TY - JOUR AU - Qian, W. AU - Yang, J. R. AU - Pearson, N. M. AU - Maclean, C. AU - Zhang, J. PY - 2012 DA - 2012// TI - Balanced codon usage optimizes eukaryotic translational efficiency JO - PLoS Genet VL - 8 UR - https://doi.org/10.1371/journal.pgen.1002603 DO - 10.1371/journal.pgen.1002603 ID - Qian2012 ER - TY - JOUR AU - Novoa, E. M. AU - Ribas de Pouplana, L. PY - 2012 DA - 2012// TI - Speeding with control: codon usage, tRNAs, and ribosomes JO - Trends Genet VL - 28 UR - https://doi.org/10.1016/j.tig.2012.07.006 DO - 10.1016/j.tig.2012.07.006 ID - Novoa2012 ER - TY - JOUR AU - Gingold, H. AU - Tehler, D. AU - Christoffersen, N. R. AU - Nielsen, M. M. AU - Asmar, F. AU - Kooistra, S. M. PY - 2014 DA - 2014// TI - A dual program for translation regulation in cellular proliferation and differentiation JO - Cell VL - 158 UR - https://doi.org/10.1016/j.cell.2014.08.011 DO - 10.1016/j.cell.2014.08.011 ID - Gingold2014 ER - TY - JOUR AU - Pelechano, V. AU - Wei, W. AU - Steinmetz, L. M. PY - 2015 DA - 2015// TI - Widespread co-translational RNA decay reveals ribosome dynamics JO - Cell VL - 161 UR - https://doi.org/10.1016/j.cell.2015.05.008 DO - 10.1016/j.cell.2015.05.008 ID - Pelechano2015 ER - TY - JOUR AU - Pang, Y. L. AU - Abo, R. AU - Levine, S. S. AU - Dedon, P. C. PY - 2014 DA - 2014// TI - Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku945 DO - 10.1093/nar/gku945 ID - Pang2014 ER - TY - JOUR AU - Schorn, A. J. AU - Gutbrod, M. J. AU - LeBlanc, C. AU - Martienssen, R. PY - 2017 DA - 2017// TI - LTR-Retrotransposon control by tRNA-derived small RNAs JO - Cell VL - 170 UR - https://doi.org/10.1016/j.cell.2017.06.013 DO - 10.1016/j.cell.2017.06.013 ID - Schorn2017 ER - TY - JOUR AU - Goodarzi, H. AU - Liu, X. AU - Nguyen, H. C. AU - Zhang, S. AU - Fish, L. AU - Tavazoie, S. F. PY - 2015 DA - 2015// TI - Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement JO - Cell VL - 161 UR - https://doi.org/10.1016/j.cell.2015.02.053 DO - 10.1016/j.cell.2015.02.053 ID - Goodarzi2015 ER - TY - JOUR AU - Goodarzi, H. AU - Nguyen, H. C. B. AU - Zhang, S. AU - Dill, B. D. AU - Molina, H. AU - Tavazoie, S. F. PY - 2016 DA - 2016// TI - Modulated expression of specific tRNAs drives gene expression and cancer progression JO - Cell VL - 165 UR - https://doi.org/10.1016/j.cell.2016.05.046 DO - 10.1016/j.cell.2016.05.046 ID - Goodarzi2016 ER - TY - JOUR AU - Phizicky, E. M. AU - Hopper, A. K. PY - 2010 DA - 2010// TI - tRNA biology charges to the front JO - Genes Dev VL - 24 UR - https://doi.org/10.1101/gad.1956510 DO - 10.1101/gad.1956510 ID - Phizicky2010 ER - TY - JOUR AU - Kutter, C. AU - Brown, G. D. AU - Goncalves, A. AU - Wilson, M. D. AU - Watt, S. AU - Brazma, A. PY - 2011 DA - 2011// TI - Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.906 DO - 10.1038/ng.906 ID - Kutter2011 ER - TY - JOUR AU - Schmitt, B. M. AU - Rudolph, K. L. AU - Karagianni, P. AU - Fonseca, N. A. AU - White, R. J. AU - Talianidis, I. PY - 2014 DA - 2014// TI - High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.176784.114 DO - 10.1101/gr.176784.114 ID - Schmitt2014 ER - TY - JOUR AU - Roberts, D. N. AU - Stewart, A. J. AU - Huff, J. T. AU - Cairns, B. R. PY - 2003 DA - 2003// TI - The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.2435566100 DO - 10.1073/pnas.2435566100 ID - Roberts2003 ER - TY - JOUR AU - Cozen, A. E. AU - Quartley, E. AU - Holmes, A. D. AU - Hrabeta-Robinson, E. AU - Phizicky, E. M. AU - Lowe, T. M. PY - 2015 DA - 2015// TI - ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3508 DO - 10.1038/nmeth.3508 ID - Cozen2015 ER - TY - JOUR AU - Zheng, G. AU - Qin, Y. AU - Clark, W. C. AU - Dai, Q. AU - Yi, C. AU - He, C. PY - 2015 DA - 2015// TI - Efficient and quantitative high-throughput tRNA sequencing JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3478 DO - 10.1038/nmeth.3478 ID - Zheng2015 ER - TY - JOUR AU - Liu, F. AU - Clark, W. AU - Luo, G. AU - Wang, X. AU - Fu, Y. AU - Wei, J. PY - 2016 DA - 2016// TI - ALKBH1-mediated tRNA demethylation regulates translation JO - Cell VL - 167 UR - https://doi.org/10.1016/j.cell.2016.11.045 DO - 10.1016/j.cell.2016.11.045 