My Bibliography

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Rambout X, Cho H, Blanc R, Lyu Q, Miano JM, Chakkalakal JV, Nelson GM, Yalamanchili HK, Adelman K, Maquat LE. PGC-1α senses the CBC of pre-mRNA to dictate the fate of promoter-proximally paused RNAPII. Mol Cell. 2023 Jan 19;83(2):186-202.e11. doi: 10.1016/j.molcel.2022.12.022. PubMed PMID: 36669479.

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Wagner EJ, Tong L, Adelman K. Integrator is a global promoter-proximal termination complex. Mol Cell. 2023 Jan 4;. doi: 10.1016/j.molcel.2022.11.012. [Epub ahead of print] Review. PubMed PMID: 36634676.

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Luppino JM, Field A, Nguyen SC, Park DS, Shah PP, Abdill RJ, Lan Y, Yunker R, Jain R, Adelman K, Joyce EF. Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression. PLoS Genet. 2022 Nov;18(11):e1010528. doi: 10.1371/journal.pgen.1010528. eCollection 2022 Nov. PubMed PMID: 36449519; PubMed Central PMCID: PMC9744307.

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Stein CB, Field AR, Mimoso CA, Zhao C, Huang KL, Wagner EJ, Adelman K. Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci. Mol Cell. 2022 Nov 17;82(22):4232-4245.e11. doi: 10.1016/j.molcel.2022.10.004. Epub 2022 Oct 28. PubMed PMID: 36309014; PubMed Central PMCID: PMC9680917.

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Mehta S, Buyanbat A, Kai Y, Karayel O, Goldman SR, Seruggia D, Zhang K, Fujiwara Y, Donovan KA, Zhu Q, Yang H, Nabet B, Gray NS, Mann M, Fischer ES, Adelman K, Orkin SH. Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells. Cell Chem Biol. 2022 Aug 18;29(8):1273-1287.e8. doi: 10.1016/j.chembiol.2022.06.007. Epub 2022 Jul 14. PubMed PMID: 35839780; PubMed Central PMCID: PMC9391307.

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Replogle JM, Saunders RA, Pogson AN, Hussmann JA, Lenail A, Guna A, Mascibroda L, Wagner EJ, Adelman K, Lithwick-Yanai G, Iremadze N, Oberstrass F, Lipson D, Bonnar JL, Jost M, Norman TM, Weissman JS. Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq. Cell. 2022 Jul 7;185(14):2559-2575.e28. doi: 10.1016/j.cell.2022.05.013. Epub 2022 Jun 9. PubMed PMID: 35688146; PubMed Central PMCID: PMC9380471.

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Vlaming H, Mimoso CA, Field AR, Martin BJE, Adelman K. Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential. Nat Struct Mol Biol. 2022 Jun;29(6):613-620. doi: 10.1038/s41594-022-00785-9. Epub 2022 Jun 9. PubMed PMID: 35681023; PubMed Central PMCID: PMC9672417.

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Zhou H, Stein CB, Shafiq TA, Shipkovenska G, Kalocsay M, Paulo JA, Zhang J, Luo Z, Gygi SP, Adelman K, Moazed D. Rixosomal RNA degradation contributes to silencing of Polycomb target genes. Nature. 2022 Apr;604(7904):167-174. doi: 10.1038/s41586-022-04598-0. Epub 2022 Mar 30. PubMed PMID: 35355014; PubMed Central PMCID: PMC8986528.

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Wu W, Nelson GM, Koch R, Donovan KA, Nowak RP, Heavican-Foral TB, Nirmal AJ, Liu H, Yang L, Duffy J, Powers F, Stevenson KE, Jones MK, Ng SY, Wu G, Jain S, Xu R, Amaka S, Trevisani C, Donaldson NL, Hagner PR, de Leval L, Gaulard P, Iqbal J, Thakurta A, Fischer ES, Adelman K, Weinstock DM. Overcoming IMiD resistance in T-cell lymphomas through potent degradation of ZFP91 and IKZF1. Blood. 2022 Mar 31;139(13):2024-2037. doi: 10.1182/blood.2021014701. PubMed PMID: 34936696; PubMed Central PMCID: PMC8972091.

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Xu W, He C, Kaye EG, Li J, Mu M, Nelson GM, Dong L, Wang J, Wu F, Shi YG, Adelman K, Lan F, Shi Y, Shen H. Dynamic control of chromatin-associated m⁶A methylation regulates nascent RNA synthesis. Mol Cell. 2022 Mar 17;82(6):1156-1168.e7. doi: 10.1016/j.molcel.2022.02.006. Epub 2022 Feb 25. PubMed PMID: 35219383; PubMed Central PMCID: PMC8969783.

