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Chen H, Levo M, Barinov L, Fujioka M, Jaynes JB, Gregor T. Dynamic interplay between enhancer-promoter topology and gene activity. Nat Genet. 2018 ;50(9):1296-1303.
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Ding Q, Nimgaonkar I, Archer NF, Bram Y, Heller B, Schwartz RE, et al. Identification of the Intragenomic Promoter Controlling Hepatitis E Virus Subgenomic RNA Transcription. mBio. 2018 ;9(3).
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Fukaya T, Lim B, Levine M. Enhancer Control of Transcriptional Bursting. Cell. 2016 ;166(2):358-368.
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Gilbertson S, Federspiel JD, Hartenian E, Cristea IM, Glaunsinger B. Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. Elife. 2018 ;7.
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Kachaev ZM, Lebedeva LA, Kozlov EN, Toropygin IY, Schedl P, Shidlovskii YV. Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila. Cell Cycle. 2018 ;17(14):1708-1720.
Kyrchanova O, Mogila V, Wolle D, Deshpande G, Parshikov A, Cleard F, et al. Functional Dissection of the Blocking and Bypass Activities of the Fab-8 Boundary in the Drosophila Bithorax Complex. PLoS Genet. 2016 ;12(7):e1006188.
Kyrchanova O, Mogila V, Wolle D, Magbanua JPaolo, White R, Georgiev P, et al. The boundary paradox in the Bithorax complex. Mech Dev. 2015 ;138 Pt 2:122-132.
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Lenz DH, Bassler BL. The small nucleoid protein Fis is involved in Vibrio cholerae quorum sensing. Mol Microbiol. 2007 ;63(3):859-71.
Levine M, Cattoglio C, Tjian R. Looping back to leap forward: transcription enters a new era. Cell. 2014 ;157(1):13-25.
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Mallarino R, Henegar C, Mirasierra M, Manceau M, Schradin C, Vallejo M, et al. Developmental mechanisms of stripe patterns in rodents. Nature. 2016 ;539(7630):518-523.
Mok WWK, Park JO, Rabinowitz JD, Brynildsen MP. RNA Futile Cycling in Model Persisters Derived from MazF Accumulation. mBio. 2015 ;6(6):e01588-15.
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Oktaba K, Zhang W, Lotz TSabrina, Jun DJayhyun, Lemke SBeatrice, Ng SPak, et al. ELAV links paused Pol II to alternative polyadenylation in the Drosophila nervous system. Mol Cell. 2015 ;57(2):341-8.
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Papenfort K, Förstner KU, Cong J-P, Sharma CM, Bassler BL. Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation. Proc Natl Acad Sci U S A. 2015 ;112(7):E766-75.
Pompeani AJ, Irgon JJ, Berger MF, Bulyk ML, Wingreen NS, Bassler BL. The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters. Mol Microbiol. 2008 ;70(1):76-88.
Postika N, Metzler M, Affolter M, Müller M, Schedl P, Georgiev P, et al.. Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex. PLoS Genet. 2018 ;14(12):e1007702.
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Santos JMendonca, Josling G, Ross P, Joshi P, Orchard L, Campbell T, et al. Red Blood Cell Invasion by the Malaria Parasite Is Coordinated by the PfAP2-I Transcription Factor. Cell Host Microbe. 2017 ;21(6):731-741.e10.
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Truong TT, Seyedsayamdost M, E Greenberg P, Chandler JR. A Burkholderia thailandensis Acyl-Homoserine Lactone-Independent Orphan LuxR Homolog That Activates Production of the Cytotoxin Malleilactone. J Bacteriol. 2015 ;197(21):3456-62.
Tu KC, Waters CM, Svenningsen SL, Bassler BL. A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi. Mol Microbiol. 2008 ;70(4):896-907.
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Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet. 2018 ;50(8):1171-1179.
Zoller B, Little SC, Gregor T. Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. Cell. 2018 ;175(3):835-847.e25.