Epigenetic regulation of TTF-I-mediated promoter-terminator interactions of rRNA genes
Open accessAbstract
Ribosomal RNA synthesis is the eukaryotic cell's main transcriptional activity, but little is known about the chromatin domain organization and epigenetics of actively transcribed rRNA genes. Here, we show epigenetic and spatial organization of mouse rRNA genes at the molecular level. TTF-I-binding sites subdivide the rRNA transcription unit into functional chromatin domains and sharply delimit transcription factor occupancy. H2A.Z-containing nucleosomes occupy the spacer promoter next to a newly characterized TTF-I-binding site. The spacer and the promoter proximal TTF-I-binding sites demarcate the enhancer. DNA from both the enhancer and the coding region is hypomethylated in actively transcribed repeats. 3C analysis revealed an interaction between promoter and terminator regions, which brings the beginning and end of active rRNA genes into close contact. Reporter assays show that TTF-I mediates this interaction, thereby linking topology and epigenetic regulation of the rRNA genes.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Studies on mammalian cells show that rDNA repeats in the nucleolus form loops connecting promoter and termination regions or more complex structures, in which the transcribed rDNA region is wrapped around the core formed by SL1.
“Studies on mammalian cells show that rDNA repeats in the nucleolus form loops connecting promoter and termination regions (91,92) or more complex structures, in which the transcribed rDNA region is wrapped around the core formed by SL1 (93).”
From Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon (2022) · cites this paper as [91]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652 · see citing works
Genomic DNA methylation: the mark and its mediators.
Klose, R. J., & Bird, A. P. (2006) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.12.008 · Cited by 2,501 · see citing works
Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., & de Laat, W. (2006) · Nature Genetics · doi:10.1038/ng1896 · Cited by 1,386 · see citing works
Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus
Tolhuis, B., Palstra, R.-J., Splinter, E., Grosveld, F., & de Laat, W. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00781-5 · Cited by 1,344 · see citing works
Dostie, J., Richmond, T., Arnaout, R., Selzer, R. R., Lee, W. L., Honan, T., Rubio, E. D., Krumm, A., Lamb, J., Nusbaum, C., et al. (2006) · Genome Research · doi:10.1101/gr.5571506 · Cited by 1,182 · see citing works
Zhao, Z., Tavoosidana, G., Sjölinder, M., Göndör, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K. S., Singh, U., et al. (2006) · Nature Genetics · doi:10.1038/ng1891 · Cited by 957 · see citing works
Self-citationHistone H3 lysine 4 methylation patterns in higher eukaryotic genes
Schneider, R., Bannister, A. J., Myers, F. A., Thorne, A. W., Crane‐Robinson, C., & Kouzarides, T. (2003) · Nature Cell Biology · doi:10.1038/ncb1076 · Cited by 792 · see citing works
c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I
Grandori, C., Gomez-Roman, N., Felton-Edkins, Z. A., Ngouenet, C., Galloway, D. A., Eisenman, R. N., & White, R. J. (2005) · Nature Cell Biology · doi:10.1038/ncb1224 · Cited by 659 · see citing works
Meneghini, M. D., Wu, M. K. Y., & Madhani, H. D. (2003) · Cell · doi:10.1016/s0092-8674(03)00123-5 · Cited by 627 · see citing works
Kurukuti, S., Tiwari, V. K., Tavoosidana, G., Pugacheva, E., Murrell, A., Zhao, Z., Lobanenkov, V., Reik, W., & Ohlsson, R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600326103 · Cited by 511 · see citing works
Self-citationCTCF Mediates Interchromosomal Colocalization Between Igf2/H19 and Wsb1/Nf1