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Cermakova K, Demeulemeester J, Lux V, Nedomova M, Goldman SR, Smith EA, Srb P, Hexnerova R, Fabry M, Madlikova M, Horejsi M, De Rijck J, Debyser Z, Adelman K, Hodges HC, Veverka V. A ubiquitous disordered protein interaction module orchestrates transcription elongation. Science. 2021 Nov 26;374(6571):1113-1121. doi: 10.1126/science.abe2913. Epub 2021 Nov 25. PubMed PMID: 34822292; PubMed Central PMCID: PMC8943916.

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Robinson DCL, Ritso M, Nelson GM, Mokhtari Z, Nakka K, Bandukwala H, Goldman SR, Park PJ, Mounier R, Chazaud B, Brand M, Rudnicki MA, Adelman K, Dilworth FJ. Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation. Dev Cell. 2021 Apr 5;56(7):1014-1029.e7. doi: 10.1016/j.devcel.2021.02.025. Epub 2021 Mar 17. PubMed PMID: 33735618; PubMed Central PMCID: PMC8357161.

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Reimer KA, Mimoso CA, Adelman K, Neugebauer KM. Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis. Mol Cell. 2021 Mar 4;81(5):998-1012.e7. doi: 10.1016/j.molcel.2020.12.018. Epub 2021 Jan 12. PubMed PMID: 33440169; PubMed Central PMCID: PMC8038867.

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Huang KL, Jee D, Stein CB, Elrod ND, Henriques T, Mascibroda LG, Baillat D, Russell WK, Adelman K, Wagner EJ. Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination. Mol Cell. 2020 Oct 15;80(2):345-358.e9. doi: 10.1016/j.molcel.2020.08.016. Epub 2020 Sep 22. PubMed PMID: 32966759; PubMed Central PMCID: PMC7660970.

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Field A, Adelman K. Evaluating Enhancer Function and Transcription. Annu Rev Biochem. 2020 Jun 20;89:213-234. doi: 10.1146/annurev-biochem-011420-095916. Epub 2020 Mar 20. Review. PubMed PMID: 32197056.

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Rogers JM, Guo B, Egan ED, Aster JC, Adelman K, Blacklow SC. MAML1-Dependent Notch-Responsive Genes Exhibit Differing Cofactor Requirements for Transcriptional Activation. Mol Cell Biol. 2020 May 14;40(11). doi: 10.1128/MCB.00014-20. Print 2020 May 14. PubMed PMID: 32179552; PubMed Central PMCID: PMC7225564.

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Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells. Nat Cell Biol. 2020 Apr;22(4):372-379. doi: 10.1038/s41556-020-0493-0. Epub 2020 Mar 30. PubMed PMID: 32231306; PubMed Central PMCID: PMC7185069.

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Elrod ND, Henriques T, Huang KL, Tatomer DC, Wilusz JE, Wagner EJ, Adelman K. The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes. Mol Cell. 2019 Dec 5;76(5):738-752.e7. doi: 10.1016/j.molcel.2019.10.034. PubMed PMID: 31809743; PubMed Central PMCID: PMC6952639.

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Tatomer DC, Elrod ND, Liang D, Xiao MS, Jiang JZ, Jonathan M, Huang KL, Wagner EJ, Cherry S, Wilusz JE. The Integrator complex cleaves nascent mRNAs to attenuate transcription. Genes Dev. 2019 Nov 1;33(21-22):1525-1538. doi: 10.1101/gad.330167.119. Epub 2019 Sep 17. PubMed PMID: 31530651; PubMed Central PMCID: PMC6824465.

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Etchegaray JP, Zhong L, Li C, Henriques T, Ablondi E, Nakadai T, Van Rechem C, Ferrer C, Ross KN, Choi JE, Samarakkody A, Ji F, Chang A, Sadreyev RI, Ramaswamy S, Nechaev S, Whetstine JR, Roeder RG, Adelman K, Goren A, Mostoslavsky R. The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing. Mol Cell. 2019 Aug 22;75(4):683-699.e7. doi: 10.1016/j.molcel.2019.06.034. Epub 2019 Aug 6. PubMed PMID: 31399344; PubMed Central PMCID: PMC6907403.

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Sendinc E, Valle-Garcia D, Dhall A, Chen H, Henriques T, Navarrete-Perea J, Sheng W, Gygi SP, Adelman K, Shi Y. PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression. Mol Cell. 2019 Aug 8;75(3):620-630.e9. doi: 10.1016/j.molcel.2019.05.030. Epub 2019 Jul 3. PubMed PMID: 31279659; PubMed Central PMCID: PMC6688901.

