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Low RNA Polymerase III activity results in up regulation of HXT2 glucose transporter independently of glucose signaling and despite changing environment.

Adamczyk M, Szatkowska R.

PLoS One. 2017 Sep 29;12(9):e0185516. doi: 10.1371/journal.pone.0185516. eCollection 2017.


How transcription circuits explore alternative architectures while maintaining overall circuit output.

Dalal CK, Johnson AD.

Genes Dev. 2017 Jul 15;31(14):1397-1405. doi: 10.1101/gad.303362.117. Review.


Profiling of transcription factor binding events by chromatin immunoprecipitation sequencing (ChIP-seq).

Song L, Koga Y, Ecker JR.

Curr Protoc Plant Biol. 2016;1(2):293-306. doi: 10.1002/cppb.20014. Epub 2016 Jun 10.


Modeling gene regulation from paired expression and chromatin accessibility data.

Duren Z, Chen X, Jiang R, Wang Y, Wong WH.

Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):E4914-E4923. doi: 10.1073/pnas.1704553114. Epub 2017 Jun 2.


A fast, efficient chromatin immunoprecipitation method for studying protein-DNA binding in Arabidopsis mesophyll protoplasts.

Lee JH, Jin S, Kim SY, Kim W, Ahn JH.

Plant Methods. 2017 May 22;13:42. doi: 10.1186/s13007-017-0192-4. eCollection 2017.


Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice.

Kim JS, Chae S, Jun KM, Pahk YM, Lee TH, Chung PJ, Kim YK, Nahm BH.

Rice (N Y). 2017 Dec;10(1):16. doi: 10.1186/s12284-017-0155-4. Epub 2017 Apr 26.


Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility.

Chen X, Yu B, Carriero N, Silva C, Bonneau R.

Nucleic Acids Res. 2017 May 5;45(8):4315-4329. doi: 10.1093/nar/gkx174.


Systematic dissection of genomic features determining transcription factor binding and enhancer function.

Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1291-E1300. doi: 10.1073/pnas.1621150114. Epub 2017 Jan 30.


Gene-Centered Yeast One-Hybrid Assays.

Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ.

Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.top077669. doi: 10.1101/pdb.top077669.


GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.

Yevshin I, Sharipov R, Valeev T, Kel A, Kolpakov F.

Nucleic Acids Res. 2017 Jan 4;45(D1):D61-D67. doi: 10.1093/nar/gkw951. Epub 2016 Oct 24.


UV-Induced DNA Damage and Mutagenesis in Chromatin.

Mao P, Wyrick JJ, Roberts SA, Smerdon MJ.

Photochem Photobiol. 2017 Jan;93(1):216-228. doi: 10.1111/php.12646. Epub 2016 Nov 7. Review.


Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network.

Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT.

Elife. 2016 Sep 30;5. pii: e19027. doi: 10.7554/eLife.19027.


Analysis of PBase Binding Profile Indicates an Insertion Target Selection Mechanism Dependent on TTAA, But Not Transcriptional Activity.

Yang D, Liao R, Zheng Y, Sun L, Xu T.

Int J Biol Sci. 2016 Jul 18;12(9):1074-82. doi: 10.7150/ijbs.15589. eCollection 2016.


Disruption of promoter memory by synthesis of a long noncoding RNA.

Yu Y, Yarrington RM, Chuong EB, Elde NC, Stillman DJ.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9575-80. doi: 10.1073/pnas.1601793113. Epub 2016 Aug 9.


Modeling protein-DNA binding via high-throughput in vitro technologies.

Orenstein Y, Shamir R.

Brief Funct Genomics. 2017 May 1;16(3):171-180. doi: 10.1093/bfgp/elw030.


A basic domain in the histone H2B N-terminal tail is important for nucleosome assembly by FACT.

Mao P, Kyriss MN, Hodges AJ, Duan M, Morris RT, Lavine MD, Topping TB, Gloss LM, Wyrick JJ.

Nucleic Acids Res. 2016 Nov 2;44(19):9142-9152. Epub 2016 Jul 1.


Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae.

Liu G, Bergenholm D, Nielsen J.

MBio. 2016 May 3;7(3). pii: e00559-16. doi: 10.1128/mBio.00559-16.


FabR regulates Salmonella biofilm formation via its direct target FabB.

Hermans K, Roberfroid S, Thijs IM, Kint G, De Coster D, Marchal K, Vanderleyden J, De Keersmaecker SC, Steenackers HP.

BMC Genomics. 2016 Mar 22;17:253. doi: 10.1186/s12864-016-2387-x.


Ensembl regulation resources.

Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D, Keefe D, Gräf S, Ahmed I, Kinsella R, Pritchard B, Brent S, Amode R, Parker A, Trevanion S, Birney E, Dunham I, Flicek P.

Database (Oxford). 2016 Feb 17;2016. pii: bav119. doi: 10.1093/database/bav119. Print 2016.

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