Ling, J. Q., Li, T., Hu, J., Vu, T. H., Chen, H. L., Qiu, X. W., Cherry, A. M., & Hoffman, A. R. (2006) · Science · doi:10.1126/science.1123191 · Cited by 434 · see citing works
Long-range intrachromosomal interactions in the T helper type 2 cytokine locus
Spilianakis, C. G., & Flavell, R. A. (2004) · Nature Immunology · doi:10.1038/ni1115 · Cited by 425 · see citing works
Santoro, R., Li, J., & Grummt, I. (2002) · Nature Genetics · doi:10.1038/ng1010 · Cited by 406 · see citing works
Nuclear actin and myosin I are required for RNA polymerase I transcription
Philimonenko, V. V., Zhao, J., Iben, S., Dingová, H., Gaplovská-Kyselá, K., Kahle, M., Zentgraf, H., Hofmann, W. A., de Lanerolle, P., Hozák, P., et al. (2004) · Nature Cell Biology · doi:10.1038/ncb1190 · Cited by 398 · see citing works
Spatial organization of gene expression: the active chromatin hub
de Laat, W. L., & Grosveld, F. G. (2003) · Chromosome Research · doi:10.1023/a:1024922626726 · Cited by 349 · see citing works
The three 'C' s of chromosome conformation capture: controls, controls, controls
Dekker, J. (2005) · Nature Methods · doi:10.1038/nmeth823 · Cited by 347 · see citing works
Gene loops juxtapose promoters and terminators in yeast
O'Sullivan, J. M., Tan‐Wong, S. M., Morillon, A., Lee, B., Coles, J., Mellor, J., & Proudfoot, N. J. (2004) · Nature Genetics · doi:10.1038/ng1411 · Cited by 346 · see citing works
Lawrence, R. J., Earley, K. W., Pontes, O., Silva, M., Chen, Z. J., Neves, N., Viegas, W. S., & Pikaard, C. S. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00064-4 · Cited by 343 · see citing works
Intergenic Transcripts Regulate the Epigenetic State of rRNA Genes
Mayer, C., Schmitz, K., Li, J., Grummt, I., & Santoro, R. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.03.028 · Cited by 327 · see citing works
Epigenetic silencing of RNA polymerase I transcription
Grummt, I., & Pikaard, C. S. (2003) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1171 · Cited by 298 · see citing works
RNA-polymerase-I-directed rDNA transcription, life and works
Russell, J., & Zomerdijk, J. C. B. M. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2004.12.008 · Cited by 291 · see citing works
Mutagenesis at Methylated CpG Sequences
Pfeifer, G. P. (2006) · Springer eBooks · doi:10.1007/3-540-31390-7_10 · Cited by 267 · see citing works
Molecular Mechanisms Mediating Methylation-Dependent Silencing of Ribosomal Gene Transcription
Santoro, R., & Grummt, I. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00317-3 · Cited by 254 · see citing works
O’Sullivan, A., Sullivan, G. J., & McStay, B. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.2.657-668.2002 · Cited by 215 · see citing works
Ghoshal, K., Majumder, S., Datta, J., Motiwala, T., Bai, S., Sharma, S. M., Frankel, W. L., & Jacob, S. T. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309393200 · Cited by 205 · see citing works
Martin, M., Cho, J., Cesare, A. J., Griffith, J. D., & Attardi, G. M. (2005) · Cell · doi:10.1016/j.cell.2005.09.040 · Cited by 192 · see citing works
UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machineryPreprint
Mais, C., Wright, J. E., Prieto, J.-L., Raggett, S. L., & McStay, B. (2004) · Genes & Development · doi:10.1101/gad.310705 · Cited by 179 · see citing works
Preuss, S. B., & Pikaard, C. S. (2007) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/j.bbaexp.2007.02.005 · Cited by 150 · see citing works
A transcription terminator located upstream of the mouse rDNA initiation site affects rRNA synthesis
Grummt, I., Kuhn, A., Bartsch, I., & Rosenbauer, H. (1986) · Cell · doi:10.1016/0092-8674(86)90805-6 · Cited by 144 · see citing works
Grummt, I., Rosenbauer, H., Niedermeyer, I., Maier, U., & Öhrlein, A. (1986) · Cell · doi:10.1016/0092-8674(86)90558-1 · Cited by 141 · see citing works
3′‐End formation of transcripts from the yeast rRNA operon.