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Core L, Adelman K. Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. Genes Dev. 2019 Aug 1;33(15-16):960-982. doi: 10.1101/gad.325142.119. Epub 2019 May 23. Review. PubMed PMID: 31123063; PubMed Central PMCID: PMC6672056.

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Oldfield AJ, Henriques T, Kumar D, Burkholder AB, Cinghu S, Paulet D, Bennett BD, Yang P, Scruggs BS, Lavender CA, Rivals E, Adelman K, Jothi R. NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region. Nat Commun. 2019 Jul 11;10(1):3072. doi: 10.1038/s41467-019-10905-7. PubMed PMID: 31296853; PubMed Central PMCID: PMC6624317.

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Hewitt SC, Li R, Adams N, Winuthayanon W, Hamilton KJ, Donoghue LJ, Lierz SL, Garcia M, Lydon JP, DeMayo FJ, Adelman K, Korach KS. Negative elongation factor is essential for endometrial function. FASEB J. 2019 Feb;33(2):3010-3023. doi: 10.1096/fj.201801752. Epub 2018 Oct 17. PubMed PMID: 30332301; PubMed Central PMCID: PMC6338652.

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Kaikkonen MU, Adelman K. Emerging Roles of Non-Coding RNA Transcription. Trends Biochem Sci. 2018 Sep;43(9):654-667. doi: 10.1016/j.tibs.2018.06.002. Epub 2018 Jun 28. Review. PubMed PMID: 30145998.

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Pai AA, Paggi JM, Yan P, Adelman K, Burge CB. Numerous recursive sites contribute to accuracy of splicing in long introns in flies. PLoS Genet. 2018 Aug;14(8):e1007588. doi: 10.1371/journal.pgen.1007588. eCollection 2018 Aug. PubMed PMID: 30148878; PubMed Central PMCID: PMC6110457.

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Adelman K, Henriques T. Transcriptional speed bumps revealed in high resolution. Nature. 2018 Aug;560(7720):560-561. doi: 10.1038/d41586-018-05971-8. PubMed PMID: 30143755.

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Meers MP, Adelman K, Duronio RJ, Strahl BD, McKay DJ, Matera AG. Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. BMC Genomics. 2018 Feb 21;19(1):157. doi: 10.1186/s12864-018-4510-7. PubMed PMID: 29466941; PubMed Central PMCID: PMC5822475.

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Henriques T, Scruggs BS, Inouye MO, Muse GW, Williams LH, Burkholder AB, Lavender CA, Fargo DC, Adelman K. Widespread transcriptional pausing and elongation control at enhancers. Genes Dev. 2018 Jan 1;32(1):26-41. doi: 10.1101/gad.309351.117. Epub 2018 Jan 29. PubMed PMID: 29378787; PubMed Central PMCID: PMC5828392.

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Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. Elife. 2017 Dec 27;6. doi: 10.7554/eLife.32537. PubMed PMID: 29280736; PubMed Central PMCID: PMC5762160.

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Urban J, Kuzu G, Bowman S, Scruggs B, Henriques T, Kingston R, Adelman K, Tolstorukov M, Larschan E. Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein. PLoS One. 2017;12(10):e0186855. doi: 10.1371/journal.pone.0186855. eCollection 2017. PubMed PMID: 29077765; PubMed Central PMCID: PMC5659772.

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Cinghu S, Yang P, Kosak JP, Conway AE, Kumar D, Oldfield AJ, Adelman K, Jothi R. Intragenic Enhancers Attenuate Host Gene Expression. Mol Cell. 2017 Oct 5;68(1):104-117.e6. doi: 10.1016/j.molcel.2017.09.010. PubMed PMID: 28985501; PubMed Central PMCID: PMC5683415.

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Lavender CA, Shapiro AJ, Burkholder AB, Bennett BD, Adelman K, Fargo DC. ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data. Nucleic Acids Res. 2017 Jun 2;45(10):5678-5690. doi: 10.1093/nar/gkx270. PubMed PMID: 28402545; PubMed Central PMCID: PMC5449597.

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Dorighi KM, Swigut T, Henriques T, Bhanu NV, Scruggs BS, Nady N, Still CD 2nd, Garcia BA, Adelman K, Wysocka J. Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation. Mol Cell. 2017 May 18;66(4):568-576.e4. doi: 10.1016/j.molcel.2017.04.018. Epub 2017 May 5. PubMed PMID: 28483418; PubMed Central PMCID: PMC5662137.

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Meers MP, Henriques T, Lavender CA, McKay DJ, Strahl BD, Duronio RJ, Adelman K, Matera AG. Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity. Elife. 2017 Mar 27;6. doi: 10.7554/eLife.23249. PubMed PMID: 28346137; PubMed Central PMCID: PMC5404926.