ID - Liu2016 ER - TY - JOUR AU - Hrabeta-Robinson, E. AU - Marcus, E. AU - Cozen, A. E. AU - Phizicky, E. M. AU - Lowe, T. M. PY - 2017 DA - 2017// TI - High-throughput small RNA sequencing enhanced by AlkB-facilitated RNA de-methylation (ARM-Seq) JO - Methods Mol Biol VL - 1562 UR - https://doi.org/10.1007/978-1-4939-6807-7_15 DO - 10.1007/978-1-4939-6807-7_15 ID - Hrabeta-Robinson2017 ER - TY - JOUR AU - Phizicky, E. M. AU - Hopper, A. K. PY - 2015 DA - 2015// TI - tRNA processing, modification, and subcellular dynamics: past, present, and future JO - RNA VL - 21 UR - https://doi.org/10.1261/rna.049932.115 DO - 10.1261/rna.049932.115 ID - Phizicky2015 ER - TY - JOUR AU - Mahat, D. B. AU - Kwak, H. AU - Booth, G. T. AU - Jonkers, I. H. AU - Danko, C. G. AU - Patel, R. K. PY - 2016 DA - 2016// TI - Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) JO - Nat Protoc VL - 11 UR - https://doi.org/10.1038/nprot.2016.086 DO - 10.1038/nprot.2016.086 ID - Mahat2016 ER - TY - JOUR AU - Jordan-Pla, A. AU - Gupta, I. AU - Miguel-Jimenez, L. AU - Steinmetz, L. M. AU - Chavez, S. AU - Pelechano, V. PY - 2015 DA - 2015// TI - Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1349 DO - 10.1093/nar/gku1349 ID - Jordan-Pla2015 ER - TY - JOUR AU - Jordan-Pla, A. AU - Miguel, A. AU - Serna, E. AU - Pelechano, V. AU - Perez-Ortin, J. E. PY - 2016 DA - 2016// TI - Biotin-Genomic Run-On (Bio-GRO): A high-resolution method for the analysis of nascent transcription in yeast JO - Methods Mol Biol VL - 1361 UR - https://doi.org/10.1007/978-1-4939-3079-1_8 DO - 10.1007/978-1-4939-3079-1_8 ID - Jordan-Pla2016 ER - TY - JOUR AU - James Faresse, N. AU - Canella, D. AU - Praz, V. AU - Michaud, J. AU - Romascano, D. AU - Hernandez, N. PY - 2012 DA - 2012// TI - Genomic study of RNA polymerase II and III SNAPc-bound promoters reveals a gene transcribed by both enzymes and a broad use of common activators JO - PLoS Genet VL - 8 UR - https://doi.org/10.1371/journal.pgen.1003028 DO - 10.1371/journal.pgen.1003028 ID - James Faresse2012 ER - TY - JOUR AU - Symmons, O. AU - Uslu, V. V. AU - Tsujimura, T. AU - Ruf, S. AU - Nassari, S. AU - Schwarzer, W. PY - 2014 DA - 2014// TI - Functional and topological characteristics of mammalian regulatory domains JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.163519.113 DO - 10.1101/gr.163519.113 ID - Symmons2014 ER - TY - JOUR AU - Lupianez, D. G. AU - Kraft, K. AU - Heinrich, V. AU - Krawitz, P. AU - Brancati, F. AU - Klopocki, E. PY - 2015 DA - 2015// TI - Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions JO - Cell VL - 161 UR - https://doi.org/10.1016/j.cell.2015.04.004 DO - 10.1016/j.cell.2015.04.004 ID - Lupianez2015 ER - TY - JOUR AU - Hnisz, D. AU - Day, D. S. AU - Young, R. A. PY - 2016 DA - 2016// TI - Insulated neighborhoods: structural and functional units of mammalian gene control JO - Cell VL - 167 UR - https://doi.org/10.1016/j.cell.2016.10.024 DO - 10.1016/j.cell.2016.10.024 ID - Hnisz2016 ER - TY - JOUR AU - Dowen, J. M. AU - Fan, Z. P. AU - Hnisz, D. AU - Ren, G. AU - Abraham, B. J. AU - Zhang, L. N. PY - 2014 DA - 2014// TI - Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes JO - Cell VL - 159 UR - https://doi.org/10.1016/j.cell.2014.09.030 DO - 10.1016/j.cell.2014.09.030 ID - Dowen2014 ER - TY - JOUR AU - Symmons, O. AU - Pan, L. AU - Remeseiro, S. AU - Aktas, T. AU - Klein, F. AU - Huber, W. PY - 2016 DA - 2016// TI - The Shh topological domain facilitates the action of remote enhancers by reducing the effects of genomic distances JO - Dev Cell VL - 39 UR - https://doi.org/10.1016/j.devcel.2016.10.015 DO - 10.1016/j.devcel.2016.10.015 ID - Symmons2016 ER - TY - JOUR AU - Andrey, G. AU - Montavon, T. AU - Mascrez, B. AU - Gonzalez, F. AU - Noordermeer, D. AU - Leleu, M. PY - 2013 DA - 2013// TI - A switch between topological domains underlies HoxD genes collinearity in mouse limbs JO - Science VL - 340 UR - https://doi.org/10.1126/science.1234167 DO - 10.1126/science.1234167 ID - Andrey2013 ER - TY - JOUR AU - Dixon, J. R. AU - Selvaraj, S. AU - Yue, F. AU - Kim, A. AU - Li, Y. AU - Shen, Y. PY - 2012 DA - 