Kempers-Veenstra, A. E., Oliemans, J., Offenberg, H. H., Dekker, A. F., Piper, P. W., Planta, R. J., & Klootwijk, J. (1986) · The EMBO Journal · doi:10.1002/j.1460-2075.1986.tb04554.x · Cited by 132 · see citing works
Längst, G., Blank, T. A., Becker, P. B., & Grummt, I. (1997) · The EMBO Journal · doi:10.1093/emboj/16.4.760 · Cited by 109 · see citing works
Self-citationTTF‐I determines the chromatin architecture of the active rDNA promoter
Längst, G., Becker, P. B., & Grummt, I. (1998) · The EMBO Journal · doi:10.1093/emboj/17.11.3135 · Cited by 108 · see citing works
Self-citationGuillemette, B. I., & Gaudreau, L. R. (2006) · Biochemistry and Cell Biology · doi:10.1139/o06-077 · Cited by 106 · see citing works
Eberhard, D., Tora, L., Egly, J., & Grummt, I. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.18.4180 · Cited by 96 · see citing works
Németh, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh732 · Cited by 65 · see citing works
Self-citationMosaic methylation of the repeat unit of the human ribosomal RNA genes
Brock, G., & Bird, A. P. (1997) · Human Molecular Genetics · doi:10.1093/hmg/6.3.451 · Cited by 53 · see citing works
Sander, E. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.6.1142 · Cited by 28 · see citing works
A test of ‘polymerase handover’ as a mechanism for stimulating initiation by RNA polymerase I
Lucchini, R., & Reeder, R. H. (1989) · Nucleic Acids Research · doi:10.1093/nar/17.1.373 · Cited by 14 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
A decade of 3C technologies: insights into nuclear organizationPreprint
de Wit, E., & de Laat, W. L. (2012) · Genes & Development · doi:10.1101/gad.179804.111 · Cited by 701 · see citing works
Genome organization in and around the nucleolus
Németh, A., & Längst, G. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.01.002 · Cited by 208 · see citing works
Self-citationBasic mechanisms in RNA polymerase i transcription of the ribosomal RNA genes
Goodfellow, S. J., & Zomerdijk, J. C. B. M. (2013) · Subcellular Biochemistry · doi:10.1007/978-94-007-4525-4_10 · Cited by 197 · see citing works
Nucleolus and nuclear periphery: Velcro for heterochromatin
Padeken, J., & Heun, P. (2014) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2014.03.001 · Cited by 179 · see citing works
Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription
Cong, R., Das, S., Ugrinova, I., Kumar, S., Mongelard, F., Wong, J., & Bouvet, P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks720 · Cited by 155 · see citing works
Chromosome crosstalk in three dimensions
Göndör, A., & OHLSSON, R. I. (2009) · Nature · doi:10.1038/nature08453 · Cited by 151 · see citing works
Self-citationSchmolke, M., Manicassamy, B., Pena, L., Sutton, T. C., Hai, R., Varga, Z. T., Hale, B. G., Steel, J., Perez, D. R., & García‐Sastre, A. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002186 · Cited by 148 · see citing works
Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional terminationPreprint
Kawauchi, J., Mischo, H. E., Braglia, P., Rondón, A. G., & Proudfoot, N. J. (2008) · Genes & Development · doi:10.1101/gad.463408 · Cited by 145 · see citing works
Epigenetic control of RNA polymerase I transcription in mammalian cells
Grummt, I., & Längst, G. (2013) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.10.004 · Cited by 132 · see citing works
Self-citationStructural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases
Girbig, M., Misiaszek, A. D., & Müller, C. W. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00476-9 · Cited by 125 · see citing works
FACT facilitates chromatin transcription by RNA polymerases I and III
Birch, J. L., Tan, B. C., Panov, K. I., Panova, T. B., Andersen, J., Owen‐Hughes, T., Russell, J., Lee, S.-C., & Zomerdijk, J. C. B. M. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.33 · Cited by 125 · see citing works
Scholz, B. A., Sumida, N., de Lima, C. D. M., Chachoua, I., Martino, M., Tzelepis, I., Nikoshkov, A., Zhao, H., Mehmood, R., Sifakis, E. G., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0535-3 · Cited by 114 · see citing works
