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Research: The human ribosomal DNA array is composed of highly homogenized tandem clusters
- Yutaro Hori,
- Akira Shimamoto,
- and Takehiko Kobayashi
Genome Res. November 2021 31: 1971-1982; Published in Advance August 18, 2021, doi:10.1101/gr.275838.121
...abundant repetitive gene region in eukaryotic cells. In the budding yeast Saccharomyces cerevisiae, the structure and function of rDNA have been well studied, establishing rDNA as a unique region in the . Each unit (9.2 kb) of rDNA includes two coding regions, 35S precursor ribosomal RNA (rRNA) and 5S rRNA...
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LETTER: Genomic architecture and inheritance of human ribosomal RNA gene clusters
- Dawn M. Stults,
- Michael W. Killen,
- Heather H. Pierce,
- and Andrew J. Pierce
Genome Res. January 2008 18: 13-18; Published in Advance November 19, 2007, doi:10.1101/gr.6858507
...of an inverted chromosome 22 results in a recombinant chromosome with duplication of the distal long arm . Am. J. Med. Genet. A 138 : 355 – 360 . ↵ Caburet, S. , Conti, C. , Schurra, C. , Lebofsky, R. , Edelstein, S.J. , Bensimon, A. ( 2005 ) Human ribosomal RNA gene arrays display a broad range of palindromic...
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Letter: Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing
- Stephen A. James,
- Michael J.T. O'Kelly,
- David M. Carter,
- Robert P. Davey,
- Alexander van Oudenaarden,
- and Ian N. Roberts
Genome Res. April 2009 19: 626-635; Published in Advance January 13, 2009, doi:10.1101/gr.084517.108
.... cerevisiae , each repeat comprises of four ribosomal RNA (rRNA) genes, the large subunit (LSU) (also referred to as the 26S rRNA), small subunit (SSU) (also referred to as the 18S rRNA), 5.8S and 5S rRNA genes, as well as two internal transcribed spacers (ITS1 and ITS2), two external transcribed spacers (ETS...
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LETTER: Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data
- Austen R.D. Ganley and
- Takehiko Kobayashi
Genome Res. February 2007 17: 184-191; Published in Advance January 2, 2007, doi:10.1101/gr.5457707
.... , Edelstein, S.J. , Bensimon, A. ( 2005 ) Human ribosomal RNA gene arrays display a broad range of palindromic structures . Genome Res. 15 : 1079 – 1085 . ↵ Carbone, I. , Kohn, L.M. ( 2001 ) A microbial population-species interface: Nested cladistic and coalescent inference with multilocus data . Mol. Ecol...
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Research: The shared genomic architecture of human nucleolar organizer regions
- Ioanna Floutsakou,
- Saumya Agrawal,
- Thong T. Nguyen,
- Cathal Seoighe,
- Austen R.D. Ganley,
- and Brian McStay
Genome Res. December 2013 23: 2003-2012; Published in Advance August 29, 2013, doi:10.1101/gr.157941.113
...C, Schurra C, Lebofsky R, Edelstein SJ, Bensimon A Caburet S, Conti C, Schurra C, Lebofsky R, Edelstein SJ, Bensimon A. 2005. Human ribosomal RNA gene arrays display a broad range of palindromic structures. Genome Res 15: 1079–1085. ↵ Derenzini M, Montanaro L, Trere D Derenzini M, Montanaro L, Trere...
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Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
- Alexandra Dallaire,
- Bethan F. Manley,
- Maya Wilkens,
- Iliana Bista,
- Clement Quan,
- Edouard Evangelisti,
- Charles R. Bradshaw,
- Navin B. Ramakrishna,
- Sebastian Schornack,
- Falk Butter,
- Uta Paszkowski,
- and Eric A. Miska
Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
...of genes that produced sRNA had no known protein domain (Class B). sRNA loci derived from nonexpressed TEs were, in general, highly methylated, whereas sRNA loci derived from expressed TEs had lower methylation scores (Fig. 6B). sRNA loci originating from unannotated regions displayed a bimodal...
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Method: Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
- Michael P. McGurk and
- Daniel A. Barbash
Genome Res. May 2018 28: 714-725; Published in Advance March 27, 2018, doi:10.1101/gr.231472.117
...duplications (TSDs) upon insertion. One example is a tandem array of the non-LTR retrotransposon R1 on the X Chromosome in D. melanogaster (Kidd and Glover 1980; Peacock et al. 1981). R1 has the unusual property of only inserting at a specific site in the multicopy ribosomal RNA genes (rDNA). The tandem...
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Research: mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
- Matthieu Legendre,
- Stéphane Audic,
- Olivier Poirot,
- Pascal Hingamp,
- Virginie Seltzer,
- Deborah Byrne,
- Audrey Lartigue,
- Magali Lescot,
- Alain Bernadac,
- Julie Poulain,
- Chantal Abergel,
- and Jean-Michel Claverie
Genome Res. May 2010 20: 664-674; Published in Advance April 1, 2010, doi:10.1101/gr.102582.109
.... It also revealed a new promoter element correlating with late gene expression, which is also prominent in Sputnik, the recently described Mimivirus ‘‘virophage.’’ These results—validated -wide by the hybridization of total RNA extracted from infected Acanthamoeba cells on a tiling array (Agilent...
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Method: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
- Ruben Boers,
- Joachim Boers,
- Bas de Hoon,
- Christel Kockx,
- Zeliha Ozgur,
- Anco Molijn,
- Wilfred van IJcken,
- Joop Laven,
- and Joost Gribnau
Genome Res. January 2018 28: 88-99; Published in Advance December 8, 2017, doi:10.1101/gr.222885.117
...of highly repetitive genes and regions such as ribosomal RNA and DUX clusters. Previous work has shown that ribosomal RNA genes are located, as tandem arrays, on the five acrocentric chromosomes in humans (Caburet et al. 2005). A large subset of these genes are transcriptionally repressed by DNA methylation...
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LETTER: Processed Pseudogenes of Human Endogenous Retroviruses Generated by LINEs: Their Integration, Stability, and Distribution
- Adam Pavlíček,
- Jan Pačes,
- Daniel Elleder,
- and Jiří Hejnar
Genome Res. March 1, 2002 12: 391-399; Published in Advance February 15, 2002, doi:10.1101/gr.216902
...by the LINE machinery is called processed pseudogenes. They were first described as pseudogenes structurally colinear with gene mRNA, lacking promoters, introns, and, in general, without protein-coding capacity due to mutations and frequent stop codons. Their mRNA-derived structure, poly(A) tails at the 3...

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