2012// TI - Topological domains in mammalian genomes identified by analysis of chromatin interactions JO - Nature VL - 485 UR - https://doi.org/10.1038/nature11082 DO - 10.1038/nature11082 ID - Dixon2012 ER - TY - JOUR AU - Nora, E. P. AU - Lajoie, B. R. AU - Schulz, E. G. AU - Giorgetti, L. AU - Okamoto, I. AU - Servant, N. PY - 2012 DA - 2012// TI - Spatial partitioning of the regulatory landscape of the X-inactivation centre JO - Nature VL - 485 UR - https://doi.org/10.1038/nature11049 DO - 10.1038/nature11049 ID - Nora2012 ER - TY - JOUR AU - Rao, S. S. AU - Huntley, M. H. AU - Durand, N. C. AU - Stamenova, E. K. AU - Bochkov, I. D. AU - Robinson, J. T. PY - 2014 DA - 2014// TI - A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping JO - Cell VL - 159 UR - https://doi.org/10.1016/j.cell.2014.11.021 DO - 10.1016/j.cell.2014.11.021 ID - Rao2014 ER - TY - JOUR AU - Darrow, E. M. AU - Huntley, M. H. AU - Dudchenko, O. AU - Stamenova, E. K. AU - Durand, N. C. AU - Sun, Z. PY - 2016 DA - 2016// TI - Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture JO - Proc Natl Acad Sci U S A VL - 113 UR - https://doi.org/10.1073/pnas.1609643113 DO - 10.1073/pnas.1609643113 ID - Darrow2016 ER - TY - JOUR AU - Dixon, J. R. AU - Jung, I. AU - Selvaraj, S. AU - Shen, Y. AU - Antosiewicz-Bourget, J. E. AU - Lee, A. Y. PY - 2015 DA - 2015// TI - Chromatin architecture reorganization during stem cell differentiation JO - Nature VL - 518 UR - https://doi.org/10.1038/nature14222 DO - 10.1038/nature14222 ID - Dixon2015 ER - TY - JOUR AU - Zuin, J. AU - Dixon, J. R. AU - Reijden, M. I. AU - Ye, Z. AU - Kolovos, P. AU - Brouwer, R. W. PY - 2014 DA - 2014// TI - Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1317788111 DO - 10.1073/pnas.1317788111 ID - Zuin2014 ER - TY - JOUR AU - Heidari, N. AU - Phanstiel, D. H. AU - He, C. AU - Grubert, F. AU - Jahanbani, F. AU - Kasowski, M. PY - 2014 DA - 2014// TI - Genome-wide map of regulatory interactions in the human genome JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.176586.114 DO - 10.1101/gr.176586.114 ID - Heidari2014 ER - TY - JOUR AU - Bortle, K. AU - Nichols, M. H. AU - Li, L. AU - Ong, C. T. AU - Takenaka, N. AU - Qin, Z. S. PY - 2014 DA - 2014// TI - Insulator function and topological domain border strength scale with architectural protein occupancy JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/gb-2014-15-5-r82 DO - 10.1186/gb-2014-15-5-r82 ID - Bortle2014 ER - TY - JOUR AU - Sanborn, A. L. AU - Rao, S. S. AU - Huang, S. C. AU - Durand, N. C. AU - Huntley, M. H. AU - Jewett, A. I. PY - 2015 DA - 2015// TI - Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1518552112 DO - 10.1073/pnas.1518552112 ID - Sanborn2015 ER - TY - JOUR AU - Nichols, M. H. AU - Corces, V. G. PY - 2015 DA - 2015// TI - A CTCF code for 3D genome architecture JO - Cell VL - 162 UR - https://doi.org/10.1016/j.cell.2015.07.053 DO - 10.1016/j.cell.2015.07.053 ID - Nichols2015 ER - TY - JOUR AU - Nora, E. P. AU - Goloborodko, A. AU - Valton, A. L. AU - Gibcus, J. H. AU - Uebersohn, A. AU - Abdennur, N. PY - 2017 DA - 2017// TI - Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization JO - Cell VL - 169 UR - https://doi.org/10.1016/j.cell.2017.05.004 DO - 10.1016/j.cell.2017.05.004 ID - Nora2017 ER - TY - JOUR AU - Haarhuis, J. H. I. AU - Weide, R. H. AU - Blomen, V. A. AU - Yanez-Cuna, J. O. AU - Amendola, M. AU - Ruiten, M. S. PY - 2017 DA - 2017// TI - The cohesin release factor WAPL restricts chromatin loop extension JO - Cell VL - 169 UR - https://doi.org/10.1016/j.cell.2017.04.013 DO - 10.1016/j.cell.2017.04.013 ID - Haarhuis2017 ER - TY - JOUR AU - Fudenberg, G. AU - Imakaev, M. AU - Lu, C. AU - Goloborodko, A. AU - Abdennur, N. AU - Mirny, L. A. PY - 2016 DA - 2016// TI - Formation of chromosomal domains by loop extrusion JO - Cell Rep VL - 15 UR - https://doi.org/10.1016/j.celrep.2016.04.085 DO - 10.1016/j.celrep.2016.04.085 ID - Fudenberg2016 ER - TY - JOUR AU - Snider, C. E. AU - Stephens, A. D. AU - Kirkland, J. G. AU - Hamdani, O. AU - Kamakaka, R. T. AU - Bloom, K. PY - 2014 DA - 2014// TI - Dyskerin, tRNA genes, and condensin