Self-citationRibosomal DNA and the nucleolus in the context of genome organization
Potapova, T., & Gerton, J. L. (2019) · Chromosome Research · doi:10.1007/s10577-018-9600-5 · Cited by 96 · see citing works
Poortinga, G., Wall, M., Sanij, E., Siwicki, K., Ellul, J., Brown, D. V., Holloway, T. P., Hannan, R. D., & McArthur, G. A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1205 · Cited by 98 · see citing works
Keeping ribosomal DNA intact: a repeating challenge
Warmerdam, D. O., & Wolthuis, R. M. F. (2018) · Chromosome Research · doi:10.1007/s10577-018-9594-z · Cited by 95 · see citing works
CTCF regulates the local epigenetic state of ribosomal DNA repeats
van de Nobelen, S., Rosa‐Garrido, M., Leers, J., Heath, H., Soochit, W., Joosen, L., Jonkers, I. H., Demmers, J., van der Reijden, M. I. J. A., Torrano, V., et al. (2010) · Epigenetics & Chromatin · doi:10.1186/1756-8935-3-19 · Cited by 90 · see citing works
Herdman, C., Mars, J.-C., Stefanovsky, V. Y., Tremblay, M. G., Sabourin‐Félix, M., Lindsay, H. A., Robinson, M. D., & Moss, T. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006899 · Cited by 89 · see citing works
Akamatsu, Y., & Kobayashi, T. (2015) · Molecular and Cellular Biology · doi:10.1128/mcb.01521-14 · Cited by 89 · see citing works
Nucleolin: Dual roles in rDNA chromatin transcription
Durut, N., & Sáez‐Vasquez, J. (2014) · Gene · doi:10.1016/j.gene.2014.09.023 · Cited by 88 · see citing works
Hamdane, N., Stefanovsky, V. Y., Tremblay, M. G., Németh, A., Paquet, É. R., Lessard, F., Sanij, E., Hannan, R. D., & Moss, T. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004505 · Cited by 87 · see citing works
Self-citationThe Nucleolus: In Genome Maintenance and Repair
Tsekrekou, M., Stratigi, K., & Chatzinikolaou, G. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18071411 · Cited by 82 · see citing works
Dicer Is Associated with Ribosomal DNA Chromatin in Mammalian Cells
Sinkkonen, L., Hugenschmidt, T., Filipowicz, W., & Svoboda, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012175 · Cited by 83 · see citing works
The conservation landscape of the human ribosomal RNA gene repeats
Agrawal, S., & Ganley, A. R. D. (2018) · PLoS ONE · doi:10.1371/journal.pone.0207531 · Cited by 76 · see citing works
Archacki, R., Yatusevich, R., Buszewicz, D., Krzyczmonik, K., Patryn, J., Iwanicka‐Nowicka, R., Biecek, P., Wilczyński, B., Koblowska, M., Jerzmanowski, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1273 · Cited by 75 · see citing works
Targeting RNA polymerase I to treat MYC-driven cancer
Poortinga, G., Quinn, L. M., & Hannan, R. D. (2014) · Oncogene · doi:10.1038/onc.2014.13 · Cited by 74 · see citing works
de Paz, A. M., Khajavi, L., Martin, H., Claveria‐Gimeno, R., Dieck, S. T., Cheema, M. S., Sanchez-Mut, J. V., Moksa, M. M., Carles, A., Brodie, N. I., et al. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0298-1 · Cited by 68 · see citing works
c-Myc induces changes in higher order rDNA structure on stimulation of quiescent cells
Shiue, C.-N., Berkson, R. G., & Wright, A. P. H. (2009) · Oncogene · doi:10.1038/onc.2009.21 · Cited by 69 · see citing works
Structure and function of ribosomal RNA gene chromatin
Birch, J. L., & Zomerdijk, J. C. B. M. (2008) · Biochemical Society Transactions · doi:10.1042/bst0360619 · Cited by 68 · see citing works
Ray, S., Panova, T. B., Miller, G., Volkov, A., Porter, A. C. G., Russell, J., Panov, K. I., & Zomerdijk, J. C. B. M. (2013) · Nature Communications · doi:10.1038/ncomms2599 · Cited by 64 · see citing works
Super-resolution in situ analysis of active ribosomal DNA chromatin organization in the nucleolus
Maiser, A., Dillinger, S., Längst, G., Schermelleh, L., Leonhardt, H., & Németh, A. (2020) · Scientific Reports · doi:10.1038/s41598-020-64589-x · Cited by 65 · see citing works
Self-citationPTRF/Cavin-1 promotes efficient ribosomal RNA transcription in response to metabolic challenges
