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Aeby2020decapping https://doi.org/10.1038/s41556-020-0558-0
Agarwal2021kdm1a https://doi.org/10.1101/gr.234559.118
Aho2019displacement https://doi.org/10.1016/j.celrep.2019.02.047
Akulenko2018transcriptional https://doi.org/10.1261/rna.062851.117
Alexander2019imprinted
Alhusini2017genomewide https://doi.org/10.1038/s41598-017-07062-6
Allen2014global https://doi.org/10.7554/eLife.02200
Anderson2020defining https://doi.org/10.1093/bioinformatics/btaa011
Andersson2014nuclear https://doi.org/10.1038/ncomms6336
Andrade2015dna https://doi.org/10.1093/nar/gkv148
Andrysik2017identification https://doi.org/10.1101/gr.220533.117
Aoi2020nelf https://doi.org/10.1016/j.molcel.2020.02.014
Aprile-garcia2019nascent https://doi.org/10.1038/s41594-018-0182-x
Ba2020ctcf https://doi.org/10.1038/s41586-020-2578-0
Bahat2019targeting https://doi.org/10.1016/j.molcel.2019.08.024
Barbieri2020rapid https://doi.org/10.1016/j.celrep.2020.108373
Barucci2020small https://doi.org/10.1038/s41556-020-0462-7
Beckedorff2020human https://doi.org/10.1016/j.celrep.2020.107917
Bi2020enhancer https://doi.org/10.1038/s41556-020-0514-z
Birkenheuer2018herpes https://doi.org/10.1128/JVI.02184-17
Birkenheuer2020rna https://doi.org/10.1128/JVI.02035-19
Blumberg2021characterizing https://doi.org/10.1186/s12915-021-00949-x
Boija2017cbp https://doi.org/10.1016/j.molcel.2017.09.031
Bonelt2019precocious https://doi.org/10.15252/embj.2018100010
Booth2016divergence https://doi.org/10.1101/gr.204578.116
Booth2018cdk9 https://doi.org/10.1038/s41467-018-03006-4
Bouvyliivrand2017analysis https://doi.org/10.1093/nar/gkx680
Boxer2020mecp2 https://doi.org/10.1016/j.molcel.2019.10.032
Busslinger2017cohesin https://doi.org/10.1038/nature22063
Cardamone2018mitochondrial https://doi.org/10.1016/j.molcel.2018.01.037
Cecere2013zfp1 https://doi.org/10.1016/j.molcel.2013.06.002
Cecere2014global https://doi.org/10.1038/nsmb.2801
Chen2014gene https://doi.org/10.1101/gad.250449.114
Chen2015paf1 https://doi.org/10.1016/j.cell.2015.07.042
Chen2016cutoff https://doi.org/10.1016/j.molcel.2016.05.010
Chen2017rchip https://doi.org/10.1016/j.molcel.2017.10.008
Chen2018augmented https://doi.org/10.1016/j.molcel.2017.12.029
Chen2018rna https://doi.org/10.1038/s41422-018-0076-9
Chivu2020unpublished
Chu2018chromatin https://doi.org/10.1038/s41588-018-0244-3
Compagno2017phosphatidylinositol https://doi.org/10.1038/nature21406
Core2008nascent https://doi.org/10.1126/science.1162228
Core2012defining https://doi.org/10.1016/j.celrep.2012.08.034
Core2014analysis https://doi.org/10.1038/ng.3142
Cosby2021recurrent https://doi.org/10.1126/science.abc6405
Cuartero2020control https://doi.org/10.1038/s41590-018-0184-1
Czimmerer2018transcription https://doi.org/10.1016/j.immuni.2017.12.010
Dai2020loop https://doi.org/10.1038/s41586-020-03121-7
Daniel2018nuclear https://doi.org/10.1016/j.immuni.2018.09.005
Danko2013signaling https://doi.org/10.1016/j.molcel.2013.02.015
Danko2015identification https://doi.org/10.1038/nmeth.3329
Danko2018dynamic https://doi.org/10.1038/s41559-017-0447-5
Delgado-benito2018chromatin https://doi.org/10.1016/j.molcel.2018.08.042
Dorighi2017mll3 https://doi.org/10.1016/j.molcel.2017.04.018
Douillet2020uncoupling https://doi.org/10.1038/s41588-020-0618-1
