Cited by 177Genomics and Chromatin DynamicsNuclear Structure and FunctionChromosomal and Genetic Variations

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Integrative genomic analysis of human ribosomal DNA

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Zentner, Gabriel E., Saiakhova, Alina, Manaenkov, Pavel, Adams, Mark D., Scacheri, Peter C.·2011·Nucleic Acids Research

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Abstract

The transcription of ribosomal RNA (rRNA) is critical to life. Despite its importance, ribosomal DNA (rDNA) is not included in current genome assemblies and, consequently, genomic analyses to date have excluded rDNA. Here, we show that short sequence reads can be aligned to a genome assembly containing a single rDNA repeat. Integrated analysis of ChIP-seq, DNase-seq, MNase-seq and RNA-seq data reveals several novel findings. First, the coding region of active rDNA is contained within nucleosome-depleted open chromatin that is highly transcriptionally active. Second, histone modifications are located not only at the rDNA promoter but also at novel sites within the intergenic spacer. Third, the distributions of active modifications are more similar within and between different cell types than repressive modifications. Fourth, UBF, a positive regulator of rRNA transcription, binds to sites throughout the genome. Lastly, the insulator binding protein CTCF associates with the spacer promoter of rDNA, suggesting that transcriptional insulation plays a role in regulating the transcription of rRNA. Taken together, these analyses confirm and expand the results of previous ChIP studies of rDNA and provide novel avenues for exploration of chromatin-mediated regulation of rDNA.

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Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Summaries of Affymetrix GeneChip probe level data
Irizarry, R. A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gng015 · Cited by 4,837
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 2×
“This scenario is reminiscent of that in the nucleoplasm, where marks associated with promoters tend to be invariant between cell types while marks associated with enhancers display cell-type specificity (34).”
Background
Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
Chen, X., Han, X., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.04.043 · Cited by 2,547
Widespread transcription at neuronal activity-regulated enhancers
Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450
ChIP–seq: advantages and challenges of a maturing technology
Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217
CTCF: Master Weaver of the Genome
Phillips‐Cremins, J. E., & Corces, V. G. (2009) · Cell · doi:10.1016/j.cell.2009.06.001 · Cited by 1,585
Dynamic Regulation of Nucleosome Positioning in the Human Genome
Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,473

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Additional file 12 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702674
Additional file 4 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702650
Additional file 1 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25556497
Additional file 2 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25556658
Additional file 13 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702677
Additional file 14 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702680
Additional file 7 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702659
Additional file 10 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702668
Additional file 3 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702647
Additional file 5 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702653
Additional file 9 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702665
Additional file 6 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702656
Additional file 8 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702662
Additional file 11 of HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells
Liao, M., Cao, J., Chen, W., Wang, M., Jin, Z., Ye, J., Ren, Y., Wei, Y., Xue, Y., Chen, D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26702671
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Ribosomal RNA transcription in normal and leukemic hematopoiesis
Henrich, J. A., Sams, E. I., & Paralkar, V. R. (2026) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2026.06.008

Authors: Zentner, G. E., Saiakhova, A., Manaenkov, P., Adams, M. D., & Scacheri, P. C.
Affiliations: Case Comprehensive Cancer Center (US)
Corresponding author: Scacheri, Peter C.
ORCID: Zentner, Gabriel E.
Adams, Mark D.
Scacheri, Peter C.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2011-02-25
Volume: 39
Issue: 12
Pages: 4949-4960
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkq1326
PMC: PMC3130253
OpenAlex: W2114591008
Cited by: 165
References: 53
Citations by year: 2026: 6 · 2025: 3 · 2024: 15 · 2023: 9 · 2022: 11 · 2021: 11 · 2020: 10 · 2019: 18 · 2018: 11 · 2017: 10 · 2016: 13 · 2015: 12 · 2014: 14 · 2013: 16 · 2012: 4
FWCI: 4.67
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/2.5 (vor, 2082 d)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
Funders: National Human Genome Research Institute (R01HG004722)
National Institute of General Medical Sciences (T32GM008613)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD056369)
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 › Genetics › Chromosomal and Genetic Variations
Keywords: ribosomal DNA, rRNA transcription, histone modifications, intergenic spacer, UBF, CTCF, chromatin regulation, rDNA promoter, cell type variation
MeSH terms: CCCTC-Binding Factor, Chromatin, DNA, Ribosomal, Histones, Humans, Nucleosomes, Promoter Regions, Genetic, Repressor Proteins, RNA Polymerase I, RNA, Ribosomal, Transcription, Genetic, Genome, Human, Sequence Alignment, Sequence Analysis, DNA, K562 Cells, Genomics, Pol1 Transcription Initiation Complex Proteins, Chromatin Immunoprecipitation, HEK293 Cells, High-Throughput Nucleotide Sequencing

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Integrative genomic analysis of human ribosomal DNA

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