Liu, L., & Pilch, P. F. (2016) · eLife · doi:10.7554/elife.17508 · Cited by 64 · see citing works
Genetic and epigenetic regulation of skeletal muscle ribosome biogenesis with exercise
Figueiredo, V. C., Wen, Y., Alkner, B., Fernandez‐Gonzalo, R., Norrbom, J., Vechetti, I. J., Valentino, T., Mobley, C. B., Zentner, G. E., Peterson, C. A., et al. (2021) · The Journal of Physiology · doi:10.1113/jp281244 · Cited by 64 · see citing works
Dual ARID1A/ARID1B loss leads to rapid carcinogenesis and disruptive redistribution of BAF complexes
Wang, Z., Chen, K., Jia, Y., Chuang, J.-C., Sun, X., Lin, Y.-H., Celen, C., Li, L., Huang, F., Liu, X., et al. (2020) · Nature Cancer · doi:10.1038/s43018-020-00109-0 · Cited by 60 · see citing works
The Reb1‐homologue Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast
Reiter, A., Hamperl, S., Seitz, H., Merkl, P., Pérez-Fernández, J., Williams, L., Gerber, J., Németh, A., Léger‐Silvestre, I., Gadal, O., et al. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.185 · Cited by 60 · see citing works
Self-citationThe chromatin landscape of the ribosomal RNA genes in mouse and human
Moss, T., Mars, J.-C., Tremblay, M. G., & Sabourin‐Félix, M. (2019) · Chromosome Research · doi:10.1007/s10577-018-09603-9 · Cited by 60 · see citing works
A model for the topology of active ribosomal RNA genes
Denissov, S., Lessard, F., Mayer, C., Stefanovsky, V., van Driel, M., Grummt, I., Moss, T., & Stunnenberg, H. G. (2011) · The EMBO Reports · doi:10.1038/embor.2011.8 · Cited by 58 · see citing works
Long Noncoding RNAs and Stress Response in the Nucleolus
Пирогов, С. А., Gvozdev, V. A., & Klenov, M. S. (2019) · Cells · doi:10.3390/cells8070668 · Cited by 54 · see citing works
RNA polymerase I termination: Where is the end?
Németh, A., Pérez-Fernández, J., Merkl, P., Hamperl, S., Gerber, J., Griesenbeck, J., & Tschochner, H. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.10.007 · Cited by 45 · see citing works
Self-citationEnd-targeting proteomics of isolated chromatin segments of a mammalian ribosomal RNA gene promoter
Ide, S., & Déjardin, J. (2015) · Nature Communications · doi:10.1038/ncomms7674 · Cited by 43 · see citing works
Smith, C. L., Matheson, T. D., Trombly, D. J., Sun, X., Campeau, E., Han, X., Yates, J. R., & Kaufman, P. D. (2014) · Molecular Biology of the Cell · doi:10.1091/mbc.e14-05-1029 · Cited by 43 · see citing works
Cyclin-dependent Kinase 9 Links RNA Polymerase II Transcription to Processing of Ribosomal RNA
Burger, K., Mühl, B., Michaela, R., Coordes, B., Heidemann, M., Kellner, M., Anita, G.-E., Heissmeyer, V., Sträßer, K., & Eick, D. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.483719 · Cited by 40 · see citing works
DNA Looping Facilitates Targeting of a Chromatin Remodeling Enzyme
Yadon, A. N., Singh, B. N., Hampsey, M., & Tsukiyama, T. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.02.005 · Cited by 39 · see citing works
Almuzzaini, B., Sarshad, A. A., Rahmanto, A. S., Hansson, M. L., von Euler, A., Sangfelt, O., Visa, N., Farrants, A. Ö., & Percipalle, P. (2016) · The FASEB Journal · doi:10.1096/fj.201600280r · Cited by 38 · see citing works
Functional architecture of the Reb1-Ter complex of Schizosaccharomyces pombe
Jaiswal, R., Choudhury, M., Zzaman, S., Singh, S. K., Santosh, V., Bastia, D., & Escalante, C. R. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1525465113 · Cited by 37 · see citing works
Enhancer functions in three dimensions: beyond the flat world perspective
Göndör, A., & OHLSSON, R. I. (2018) · F1000Research · doi:10.12688/f1000research.13842.1 · Cited by 36 · see citing works
Self-citationMyb-binding Protein 1a (Mybbp1a) Regulates Levels and Processing of Pre-ribosomal RNA
Hochstatter, J., Hölzel, M., Michaela, R., Schermelleh, L., Leonhardt, H., Keough, R. A., Gonda, T. J., Imhof, A., Eick, D., Längst, G., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.303719 · Cited by 37 · see citing works
