 31431618
Nature. 2015 Jul 23;523(7561):486-90
pubmed: 26083756
RNA. 2016 Oct;22(10):1631-9
pubmed: 27512124
Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9290-5
pubmed: 18579772
Mol Cell. 2017 Apr 20;66(2):285-299.e5
pubmed: 28416141
Nat Rev Neurosci. 2007 Jun;8(6):427-37
pubmed: 17514196
Front Neuroanat. 2014 Jun 10;8:42
pubmed: 24959122
J Clin Invest. 2016 Feb;126(2):639-52
pubmed: 26752646
Nat Cell Biol. 2019 Feb;21(2):287-296
pubmed: 30532068
Genome Res. 2011 May;21(5):748-55
pubmed: 21471402
Genome Biol. 2017 Jan 24;18(1):15
pubmed: 28118844
Cell. 2013 Nov 7;155(4):934-47
pubmed: 24119843
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
Cell. 1997 Nov 14;91(4):501-10
pubmed: 9390559
Methods Enzymol. 2006;410:342-59
pubmed: 16938559
Genetics. 2012 Mar;190(3):941-9
pubmed: 22214611
BMC Cancer. 2013 Aug 05;13:371
pubmed: 23915344
Cell. 2013 Mar 14;152(6):1237-51
pubmed: 23498934
Nucleic Acids Res. 2012 Jan;40(Database issue):D1144-9
pubmed: 22086960
Curr Top Dev Biol. 2016;116:445-54
pubmed: 26970633
ACS Synth Biol. 2016 Jul 15;5(7):774-80
pubmed: 27110723
Cell. 2013 Apr 11;153(2):320-34
pubmed: 23582323
Nat Commun. 2018 Dec 21;9(1):5416
pubmed: 30575746
Cell Death Dis. 2019 May 29;10(6):421
pubmed: 31142733
Nat Biotechnol. 2015 Nov;33(11):1165-72
pubmed: 26458175
Nature. 2011 Aug 03;478(7370):524-8
pubmed: 21814200
Biom J. 2008 Jun;50(3):346-63
pubmed: 18481363
Proc Natl Acad Sci U S A. 2012 May 15;109(20):7882-7
pubmed: 22543161
Cell. 2005 Aug 12;122(3):473-83
pubmed: 16096065
Science. 2017 Aug 18;357(6352):661-667
pubmed: 28818938
Cell. 2013 Mar 28;153(1):178-92
pubmed: 23523135
Mol Cell Biol. 2010 Nov;30(21):5071-85
pubmed: 20805357
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Cell. 2013 Apr 11;153(2):307-19
pubmed: 23582322
Nat Protoc. 2007;2(6):1467-78
pubmed: 17545983
Mol Ther. 2009 Dec;17(12):2115-20
pubmed: 19809403
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Nat Neurosci. 2017 Mar;20(3):484-496
pubmed: 28166221
Nature. 2017 Oct 5;550(7674):67-73
pubmed: 28953884
Cell Rep. 2014 Oct 9;9(1):234-247
pubmed: 25263550
J Neurosci. 2012 Jun 20;32(25):8663-77
pubmed: 22723706
Nature. 2010 Dec 23;468(7327):1067-73
pubmed: 20871596
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Neurochem Int. 2013 Apr;62(5):556-65
pubmed: 22982300
Nature. 2004 Sep 23;431(7007):471-6
pubmed: 15386015
Nat Methods. 2016 Mar;13(3):229-232
pubmed: 26752769
Nucleic Acids Res. 2018 Jan 25;46(2):e9
pubmed: 29126307
Sci Rep. 2017 Mar 02;7:43613
pubmed: 28252665
Nat Rev Genet. 2013 Sep;14(9):618-30
pubmed: 23897237
Nat Cell Biol. 2019 Sep;21(9):1164-1172
pubmed: 31481796
Cell Rep. 2018 Sep 25;24(13):3619-3629.e4
pubmed: 30257220
Proc Natl Acad Sci U S A. 2006 Jul 11;103(28):10660-5
pubmed: 16818887