Duarte2016transcription https://doi.org/10.1101/gad.284430.116
Dukler2017nascent https://doi.org/10.1101/gr.222935.117
Duttke2015human https://doi.org/10.1016/j.molcel.2014.12.029
Duttke2017unpublished
Elkon2015myc https://doi.org/10.15252/embr.201540717
Elrod2019integrator https://doi.org/10.1016/j.molcel.2019.10.034
Emmett2017histone https://doi.org/10.1038/nature22819
Engreitz2016local https://doi.org/10.1038/nature20149
Erhard2015nascent https://doi.org/10.1534/genetics.115.174714
Escoubet-lozach2011mechanisms https://doi.org/10.1371/journal.pgen.1002401
Esousa2019kinetics https://doi.org/10.1101/gr.245027.118
Estaras2015smad https://doi.org/10.1016/j.molcel.2015.04.001
Etchegaray2019histone https://doi.org/10.1016/j.molcel.2019.06.034
Fan2020drb https://doi.org/10.1126/sciadv.aaz5041
Fang2014circadian https://doi.org/10.1016/j.cell.2014.10.022
Fant2020tfiid https://doi.org/10.1016/j.molcel.2020.03.008
Fei2018ndf https://doi.org/10.1101/gad.313973.118
Fleischer2017dna https://doi.org/10.1038/s41467-017-00510-x
Flynn20167skbaf https://doi.org/10.1038/nsmb.3176
Fong2014pre https://doi.org/10.1101/gad.252106.114
Fong2017rna https://doi.org/10.1016/j.molcel.2017.04.016
Fonseca2019diverse https://doi.org/10.1038/s41467-018-08236-0
Franco2015tnfalpha https://doi.org/10.1016/j.molcel.2015.02.001
Franco2018enhancer https://doi.org/10.1101/gr.226019.117
Fuda2012fcp1 https://doi.org/10.1128/MCB.00247-12
Fuda2015gaga https://doi.org/10.1371/journal.pgen.1005108
Galbraith2013hif1a https://doi.org/10.1016/j.cell.2013.04.048
Gally2020gain https://doi.org/10.1172/jci.insight.144294
Gao2017thyroid https://doi.org/10.1073/pnas.1711058114
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Gardini2014integrator https://doi.org/10.1016/j.molcel.2014.08.004
Gibson2016chemical https://doi.org/10.1126/science.aaf7865
Godfrey2017mll https://doi.org/10.1016/j.exphem.2016.11.003
Guan2018diet https://doi.org/10.1016/j.cell.2018.06.031
Hah2011rapid https://doi.org/10.1016/j.cell.2011.03.042
Hah2013enhancer https://doi.org/10.1101/gr.152306.112
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Harman2021invivo https://doi.org/10.1073/pnas.1918062118
Heinaniemi2016transcription https://doi.org/10.7554/eLife.13087
Heinz2013effect https://doi.org/10.1038/nature12615
Herold2019recruitment https://doi.org/10.1038/s41586-019-1030-9
Hetzel2016nascent https://doi.org/10.1073/pnas.1603217113
Hong2017dissociation https://doi.org/10.1038/nm.4245
Horibata2018erpositive https://doi.org/10.1371/journal.pone.0194023
Hou2019paf1c https://doi.org/10.1073/pnas.1904324116
Hu2012dicer https://doi.org/10.1038/nsmb.2400
Huang2020integrator https://doi.org/10.1016/j.molcel.2020.08.016
Ikegami2020phosphorylated https://doi.org/10.1016/j.devcel.2020.02.011
Illingworth2016polycomb https://doi.org/10.7554/eLife.14926
Incarnato2017vivo https://doi.org/10.1093/nar/gkx617
Jaeger2020selective https://doi.org/10.1038/s41588-020-0635-0
Jager2016nuclear https://doi.org/10.1074/jbc.M116.719120
Ji2011transcriptional https://doi.org/10.1038/msb.2011.69
Ji2013sr https://doi.org/10.1016/j.cell.2013.04.028
Jiang2018multi https://doi.org/10.1038/s41598-018-24039-1
Jin2013high https://doi.org/10.1038/nature12644
Jin2014chem https://doi.org/10.1073/pnas.1404303111