Self-citationEpigeneitc silencing of ribosomal RNA genes by Mybbp1a
Tan, B. C., Yang, C., Hsieh, C.-L., Chou, Y.-H., Zhong, C. Z., Yung, B. Y., & Liu, H. (2012) · Journal of Biomedical Science · doi:10.1186/1423-0127-19-57 · Cited by 34 · see citing works
Nucleolar DNA: the host and the guests
Smirnov, E., Cmarko, D., Mazel, T., Hornáček, M., & Raška, I. (2016) · Histochemistry and Cell Biology · doi:10.1007/s00418-016-1407-x · Cited by 34 · see citing works
Karahan, G., Sayar, N., GOZUM, G., Bozkurt, B., Konu, Ö., & Yuluğ, I. G. (2015) · Oncology Reports · doi:10.3892/or.2015.3940 · Cited by 33 · see citing works
Regulation of Replication Termination by Reb1 Protein-Mediated Action at a Distance
Singh, S. K., Sabatinos, S., Forsburg, S. L., & Bastia, D. (2010) · Cell · doi:10.1016/j.cell.2010.08.013 · Cited by 33 · see citing works
PAN RNA: transcriptional exhaust from a viral engine
Campbell, M., & Izumiya, Y. (2020) · Journal of Biomedical Science · doi:10.1186/s12929-020-00637-y · Cited by 28 · see citing works
Ribosomal RNA Transcription Regulation in Breast Cancer
Harold, C. M., Buhagiar, A. F., Yan, C., & Baserga, S. J. (2021) · Genes · doi:10.3390/genes12040502 · Cited by 29 · see citing works
An actin-based nucleoskeleton involved in gene regulation and genome organization
Xie, X., & Percipalle, P. (2017) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2017.11.206 · Cited by 28 · see citing works
Zillner, K., Komatsu, J., Filarsky, K., Kalepu, R., Bensimon, A., & Németh, A. (2015) · Epigenomics · doi:10.2217/epi.14.93 · Cited by 28 · see citing works
Self-citationVariations in a team: Major and minor variants ofArabidopsisthaliana rDNA genes
Abou-Ellail, M., Cooke, R., & Sáez‐Vasquez, J. (2011) · Nucleus · doi:10.4161/nucl.2.4.16561 · Cited by 28 · see citing works
Regulation of RNA Polymerase I Stability and Function
Pitts, S., & Laiho, M. (2022) · Cancers · doi:10.3390/cancers14235776 · Cited by 22 · see citing works
Recognition of hyperacetylated N-terminus of H2AZ by TbBDF2 from Trypanosoma brucei
Xiao, Y., Wu, X., Zhang, J., Zhang, X., Xu, C., Liao, S., & Tu, X. (2017) · Biochemical Journal · doi:10.1042/bcj20170619 · Cited by 25 · see citing works
Are gene loops the cause of transcriptional noise?
Hebenstreit, D. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.04.001 · Cited by 25 · see citing works
Chromatin-Specific Regulation of Mammalian rDNA Transcription by Clustered TTF-I Binding Sites
Diermeier, S. D., Németh, A., Rehli, M., Grummt, I., & Längst, G. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003786 · Cited by 24 · see citing works
Self-citationShiue, C.-N., Mahani, A., & Wright, A. P. H. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku183 · Cited by 24 · see citing works
Ribosomal RNA Genes in the Protozoan Parasite Leishmania major Possess a Nucleosomal Structure
Vizuet‐de‐Rueda, J. C., Florencio-Martínez, L. E., Padilla-Mejía, N. E., Manning-Cela, R. G., Hernández‐Rivas, R., & Martínez‐Calvillo, S. (2016) · Protist · doi:10.1016/j.protis.2016.02.001 · Cited by 22 · see citing works
DNA sequence encoded repression of rRNA gene transcription in chromatin
Felle, M., Exler, J. H., Merkl, R., Dachauer, K., Brehm, A., Grummt, I., & Längst, G. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq263 · Cited by 21 · see citing works
Self-citationNucleolar organization, growth control and cancer
Shiue, C.-N., Arabi, A., & Wright, A. P. H. (2010) · Epigenetics · doi:10.4161/epi.5.3.11376 · Cited by 18 · see citing works
Fefelova, E. A., Pleshakova, I. M., Mikhaleva, E. A., Pirogov, S. A., Poltorachenko, V. A., Abramov, Y. A., Romashin, D. D., Shatskikh, A. S., Blokh, R. S., Gvozdev, V. A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1276 · Cited by 15 · see citing works
“Studies on mammalian cells show that rDNA repeats in the nucleolus form loops connecting promoter and termination regions (91,92) or more complex structures, in which the transcribed rDNA region is wrapped around the core formed by SL1 (93).”