Trends Genet. 2016 Jan;32(1):42-56
pubmed: 26704082
Science. 2018 Sep 28;361(6409):1380-1385
pubmed: 30166440
Nat Commun. 2018 Feb 22;9(1):781
pubmed: 29472610
Cell. 2019 Jan 10;176(1-2):377-390.e19
pubmed: 30612741
Nat Commun. 2019 Jan 21;10(1):348
pubmed: 30664650
Nature. 2009 Nov 5;462(7269):58-64
pubmed: 19890323
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8
pubmed: 16381938
Mol Cell. 2018 Feb 15;69(4):648-663.e7
pubmed: 29398447
Nucleic Acids Res. 2017 Apr 20;45(7):e55
pubmed: 28082389
Nature. 2011 May 5;473(7345):43-9
pubmed: 21441907
Cell. 2018 Feb 22;172(5):1091-1107.e17
pubmed: 29474909
Nat Biotechnol. 2015 Mar;33(3):285-289
pubmed: 25599178
Mol Ther. 2016 Mar;24(3):592-606
pubmed: 26755332
Genome Biol. 2018 Dec 19;19(1):224
pubmed: 30567574
Sci Rep. 2016 Oct 14;6:34962
pubmed: 27739523
Cell. 2017 Nov 16;171(5):1151-1164.e16
pubmed: 29056337
Nat Genet. 2009 Jun;41(6):753-61
pubmed: 19412179
Nat Commun. 2019 Apr 29;10(1):1930
pubmed: 31036827
Exp Mol Med. 2018 Aug 7;50(8):1-14
pubmed: 30089861
Genomics Proteomics Bioinformatics. 2017 Oct;15(5):287-300
pubmed: 29031844
Science. 2007 Jun 8;316(5830):1497-502
pubmed: 17540862
Database (Oxford). 2016 Jul 03;2016:
pubmed: 27374120
Science. 2018 Aug 31;361(6405):
pubmed: 30093604
Nat Methods. 2011 Nov 29;8(12):989-90
pubmed: 22127213
Genome Res. 2007 Aug;17(8):1202-9
pubmed: 17623806
Nat Protoc. 2018 Apr;13(4):599-604
pubmed: 29494575
Cell. 2016 Oct 20;167(3):633-642.e11
pubmed: 27768887
Curr Protoc Cell Biol. 2001 May;Chapter 8:Unit 8.3
pubmed: 18228388
Proc Natl Acad Sci U S A. 2020 May 5;117(18):10003-10014
pubmed: 32300008
Nature. 2018 Jan 11;553(7687):212-216
pubmed: 29323290
Nature. 2018 Nov;563(7729):72-78
pubmed: 30382198
Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1531-6
pubmed: 21205896
Nat Commun. 2017 Jan 16;8:14049
pubmed: 28091601
Nature. 2005 Jun 16;435(7044):944-7
pubmed: 15959514
Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15008-13
pubmed: 17005721
Biotechniques. 2012 Jun;52(6):381-5
pubmed: 22668417
Cell. 2015 Sep 24;163(1):134-47
pubmed: 26365489
Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32
pubmed: 26527727
Genome Biol. 2007;8(2):R24
pubmed: 17324271
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Cell. 2018 May 31;173(6):1398-1412.e22
pubmed: 29731168
Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13445-50
pubmed: 18768805
Development. 2012 Jul;139(13):2299-307
pubmed: 22627280
Genome Res. 2009 Jun;19(6):1044-56
pubmed: 19273619
Nat Genet. 2019 Jun;51(6):990-998
pubmed: 31133746
Genome Res. 2014 Dec;24(12):2033-40
pubmed: 25079858
Epigenetics Chromatin. 2018 Jun 8;11(1):30
pubmed: 29884215
Nat Methods. 2015 Jun;12(6):519-22
pubmed: 25915121
Science. 2018 Jun 29;360(6396):1469-1473
pubmed: 29903884