tether pericentric chromatin to the spindle axis in mitosis JO - J Cell Biol VL - 207 UR - https://doi.org/10.1083/jcb.201405028 DO - 10.1083/jcb.201405028 ID - Snider2014 ER - TY - JOUR AU - Raab, J. R. AU - Chiu, J. AU - Zhu, J. AU - Katzman, S. AU - Kurukuti, S. AU - Wade, P. A. PY - 2012 DA - 2012// TI - Human tRNA genes function as chromatin insulators JO - EMBO J VL - 31 UR - https://doi.org/10.1038/emboj.2011.406 DO - 10.1038/emboj.2011.406 ID - Raab2012 ER - TY - JOUR AU - Ebersole, T. AU - Kim, J. H. AU - Samoshkin, A. AU - Kouprina, N. AU - Pavlicek, A. AU - White, R. J. PY - 2011 DA - 2011// TI - tRNA genes protect a reporter gene from epigenetic silencing in mouse cells JO - Cell Cycle VL - 10 UR - https://doi.org/10.4161/cc.10.16.17092 DO - 10.4161/cc.10.16.17092 ID - Ebersole2011 ER - TY - JOUR AU - Noma, K. AU - Cam, H. P. AU - Maraia, R. J. AU - Grewal, S. I. PY - 2006 DA - 2006// TI - A role for TFIIIC transcription factor complex in genome organization JO - Cell VL - 125 UR - https://doi.org/10.1016/j.cell.2006.04.028 DO - 10.1016/j.cell.2006.04.028 ID - Noma2006 ER - TY - STD TI - Phanstiel DH, Van Bortle K, Spacek DV, Hess G, Shamim MS, Machol I, et al. Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. Mol Cell. 2017. http://dx.doi.org/10.1016/j.molcel.2017.08.006. UR - http://dx.doi.org/10.1016/j.molcel.2017.08.006 ID - ref45 ER - TY - JOUR AU - Tsuchiya, S. AU - Kobayashi, Y. AU - Goto, Y. AU - Okumura, H. AU - Nakae, S. AU - Konno, T. PY - 1982 DA - 1982// TI - Induction of maturation in cultured human monocytic leukemia cells by a phorbol diester JO - Cancer Res VL - 42 ID - Tsuchiya1982 ER - TY - JOUR AU - Auwerx, J. PY - 1991 DA - 1991// TI - The human leukemia cell line, THP-1: a multifacetted model for the study of monocyte-macrophage differentiation JO - Experientia VL - 47 UR - https://doi.org/10.1007/BF02041244 DO - 10.1007/BF02041244 ID - Auwerx1991 ER - TY - JOUR AU - Daigneault, M. AU - Preston, J. A. AU - Marriott, H. M. AU - Whyte, M. K. AU - Dockrell, D. H. PY - 2010 DA - 2010// TI - The identification of markers of macrophage differentiation in PMA-stimulated THP-1 cells and monocyte-derived macrophages JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0008668 DO - 10.1371/journal.pone.0008668 ID - Daigneault2010 ER - TY - JOUR AU - Kouno, T. AU - Hoon, M. AU - Mar, J. C. AU - Tomaru, Y. AU - Kawano, M. AU - Carninci, P. PY - 2013 DA - 2013// TI - Temporal dynamics and transcriptional control using single-cell gene expression analysis JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-10-r118 DO - 10.1186/gb-2013-14-10-r118 ID - Kouno2013 ER - TY - JOUR AU - Telonis, A. G. AU - Loher, P. AU - Kirino, Y. AU - Rigoutsos, I. PY - 2016 DA - 2016// TI - Consequential considerations when mapping tRNA fragments JO - BMC Bioinf VL - 17 UR - https://doi.org/10.1186/s12859-016-0921-0 DO - 10.1186/s12859-016-0921-0 ID - Telonis2016 ER - TY - JOUR AU - Selitsky, S. R. AU - Sethupathy, P. PY - 2015 DA - 2015// TI - tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data JO - BMC Bioinf VL - 16 UR - https://doi.org/10.1186/s12859-015-0800-0 DO - 10.1186/s12859-015-0800-0 ID - Selitsky2015 ER - TY - JOUR AU - Chan, P. P. AU - Lowe, T. M. PY - 2009 DA - 2009// TI - GtRNAdb: a database of transfer RNA genes detected in genomic sequence JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn787 DO - 10.1093/nar/gkn787 ID - Chan2009 ER - TY - JOUR AU - Chan, P. P. AU - Lowe, T. M. PY - 2016 DA - 2016// TI - GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1309 DO - 10.1093/nar/gkv1309 ID - Chan2016 ER - TY - JOUR AU - Canella, D. AU - Bernasconi, D. AU - Gilardi, F. AU - LeMartelot, G. AU - Migliavacca, E. AU - Praz, V. PY - 2012 DA - 2012// TI - A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.130286.111 DO - 10.1101/gr.130286.111 ID - Canella2012 ER - TY - JOUR AU - Canella, D. AU - Praz, V. AU - Reina, J. H. AU - Cousin, P. AU - Hernandez, N. PY - 2010 DA - 2010// TI - Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.101337.109 DO - 10.1101/gr.101337.109 ID - Canella2010 ER - TY - JOUR AU - Alla, R. K. AU - Cairns, B. R. PY - 2014 DA - 2014// TI - RNA polymerase III transcriptomes in human embryonic stem cells and induced pluripotent stem cells, and relationships with pluripotency transcription factors JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0085648 DO - 10.1371/journal.pone.0085648 ID - Alla2014 ER - TY - JOUR AU - Buenrostro, J. D. AU - Giresi, P. G. AU - Zaba, L. C. AU - Chang, H. Y. AU - Greenleaf, W. J. PY - 2013 DA - 2013// TI - Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position JO - Nat Methods VL - 10 UR - https://doi.org/10.1038/nmeth.2688 DO - 10.1038/nmeth.2688 ID - Buenrostro2013 ER - TY - JOUR AU - Buenrostro, J. D. AU - Wu, B. AU - Chang, H. Y. AU - Greenleaf, W. J. PY - 2015 DA - 2015// TI - ATAC-seq: a method for assaying chromatin accessibility genome-wide JO - Curr Protoc Mol Biol VL - 109 ID - Buenrostro2015 ER - TY - JOUR AU - Sagi, D. AU - Rak, R. AU - Gingold, H. AU - Adir, I. AU - Maayan, G. AU - Dahan, O. PY - 2016 DA - 2016// TI - Tissue- and time-specific expression of otherwise identical tRNA genes JO - PLoS Genet VL - 12 UR - https://doi.org/10.1371/journal.pgen.1006264 DO - 10.1371/journal.pgen.1006264 ID - Sagi2016 ER - TY - JOUR AU - Raha, D. AU - Wang, Z. AU - Moqtaderi, Z. AU - Wu, L. AU - Zhong, G. AU - Gerstein, M. PY - 2010 DA - 2010// TI - Close association of RNA polymerase II and many transcription factors with Pol III genes JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.0911315106 DO - 10.1073/pnas.0911315106 ID - Raha2010 ER - TY - JOUR AU - Helbo, A. S. AU - Lay, F. D. AU - Jones, P. A. AU - Liang, G. AU - Gronbaek, K. PY - 2017 DA - 2017// TI - Nucleosome positioning and NDR structure at RNA polymerase III promoters JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/srep41947 DO - 10.1038/srep41947 ID - Helbo2017 ER - TY - JOUR AU - Moqtaderi, Z. AU - Wang, J. AU - Raha, D. AU - White, R. J. AU - Snyder, M. AU - Weng, Z. PY - 2010 DA - 2010// TI - Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells JO - Nat Struct Mol Biol VL - 17 UR - https://doi.org/10.1038/nsmb.1794 DO - 10.1038/nsmb.1794 ID - Moqtaderi2010 ER - TY - JOUR AU - White, R. J. PY - 2011 DA - 2011// TI - Transcription by RNA polymerase III: more complex than we thought JO - Nat Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg3001 DO - 10.1038/nrg3001 ID - White2011 ER - TY - JOUR AU - Iben, J. R. AU - Maraia, R. J. PY - 2014 DA - 2014// TI - tRNA gene copy number variation in humans JO - Gene VL - 536 UR - https://doi.org/10.1016/j.gene.2013.11.049 DO - 10.1016/j.gene.2013.11.049 ID - Iben2014 ER - TY - JOUR AU - Abecasis, G. R. AU - Auton, A. AU - Brooks, L. D. AU - DePristo, M. A. AU - Durbin, R. M. PY - 2012 DA - 2012// TI - An integrated map of genetic variation from 1,092 human genomes JO - Nature VL - 491 UR - https://doi.org/10.1038/nature11632 DO - 10.1038/nature11632 ID - Abecasis2012 ER - TY - JOUR AU - Darrow, E. M. AU - Chadwick, B. P. PY - 2014 DA - 2014// TI - A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku280 DO - 10.1093/nar/gku280 ID - Darrow2014 ER - TY - JOUR AU - Melnik, S. AU - Deng, B. AU - Papantonis, A. AU - Baboo, S. AU - Carr, I. M. AU - Cook, P. R. PY - 2011 DA - 2011// TI - The proteomes of transcription factories containing RNA polymerases I, II or III JO - Nat Methods VL - 8 UR - https://doi.org/10.1038/nmeth.1705 DO - 10.1038/nmeth.1705 ID - Melnik2011 ER - TY - JOUR AU - Oler, A. J. AU - Alla, R. K. AU - Roberts, D. N. AU - Wong, A. AU - Hollenhorst, P. C. AU - Chandler, K. J. PY - 2010 DA - 2010// TI - Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors JO - Nat Struct Mol Biol VL - 17 UR - https://doi.org/10.1038/nsmb.1801 DO - 10.1038/nsmb.1801 ID - Oler2010 ER - TY - JOUR AU - Smith, S. T. AU - Wickramasinghe, P. AU - Olson, A. AU - Loukinov, D. AU - Lin, L. AU - Deng, J. PY - 2009 DA - 2009// TI - Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization JO - Dev Biol VL - 328 UR - https://doi.org/10.1016/j.ydbio.2008.12.039 DO - 10.1016/j.ydbio.2008.12.039 ID - Smith2009 ER - TY - JOUR AU - Yuen, K. C. AU - Slaughter, B. D. AU - Gerton, J. L. PY - 2017 DA - 2017// TI - Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters JO - Sci Adv VL - 3 UR - https://doi.org/10.1126/sciadv.1700191 DO - 10.1126/sciadv.1700191 ID - Yuen2017 ER - TY - JOUR AU - Orioli, A. AU - Praz, V. AU - Lhote, P. AU - Hernandez, N. PY - 2016 DA - 2016// TI - Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest JO - Genome Res VL - 26 UR - https://doi.org/10.1101/gr.201400.115 DO - 10.1101/gr.201400.115 ID - Orioli2016 ER - TY - JOUR AU - Turowski, T. W. AU - Lesniewska, E. AU - Delan-Forino, C. AU - Sayou, C. AU - Boguta, M. AU - Tollervey, D. PY - 2016 DA - 2016// TI - Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts JO - Genome Res VL - 26 UR - https://doi.org/10.1101/gr.205492.116 DO - 10.1101/gr.205492.116 ID - Turowski2016 ER - TY - JOUR AU - Song, L. AU - Zhang, Z. AU - Grasfeder, L. L. AU - Boyle, A. P. AU - Giresi, P. G. AU - Lee, B. K. PY - 2011 DA - 2011// TI - Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.121541.111 DO - 10.1101/gr.121541.111 ID - Song2011 ER - TY - JOUR AU - Gusmao, E. G. AU - Allhoff, M. AU - Zenke, M. AU - Costa, I. G. PY - 2016 DA - 2016// TI - Analysis of computational footprinting methods for DNase sequencing experiments JO - Nat Methods VL - 13 UR - https://doi.org/10.1038/nmeth.3772 DO - 10.1038/nmeth.3772 ID - Gusmao2016 ER - TY - JOUR AU - Sherwood, R. I. AU - Hashimoto, T. AU - O’Donnell, C. W. AU - Lewis, S. AU - Barkal, A. A. AU - Hoff, J. P. PY - 2014 DA - 2014// TI - Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape JO - Nat Biotechnol VL - 32 UR - https://doi.org/10.1038/nbt.2798 DO - 10.1038/nbt.2798 ID - Sherwood2014 ER - TY - JOUR AU - Mathelier, A. AU - Fornes, O. AU - Arenillas, D. J. AU - Chen, C. Y. AU - Denay, G. AU - Lee, J. PY - 2016 DA - 2016// TI - JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1176 DO - 10.1093/nar/gkv1176 ID - Mathelier2016 ER - TY - JOUR AU - Male, G. AU - Appen, A. AU - Glatt, S. AU - Taylor, N. M. AU - Cristovao, M. AU - Groetsch, H. PY - 2015 DA - 2015// TI - Architecture of TFIIIC and its role in RNA polymerase III pre-initiation complex assembly JO - Nat Commun VL - 6 UR - https://doi.org/10.1038/ncomms8387 DO - 10.1038/ncomms8387 ID - Male2015 ER - TY - JOUR AU - Piper, J. AU - Assi, S. A. AU - Cauchy, P. AU - Ladroue, C. AU - Cockerill, P. N. AU - Bonifer, C. PY - 2015 DA - 2015// TI - Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-2081-4 DO - 10.1186/s12864-015-2081-4 ID - Piper2015 ER - TY - JOUR AU - He, H. H. AU - Meyer, C. A. AU - Chen, M. W. AU - Jordan, V. C. AU - Brown, M. AU - Liu, X. S. PY - 2012 DA - 2012// TI - Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.133280.111 DO - 10.1101/gr.133280.111 ID - He2012 ER - TY - JOUR AU - Oda, T. AU - Hirota, K. AU - Nishi, K. AU - Takabuchi, S. AU - Oda, S. AU - Yamada, H. PY - 2006 DA - 2006// TI - Activation of hypoxia-inducible factor 1 during macrophage differentiation JO - Am J Physiol Cell Physiol VL - 291 UR - https://doi.org/10.1152/ajpcell.00614.2005 DO - 10.1152/ajpcell.00614.2005 ID - Oda2006 ER - TY - JOUR AU - Akuzawa, N. AU - Kurabayashi, M. AU - Ohyama, Y. AU - Arai, M. AU - Nagai, R. PY - 2000 DA - 2000// TI - Zinc finger transcription factor Egr-1 activates Flt-1 gene expression in THP-1 cells on induction for macrophage differentiation JO - Arterioscler Thromb Vasc Biol VL - 20 UR - https://doi.org/10.1161/01.ATV.20.2.377 DO - 10.1161/01.ATV.20.2.377 ID - Akuzawa2000 ER - TY - JOUR AU - Boguta, M. PY - 2013 DA - 2013// TI - Maf1, a general negative regulator of RNA polymerase III in yeast JO - Biochim Biophys Acta VL - 1829 UR - https://doi.org/10.1016/j.bbagrm.2012.11.004 DO - 10.1016/j.bbagrm.2012.11.004 ID - Boguta2013 ER - TY - JOUR AU - Rideout, E. J. AU - Marshall, L. AU - Grewal, S. S. PY - 2012 DA - 2012// TI - Drosophila RNA polymerase III repressor Maf1 controls body size and developmental timing by modulating tRNAiMet synthesis and systemic insulin signaling JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1113311109 DO - 10.1073/pnas.1113311109 ID - Rideout2012 ER - TY - JOUR AU - Vannini, A. AU - Ringel, R. AU - Kusser, A. G. AU - Berninghausen, O. AU - Kassavetis, G. A. AU - Cramer, P. PY - 2010 DA - 2010// TI - Molecular basis of RNA polymerase III transcription repression by Maf1 JO - Cell VL - 143 UR - https://doi.org/10.1016/j.cell.2010.09.002 DO - 10.1016/j.cell.2010.09.002 ID - Vannini2010 ER - TY - JOUR AU - Gajda, A. AU - Towpik, J. AU - Steuerwald, U. AU - Muller, C. W. AU - Lefebvre, O. AU - Boguta, M. PY - 2010 DA - 2010// TI - Full repression of RNA polymerase III transcription requires interaction between two domains of its negative regulator Maf1 JO - J Biol Chem VL - 285 UR - https://doi.org/10.1074/jbc.M110.125286 DO - 10.1074/jbc.M110.125286 ID - Gajda2010 ER - TY - JOUR AU - Ciesla, M. AU - Boguta, M. PY - 2008 DA - 2008// TI - Regulation of RNA polymerase III transcription by Maf1 protein JO - Acta Biochim Pol VL - 55 ID - Ciesla2008 ER - TY - JOUR AU - Goodfellow, S. J. AU - Graham, E. L. AU - Kantidakis, T. AU - Marshall, L. AU - Coppins, B. A. AU - Oficjalska-Pham, D. PY - 2008 DA - 2008// TI - Regulation of RNA polymerase III transcription by Maf1 in mammalian cells JO - J Mol Biol VL - 378 UR - https://doi.org/10.1016/j.jmb.2008.02.060 DO - 10.1016/j.jmb.2008.02.060 ID - Goodfellow2008 ER - TY - JOUR AU - Rollins, J. AU - Veras, I. AU - Cabarcas, S. AU - Willis, I. AU - Schramm, L. PY - 2007 DA - 2007// TI - Human Maf1 negatively regulates RNA polymerase III transcription via the TFIIB family members Brf1 and Brf2 JO - Int J Biol Sci VL - 3 UR - https://doi.org/10.7150/ijbs.3.292 DO - 10.7150/ijbs.3.292 ID - Rollins2007 ER - TY - JOUR AU - Dengler, V. L. AU - Galbraith, M. D. AU - Espinosa, J. M. PY - 2014 DA - 2014// TI - Transcriptional regulation by hypoxia inducible factors JO - Crit Rev Biochem Mol Biol VL - 49 UR - https://doi.org/10.3109/10409238.2013.838205 DO - 10.3109/10409238.2013.838205 ID - Dengler2014 ER - TY - JOUR AU - Ernens, I. AU - Goodfellow, S. J. AU - Innes, F. AU - Kenneth, N. S. AU - Derblay, L. E. AU - White, R. J. PY - 2006 DA - 2006// TI - Hypoxic stress suppresses RNA polymerase III recruitment and tRNA gene transcription in cardiomyocytes JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj402 DO - 10.1093/nar/gkj402 ID - Ernens2006 ER - TY - JOUR AU - Guimaraes-Camboa, N. AU - Stowe, J. AU - Aneas, I. AU - Sakabe, N. AU - Cattaneo, P. AU - Henderson, L. PY - 2015 DA - 2015// TI - HIF1alpha represses cell stress pathways to allow proliferation of hypoxic fetal cardiomyocytes JO - Dev Cell VL - 33 UR - https://doi.org/10.1016/j.devcel.2015.04.021 DO - 10.1016/j.devcel.2015.04.021 ID - Guimaraes-Camboa2015 ER - TY - JOUR AU - Mourad, R. AU - Li, L. AU - Cuvier, O. PY - 2017 DA - 2017// TI - Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach JO - PLoS Comput Biol VL - 13 UR - https://doi.org/10.1371/journal.pcbi.1005538 DO - 10.1371/journal.pcbi.1005538 ID - Mourad2017 ER - TY - JOUR AU - Bortle, K. AU - Corces, V. G. PY - 2012 DA - 2012// TI - tDNA insulators and the emerging role of TFIIIC in genome organization JO - Transcription VL - 3 UR - https://doi.org/10.4161/trns.21579 DO - 10.4161/trns.21579 ID - Bortle2012 ER - TY - JOUR AU - Kirkland, J. G. AU - Raab, J. R. AU - Kamakaka, R. T. PY - 2013 DA - 2013// TI - TFIIIC bound DNA elements in nuclear organization and insulation JO - Biochim Biophys Acta VL - 1829 UR - https://doi.org/10.1016/j.bbagrm.2012.09.006 DO - 10.1016/j.bbagrm.2012.09.006 ID - Kirkland2013 ER - TY - JOUR AU - Haeusler, R. A. AU - Pratt-Hyatt, M. AU - Good, P. D. AU - Gipson, T. A. AU - Engelke, D. R. PY - 2008 DA - 2008// TI - Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes JO - Genes Dev VL - 22 UR - https://doi.org/10.1101/gad.1675908 DO - 10.1101/gad.1675908 ID - Haeusler2008 ER - TY - JOUR AU - Thompson, M. AU - Haeusler, R. A. AU - Good, P. D. AU - Engelke, D. R. PY - 2003 DA - 2003// TI - Nucleolar clustering of dispersed tRNA genes JO - Science VL - 302 UR - https://doi.org/10.1126/science.1089814 DO - 10.1126/science.1089814 ID - Thompson2003 ER - TY - JOUR AU - Duan, Z. AU - Andronescu, M. AU - Schutz, K. AU - McIlwain, S. AU - Kim, Y. J. AU - Lee, C. PY - 2010 DA - 2010// TI - A three-dimensional model of the yeast genome JO - Nature VL - 465 UR - https://doi.org/10.1038/nature08973 DO - 10.1038/nature08973 ID - Duan2010 ER - TY - STD TI - Woolnough JL, Schneider DA, Giles KE. The regulation of tDNA transcription during the directed differentiation of stem cells. bioRxiv. 