BackgroundThe Epigenetics of the Nucleolus: Structure and Function of Active and Silent Ribosomal RNA Genes
Santoro, R. (2011) · Springer eBooks · doi:10.1007/978-1-4614-0514-6_4 · Cited by 13 · see citing works
Dynamic chromatin loops bridge health and disease in the nuclear landscape
Göndör, A. (2013) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2013.01.002 · Cited by 13 · see citing works
Mukhopadhyay, P., Singla-Pareek, S. L., Reddy, M. K., & Sopory, S. K. (2013) · Plant and Cell Physiology · doi:10.1093/pcp/pct012 · Cited by 12 · see citing works
Ribosomal RNA Methylation and Cancer
Thérizols, G., Laforêts, F., Marcel, V., Catez, F., Bouvet, P., & Diaz, J. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-800206-3.00006-9 · Cited by 10 · see citing works
Musgrove, E. A., & Sutherland, R. L. (2010) · Cell Cycle · doi:10.4161/cc.9.23.13889 · Cited by 11 · see citing works
Eukaryotic Replication Barriers: How, Why and Where Forks Stall
Jacob, Z., Emma, L. B., & Ramsay, J. (2011) · InTech eBooks · doi:10.5772/20383 · Cited by 10 · see citing works
Transcription factor regulation of ribosomal RNA in hematopoiesis
Paralkar, V. R. (2024) · Current Opinion in Hematology · doi:10.1097/moh.0000000000000816 · Cited by 9 · see citing works
The RNA Polymerase I Transcription Machinery
Voit, R., & Grummt, I. (2011) · Springer eBooks · doi:10.1007/978-1-4614-0514-6_6 · Cited by 9 · see citing works
C-methods to study 3D organization of the eukaryotic genome
Gavrilov, A. A., Razin, S. V., & Iarovaia, O. V. (2012) · Biopolymers and Cell · doi:10.7124/bc.000056 · Cited by 8 · see citing works
Mayán, M. D. (2012) · Yeast · doi:10.1002/yea.2938 · Cited by 7 · see citing works
Rolicka, A. T., Guo, Y., Zapater, A. G., Tariq, K., Quin, J. E., Vintermist, A., Sadeghifar, F., Arsenian‐Henriksson, M., & Farrants, A. Ö. (2020) · The FASEB Journal · doi:10.1096/fj.202000411r · Cited by 7 · see citing works
Molecular and organismal changes in offspring of male mice treated with chemical stressors
Shiao, Y., Leighty, R. M., Wang, C.-J., Ge, X., Crawford, E. B., Spurrier, J. M., McCann, S. D., Fields, J. R., Fornwald, L. W., Riffle, L. A., et al. (2012) · Environmental and Molecular Mutagenesis · doi:10.1002/em.21701 · Cited by 6 · see citing works
Tiwari, K., Gangopadhyay, A., Singh, G., Singh, V. K., & Singh, S. K. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2109754 · Cited by 6 · see citing works
Chromatin Organization and the Mammalian Nucleolus
Németh, A., & Längst, G. (2013) · Springer eBooks · doi:10.1007/978-94-007-5818-6_6 · Cited by 5 · see citing works
Self-citationOdd RNA polymerases or the A(B)C of eukaryotic transcription
Sentenac, A., & Riva, M. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.10.012 · Cited by 5 · see citing works
Investigation of functional roles of transcription termination factor-1 (TTF-I) in HIV-1 replication
Park, S., Yu, K.-L., Jung, Y.-M., Lee, S.-D., Kim, M., & You, J.-C. (2018) · BMB Reports · doi:10.5483/bmbrep.2018.51.7.032 · Cited by 2 · see citing works
The Structure, Expression, and Non-Canonical Functions of Human rDNA: The Role of Non-Coding Regions
Sadova, A. A., Panteleev, D. Y., & Pavlova, G. V. (2023) · Molecular Biology · doi:10.1134/s002689332303007x · Cited by 2 · see citing works
Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription
Tariq, K., & Farrants, A. Ö. (2021) · Genes · doi:10.3390/genes12070961 · Cited by 3 · see citing works
Molecular Mechanisms of RNA Polymerase I Transcription in Health and Disease: An Overview
Walker, B. E., Chung, J., Pascual, H. G., Adala, J. D., & Knutson, B. A. (2026) · Molecular and Cellular Biology · doi:10.1080/10985549.2026.2628826 · Cited by 2 · see citing works
Human rDNA Structure, Expression, and Non-Canonical Functions: the Role of Non-Coding Regions
Sadova, A. A., Panteleev, D. Y., & Pavlova, G. V. (2023) · Molecular Biology · doi:10.31857/s0026898423030084 · Cited by 1 · see citing works
Structural characterization of DNA-binding domain of essential mammalian protein TTF 1
Singh, G., Bhopale, A. J., Khatri, S., Prakash, P., Kumar, R., Singh, S. M., & Singh, S. K. (2024) · Bioscience Reports · doi:10.1042/bsr20240800 · Cited by 1 · see citing works
Epigenetic Regulation of Nucleolar Functions
Farrants, A. Ö. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-803395-1.00010-1 · Cited by 1 · see citing works
Transcriptional Control Leading to Clinical Outcomes in Breast Cancer Cases
Aftab, A., Khan, R., Hameed, U., Abbas, T., & Ahmad, B. (2022) · Springer eBooks · doi:10.1007/978-981-19-0197-3_13 · Cited by 1 · see citing works
Yglesias, M. V., & DeRose, V. J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.09.632225 · Cited by 1 · see citing works
Sandhu, K. S. (2010) · Figshare
Birch, J. L., Tan, B. C., Panov, K. I., Panova, T. B., Andersen, J., Owen‐Hughes, T., Russell, J., Lee, S.-C., & Zomerdijk, J. C. B. M. (2009)
Genome-wide identification of nucleosome positioning determinants in schizosaccharomyces pombe
Pointner, J. (2013) · Elektronische Hochschulschriften der LMU München (Ludwig-Maximilians-Universität München) · doi:10.5282/edoc.17714
- Authors
- Németh, A., Guibert, S., Tiwari, V. K., Ohlsson, R., & Längst, G.
- Affiliations
- University of Regensburg (DE)
- Uppsala University (SE)
- Corresponding author
- Längst, Gernot
- Venue
- The EMBO Journal
- Published
- 2008-03-20
- Volume
- 27
- Issue
- 8
- Pages
- 1255-1265
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC2367401
- OpenAlex
- W2045240569
- Cited by
- 94
- References
- 39
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 2 · 2023: 2 · 2022: 5 · 2021: 4 · 2020: 4 · 2019: 5 · 2018: 4 · 2017: 4 · 2016: 7 · 2015: 5 · 2014: 6 · 2013: 9 · 2012: 13
- FWCI
- 3.02
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The EMBO Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- University of Regensburg Publication Server (University of Regensburg) (submittedVersion)
- Research Portal (Queen's University Belfast) (submittedVersion)
- Funders
- Deutsche Forschungsgemeinschaft
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- TATA-binding protein, ribosomal DNA, rDNA transcription, epigenetic regulation, chromatin domains, DNA methylation, enhancers, chromatin organization, 3D genome organization, mice
- MeSH terms
- Animals, Binding, Competitive, Cricetulus, DNA-Binding Proteins, Cricetinae, Promoter Regions, Genetic, Protein Binding, Terminator Regions, Genetic, Transcription Factors, Transcription, Genetic, CHO Cells, Genes, rRNA, NIH 3T3 Cells, Epigenesis, Genetic, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review