Johnson2017biotin https://doi.org/10.1038/nm.4406
Johnston2020nascent https://doi.org/10.1016/j.gene.2020.144758
Jones2023unpublished
Jonkers2014genome https://doi.org/10.7554/eLife.02407
Judd2020unpublished
Judd2021pioneer https://doi.org/10.1101/gad.341768.120
Kaikkonen2013remodeling https://doi.org/10.1016/j.molcel.2013.07.010
Kaikkonen2014control https://doi.org/10.1093/nar/gku1036
Kaikkonen2017genome https://doi.org/10.1161/CIRCGENETICS.117.001702
Kantidakis2016mutation https://doi.org/10.1101/gad.275453.115
Kelly2020unpublished
Khodor2011nascent https://doi.org/10.1101/gad.178962.111
Kim2018pluripotency https://doi.org/10.1038/s41586-018-0048-8
Kloetgen2020three https://doi.org/10.1038/s41588-020-0602-9
Komarov2020epigenetic https://doi.org/10.3390/cells9040922
Korkmaz2019crispr https://doi.org/10.1093/nar/gkz675
Kourtis2018oncogenic https://doi.org/10.1038/s41591-018-0105-8
Kriaucionis2019unpublished
Kristjansdottir2020population https://doi.org/10.1038/s41467-020-19829-z
Kruesi2013condensin https://doi.org/10.7554/eLife.00808
Kuosmanen2018nrf2 https://doi.org/10.1093/nar/gkx1155
Kwak2013precise https://doi.org/10.1126/science.1229386
Kwon2017locus https://doi.org/10.1038/ncomms15315
Lai2020directed https://doi.org/10.1016/j.molcel.2019.12.029
Laitem2015cdk9 https://doi.org/10.1038/nsmb.3000
Lam2013rev https://doi.org/10.1038/nature12209
Larschan2011x https://doi.org/10.1038/nature09757
Le2013mapping https://doi.org/10.1371/journal.pone.0071355
Leroy2019ledgf https://doi.org/10.1126/sciadv.aay3068
Leveille2015genome https://doi.org/10.1038/ncomms7520
Li2013functional https://doi.org/10.1038/nature12210
Li2013ncor https://doi.org/10.1016/j.cell.2013.08.054
Li2015condensin https://doi.org/10.1016/j.molcel.2015.06.002
Li2017grid https://doi.org/10.1038/nbt.3968
Li2018lncrna https://doi.org/10.1093/nar/gky087
Li2020human https://doi.org/10.1371/journal.ppat.1008402
Li2020signalosome https://doi.org/10.1161/CIRCULATIONAHA.119.044805
Li2021comprehensive https://doi.org/10.1186/s13059-021-02272-8
Liang2018targeting https://doi.org/10.1016/j.cell.2018.09.027
Lin2012global https://doi.org/10.1038/ni.2432
Link2018analysis https://doi.org/10.1016/j.cell.2018.04.018
Linnakuosmanen2020nrf2 https://doi.org/10.1093/cvr/cvaa219
Liu2013brd4 https://doi.org/10.1016/j.cell.2013.10.056
Liu2014enhancer https://doi.org/10.1016/j.cell.2014.08.027
Liu2017dynamic https://doi.org/10.1182/bloodadvances.2017008383
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Liu2018arabidopsis https://doi.org/10.1016/j.devcel.2017.12.002
Liu2018rna-directed https://doi.org/10.1038/s41477-017-0100-y
Liu2020immediate https://doi.org/10.1111/jipb.12990
Liu2021transcription https://doi.org/10.1038/s41588-021-00798-y
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Lozano2018rna
Lu2017nascent https://doi.org/10.1093/nar/gkx464
Luo2014dynamic https://doi.org/10.1186/1471-2164-15-155
Ma2020super https://doi.org/10.1016/j.celrep.2020.107532
Magnuson2015identifying https://doi.org/10.1038/srep17978
Mahat2016mammalian https://doi.org/10.1016/j.molcel.2016.02.025
Malinen2017crosstalk https://doi.org/10.1093/nar/gkw855
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Miller2015senataxin https://doi.org/10.1038/ni.3132
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