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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
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Allen2014global https://doi.org/10.7554/eLife.02200
Anderson2020defining https://doi.org/10.1093/bioinformatics/btaa011
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Ba2020ctcf https://doi.org/10.1038/s41586-020-2578-0
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Bouvyliivrand2017analysis https://doi.org/10.1093/nar/gkx680
Boxer2020mecp2 https://doi.org/10.1016/j.molcel.2019.10.032
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Chen2014gene https://doi.org/10.1101/gad.250449.114
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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
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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
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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
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Dorighi2017mll3 https://doi.org/10.1016/j.molcel.2017.04.018
Douillet2020uncoupling https://doi.org/10.1038/s41588-020-0618-1
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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
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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
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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
Hah2015inflammation https://doi.org/10.1073/pnas.1424028112
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
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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
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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
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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
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Kruesi2013condensin https://doi.org/10.7554/eLife.00808
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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
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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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Liu2017transcriptional https://doi.org/10.1073/pnas.1617636114
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
Lloret-llinares2018rna https://doi.org/10.1093/nar/gky817
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
Marazzi2012suppression https://doi.org/10.1038/nature10892
Mayer2015native https://doi.org/10.1016/j.cell.2015.03.010
Mckinlay2011genome https://doi.org/10.1534/g3.111.000810
Meng2014convergent https://doi.org/10.1016/j.cell.2014.11.014
Meyerswallen2017xx https://doi.org/10.1371/journal.pone.0186331
Miller2015senataxin https://doi.org/10.1038/ni.3132
Min2011regulating https://doi.org/10.1101/gad.2005511
Mohn2014rhino https://doi.org/10.1016/j.cell.2014.04.031
Moreau2018transcriptional https://doi.org/10.3389/fcvm.2018.00159
Mukai2020chromatin https://doi.org/10.1186/s12917-020-02395-3
Murakami2017dynamic https://doi.org/10.1101/gad.302182.117
Nair2019phase https://doi.org/10.1038/s41594-019-0190-5
Nelson2018ppar https://doi.org/10.1101/gad.312355.118
Ngoc2017human https://doi.org/10.1101/gad.293837.116
Nguyen2020dichotomous https://doi.org/10.1038/s41586-020-2576-2
Nilson2017oxidative https://doi.org/10.1093/nar/gkx724
Niskanen2015global https://doi.org/10.1186/s13059-015-0717-y
Niskanen2018endothelial https://doi.org/10.1093/nar/gkx1214
Nojima2015mammalian https://doi.org/10.1016/j.cell.2015.03.027
Oh2021enhancer https://doi.org/10.1038/s41586-021-03577-1
Oittinen2017polycomb https://doi.org/10.1002/stem.2479
Orioli2016human https://doi.org/10.1101/gr.201400.115
Parida2019nucleotide https://doi.org/10.1128/mBio.02047-18
Parikh2018critical https://doi.org/10.1074/jbc.AC118.003264
Park2020global https://doi.org/10.1073/pnas.1922216117
Parua2018cdk9-pp1 https://doi.org/10.1038/s41586-018-0214-z
Patel2020robust https://doi.org/10.1093/nar/gkaa687
Perreault2019epigenetic https://doi.org/10.1038/sdata.2019.33
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Puc2015ligand https://doi.org/10.1016/j.cell.2014.12.023
Rahnamoun2017mutant https://doi.org/10.1038/s41467-017-01117-y
Rao2017cohesin https://doi.org/10.1016/j.cell.2017.09.026
Rozhkov2013multiple https://doi.org/10.1101/gad.209767.112
Salony2016akt https://doi.org/10.1158/1535-7163.MCT-15-0414
Santoriello2020rna https://doi.org/10.1038/s41556-020-0493-0
Saponaro2014recql5 https://doi.org/10.1016/j.cell.2014.03.048