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Adelman K, Egan E. Non-coding RNA: More uses for genomic junk. Nature. 2017 Mar 8;543(7644):183-185. doi: 10.1038/543183a. PubMed PMID: 28277509.

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Scruggs BS, Gilchrist DA, Nechaev S, Muse GW, Burkholder A, Fargo DC, Adelman K. Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin. Mol Cell. 2015 Jun 18;58(6):1101-12. doi: 10.1016/j.molcel.2015.04.006. Epub 2015 May 28. PubMed PMID: 26028540; PubMed Central PMCID: PMC4475495.

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Williams LH, Fromm G, Gokey NG, Henriques T, Muse GW, Burkholder A, Fargo DC, Hu G, Adelman K. Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks. Mol Cell. 2015 Apr 16;58(2):311-322. doi: 10.1016/j.molcel.2015.02.003. Epub 2015 Mar 12. PubMed PMID: 25773599; PubMed Central PMCID: PMC4402150.

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Scruggs BS, Adelman K. The Importance of Controlling Transcription Elongation at Coding and Noncoding RNA Loci. Cold Spring Harb Symp Quant Biol. 2015;80:33-44. doi: 10.1101/sqb.2015.80.027235. Review. PubMed PMID: 27325707; PubMed Central PMCID: PMC6499063.

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Rogatsky I, Adelman K. Preparing the first responders: building the inflammatory transcriptome from the ground up. Mol Cell. 2014 Apr 24;54(2):245-54. doi: 10.1016/j.molcel.2014.03.038. Review. PubMed PMID: 24766888; PubMed Central PMCID: PMC4041192.

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Henriques T, Gilchrist DA, Nechaev S, Bern M, Muse GW, Burkholder A, Fargo DC, Adelman K. Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. Mol Cell. 2013 Nov 21;52(4):517-28. doi: 10.1016/j.molcel.2013.10.001. Epub 2013 Oct 31. PubMed PMID: 24184211; PubMed Central PMCID: PMC3845087.

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Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell. 2013 Nov 7;52(3):314-24. doi: 10.1016/j.molcel.2013.10.009. PubMed PMID: 24207025; PubMed Central PMCID: PMC3936344.

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Gupte R, Muse GW, Chinenov Y, Adelman K, Rogatsky I. Glucocorticoid receptor represses proinflammatory genes at distinct steps of the transcription cycle. Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):14616-21. doi: 10.1073/pnas.1309898110. Epub 2013 Aug 15. PubMed PMID: 23950223; PubMed Central PMCID: PMC3767553.

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Fromm G, Gilchrist DA, Adelman K. SnapShot: Transcription regulation: pausing. Cell. 2013 May 9;153(4):930-930.e1. doi: 10.1016/j.cell.2013.04.011. PubMed PMID: 23663787.

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Henriques T, Adelman K. Catching the waves: following the leading edge of elongating RNA polymerase II. Mol Cell. 2013 Apr 25;50(2):159-60. doi: 10.1016/j.molcel.2013.04.009. PubMed PMID: 23622514; PubMed Central PMCID: PMC3676273.

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Core LJ, Waterfall JJ, Gilchrist DA, Fargo DC, Kwak H, Adelman K, Lis JT. Defining the status of RNA polymerase at promoters. Cell Rep. 2012 Oct 25;2(4):1025-35. doi: 10.1016/j.celrep.2012.08.034. Epub 2012 Oct 10. PubMed PMID: 23062713; PubMed Central PMCID: PMC3483431.

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Adelman K, Lis JT. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet. 2012 Oct;13(10):720-31. doi: 10.1038/nrg3293. Review. PubMed PMID: 22986266; PubMed Central PMCID: PMC3552498.

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Gilchrist DA, Adelman K. Coupling polymerase pausing and chromatin landscapes for precise regulation of transcription. Biochim Biophys Acta. 2012 Jul;1819(7):700-6. doi: 10.1016/j.bbagrm.2012.02.015. Epub 2012 Mar 2. Review. PubMed PMID: 22406341; PubMed Central PMCID: PMC3371112.

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Gilchrist DA, Fromm G, dos Santos G, Pham LN, McDaniel IE, Burkholder A, Fargo DC, Adelman K. Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks. Genes Dev. 2012 May 1;26(9):933-44. doi: 10.1101/gad.187781.112. PubMed PMID: 22549956; PubMed Central PMCID: PMC3347791.

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Saha RN, Wissink EM, Bailey ER, Zhao M, Fargo DC, Hwang JY, Daigle KR, Fenn JD, Adelman K, Dudek SM. Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II. Nat Neurosci. 2011 May 29;14(7):848-56. doi: 10.1038/nn.2839. PubMed PMID: 21623364; PubMed Central PMCID: PMC3125443.