2017. https://doi.org/10.1101/108472. UR - https://doi.org/10.1101/108472 ID - ref98 ER - TY - JOUR AU - Bortle, K. AU - Nichols, M. H. AU - Ramos, E. AU - Corces, V. G. PY - 2015 DA - 2015// TI - Integrated tRNA, transcript, and protein profiles in response to steroid hormone signaling JO - RNA VL - 21 UR - https://doi.org/10.1261/rna.052126.115 DO - 10.1261/rna.052126.115 ID - Bortle2015 ER - TY - JOUR AU - Schwende, H. AU - Fitzke, E. AU - Ambs, P. AU - Dieter, P. PY - 1996 DA - 1996// TI - Differences in the state of differentiation of THP-1 cells induced by phorbol ester and 1,25-dihydroxyvitamin D3 JO - J Leukoc Biol VL - 59 ID - Schwende1996 ER - TY - JOUR AU - Richter, E. AU - Ventz, K. AU - Harms, M. AU - Mostertz, J. AU - Hochgrafe, F. PY - 2016 DA - 2016// TI - Induction of macrophage function in human THP-1 cells is associated with rewiring of MAPK signaling and activation of MAP3K7 (TAK1) protein kinase JO - Front Cell Dev Biol VL - 4 UR - https://doi.org/10.3389/fcell.2016.00021 DO - 10.3389/fcell.2016.00021 ID - Richter2016 ER - TY - JOUR AU - Rudolph, K. L. AU - Schmitt, B. M. AU - Villar, D. AU - White, R. J. AU - Marioni, J. C. AU - Kutter, C. PY - 2016 DA - 2016// TI - Codon-driven translational efficiency is stable across diverse mammalian cell states JO - PLoS Genet VL - 12 UR - https://doi.org/10.1371/journal.pgen.1006024 DO - 10.1371/journal.pgen.1006024 ID - Rudolph2016 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Anders, S. AU - Huber, W. PY - 2010 DA - 2010// TI - Differential expression analysis for sequence count data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-10-r106 DO - 10.1186/gb-2010-11-10-r106 ID - Anders2010 ER - TY - JOUR AU - Zhang, Y. AU - Liu, T. AU - Meyer, C. A. AU - Eeckhoute, J. AU - Johnson, D. S. AU - Bernstein, B. E. PY - 2008 DA - 2008// TI - Model-based analysis of ChIP-Seq (MACS) JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-9-r137 DO - 10.1186/gb-2008-9-9-r137 ID - Zhang2008 ER - TY - JOUR AU - Nikolayeva, O. AU - Robinson, M. D. PY - 2014 DA - 2014// TI - edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology JO - Methods Mol Biol VL - 1150 UR - https://doi.org/10.1007/978-1-4939-0512-6_3 DO - 10.1007/978-1-4939-0512-6_3 ID - Nikolayeva2014 ER - TY - JOUR AU - Robinson, M. D. AU - McCarthy, D. J. AU - Smyth, G. K. PY - 2010 DA - 2010// TI - edgeR: a Bioconductor package for differential expression analysis of digital gene expression data JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp616 DO - 10.1093/bioinformatics/btp616 ID - Robinson2010 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Ramirez, F. AU - Ryan, D. P. AU - Gruning, B. AU - Bhardwaj, V. AU - Kilpert, F. AU - Richter, A. S. PY - 2016 DA - 2016// TI - deepTools2: a next generation web server for deep-sequencing data analysis JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw257 DO - 10.1093/nar/gkw257 ID - Ramirez2016 ER - TY - JOUR AU - Ramirez, F. AU - Dundar, F. AU - Diehl, S. AU - Gruning, B. A. AU - Manke, T. PY - 2014 DA - 2014// TI - deepTools: a flexible platform for exploring deep-sequencing data JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku365 DO - 10.1093/nar/gku365 ID - Ramirez2014 ER - TY - JOUR AU - Phanstiel, D. H. AU - Boyle, A. P. AU - Araya, C. L. AU - Snyder, M. P. PY - 2014 DA - 2014// TI - Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu379 DO - 10.1093/bioinformatics/btu379 ID - Phanstiel2014 ER - TY - JOUR AU - Zhang, H. AU - Meltzer, P. AU - Davis, S. PY - 2013 DA - 2013// TI - RCircos: an R package for Circos 2D track plots JO - BMC Bioinf VL - 14 UR - https://doi.org/10.1186/1471-2105-14-244 DO - 10.1186/1471-2105-14-244 ID - Zhang2013 ER - TY - JOUR AU - Csardi, G. AU - Nepusz, T. PY - 2006 DA - 2006// TI - The igraph software package for complex network research JO - Inter J Complex Syst VL - 1695 ID - Csardi2006 ER -