Sasse2019nascent https://doi.org/10.1101/gr.248187.119
Sathyan2019improved https://doi.org/10.1101/gad.328237.119
Saunders2013extensive https://doi.org/10.1101/gad.215459.113
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Schoeberl2012biased https://doi.org/10.1101/gad.196493.112
Sen2019histone https://doi.org/10.1016/j.molcel.2019.01.021
Sendinc2019pcif1 https://doi.org/10.1016/j.molcel.2019.05.030
Shamie2020unpublished
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Sienski2012transcriptional https://doi.org/10.1016/j.cell.2012.10.040
Sigova2013divergent https://doi.org/10.1073/pnas.1221904110
Sigova2015transcription https://doi.org/10.1126/science.aad3346
Skowronskakrawczyk2014required https://doi.org/10.1038/nature13573
Slobodin2017transcription https://doi.org/10.1016/j.cell.2017.03.031
Smith2021peppro https://doi.org/10.1186/s13059-021-02349-4
Soccio2015genetic https://doi.org/10.1016/j.cell.2015.06.025
Steinparzer2019transcriptional https://doi.org/10.1016/j.molcel.2019.07.034
Stender2017structural https://doi.org/10.1016/j.molcel.2017.02.008
Stengel2019histone https://doi.org/10.1093/nar/gkz816
Stengel2020definition https://doi.org/10.1016/j.molcel.2020.12.005
Step2014antidiabetic https://doi.org/10.1101/gad.237628.114
Strikoudis2016regulation https://doi.org/10.1038/ncb3424
Sumida2018ultra https://doi.org/https://doi.org/10.1101/286583
Sun2017enhancer
Takahashi2020role https://doi.org/10.1038/s41467-020-14849-1
Tan2016stress https://doi.org/10.1016/j.molcel.2016.03.013
Tan2018dismissal https://doi.org/10.1016/j.molcel.2018.07.039
Tastemel2017transcription https://doi.org/10.1016/j.scr.2017.11.012
Telese2015lrp8 https://doi.org/10.1016/j.neuron.2015.03.033
Tena2020induction https://doi.org/10.1073/pnas.1922299117
Teppo2016genome https://doi.org/10.1101/gr.193649.115
Thomas2019interaction https://doi.org/10.1073/pnas.1910391116
Tome2018single https://doi.org/10.1038/s41588-018-0234-5
Toropainen2016global https://doi.org/10.1038/srep33510
Trizzino2018tumor https://doi.org/10.1016/j.celrep.2018.05.097
Ueberschar2019ben https://doi.org/10.1038/s41467-019-13558-8
Vaid2020release https://doi.org/10.1093/nar/gkaa234
Veloso2013genome-wide https://doi.org/10.1371/journal.pone.0078190
Vian2018energetics https://doi.org/10.1016/j.cell.2018.03.072
Vihervaara2017transcriptional https://doi.org/10.1038/s41467-017-00151-0
Vihervaara2021stress https://doi.org/10.1016/j.molcel.2021.03.007
Viiri2019extensive https://doi.org/10.1038/s41598-019-39215-0
Wan2020h2bg53d https://doi.org/10.1038/s41392-020-00219-2
Wang2011reprogramming https://doi.org/10.1038/nature10006
Wang2014rna https://doi.org/10.1016/j.celrep.2014.01.037
Wang2015epigenetic https://doi.org/10.1016/j.stem.2015.02.013
Wang2015lsd1n https://doi.org/10.1038/nn.4069
Wang2015molecular https://doi.org/10.1038/nature14482
Wang2017cell https://doi.org/10.1084/jem.20161649
Wang2018nascent https://doi.org/10.1186/s12864-018-5016-z
Wang2019identification https://doi.org/10.1101/gr.238279.118
Wang2020increased https://doi.org/10.1016/j.stem.2019.12.013
Wang2020proapoptotic https://doi.org/10.1038/s41388-020-01435-4
Wei2016long https://doi.org/10.1016/j.cell.2015.12.039
Wei2016rbfox2 https://doi.org/10.1016/j.molcel.2016.04.013
Weissmiller2019inhibition https://doi.org/10.1038/s41467-019-10022-5
Williams2015pausing https://doi.org/10.1016/j.molcel.2015.02.003
Williamson2017uv https://doi.org/10.1016/j.cell.2017.01.019
Woo2018ted https://doi.org/10.1016/j.celrep.2018.08.084
Wu2017indentifying https://doi.org/10.1038/s41598-017-00176-x
Xiao2019pervasive https://doi.org/10.1016/j.cell.2019.06.001
Yang2013lncrna https://doi.org/10.1038/nature12451
Yang2017glucocorticoid https://doi.org/10.1016/j.molcel.2017.03.019
Yu2015panoramix https://doi.org/10.1126/science.aab0700
Yu2020negative https://doi.org/10.1038/s41467-020-16209-5
Zhang2015enhancer https://doi.org/10.1073/pnas.1424228112
Zhang2016regulation https://doi.org/10.1038/srep21718
Zhang2017hepatic https://doi.org/10.1101/gad.302323.117
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Zhang2019fundamental https://doi.org/10.1038/s41586-019-1723-0
Zhang2020bcatenin https://doi.org/10.1126/sciadv.aba1593
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Zhao2016high https://doi.org/10.1016/j.celrep.2016.07.032
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Zhu2017comprehensive https://doi.org/10.1101/gad.293910.116
Zhu2018rna https://doi.org/10.1038/s41477-018-0280-0
Zhu2019non https://doi.org/10.1016/j.molcel.2019.06.010
Zhu2021calcium https://doi.org/10.1101/gad.343475.120
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