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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
....u-tokyo.ac.jpAbstractThe structure of the human ribosomal DNA (rDNA) cluster has traditionally been hard to analyze owing to its highly repetitive nature. However, the recent development of long-read sequencing technology, such as Oxford Nanopore sequencing, has enabled us to study the large-scale structure of the . Using...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
...Absolute nucleosome occupancy map for the Saccharomyces cerevisiae Elisa Oberbeckmann1,8, Michael Wolff2,8, Nils Krietenstein1,3, Mark Heron4,5, Jessica L. Ellins6, Andrea Schmid1, Stefan Krebs7, Helmut Blum7, Ulrich Gerland2 and Philipp Korber1 1Molecular Biology Division, Biomedical Center...
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Research: Ribosomal DNA harbors an evolutionarily conserved clock of biological aging
- Meng Wang and
- Bernardo Lemos
Genome Res. March 2019 29: 325-333; Published in Advance February 14, 2019, doi:10.1101/gr.241745.118
...author: blemos@hsph.harvard.eduAbstractThe ribosomal DNA (rDNA) is the most evolutionarily conserved segment of the and gives origin to the nucleolus, an energy intensive nuclear organelle and major hub influencing myriad molecular processes from cellular metabolism to epigenetic states of the . The r...
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Research: Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
- Bo Li,
- Karl A.G. Kremling,
- Penghao Wu,
- Robert Bukowski,
- Maria C. Romay,
- En Xie,
- Edward S. Buckler,
- and Mingsheng Chen
Genome Res. October 2018 28: 1555-1565; Published in Advance August 30, 2018, doi:10.1101/gr.229716.117
...of Biotechnology, Cornell University, Ithaca, New York 14853, USA; 6US Department of Agriculture–Agricultural Research Service (USDA–ARS), Ithaca, New York 14853, USA; 7University of Chinese Academy of Sciences, Beijing, China 100049 Corresponding authors: bol@genetics.ac.cn, mschen@genetics.ac.cnAbstractRibosomal...
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Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
- Konstantin Licht,
- Utkarsh Kapoor,
- Fabian Amman,
- Ernesto Picardi,
- David Martin,
- Prajakta Bajad,
- and Michael F. Jantsch
Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
...mapped reads per replicate and mapped to the mm10 RefSeq . Comparison with poly(A)-mRNA-seq shows an increased intronic coverage (Supplemental Fig. S1). Editing site detection was done using the RDDpred package (Kim et al. 2016). RNA-DNA differences (RDDs) were counted and plotted according to the type...
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Resource: Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
- Pablo Meyer,
- Geoffrey Siwo,
- Danny Zeevi,
- Eilon Sharon,
- Raquel Norel,
- DREAM6 Promoter Prediction Consortium,
- Eran Segal,
- and Gustavo Stolovitzky
Genome Res. November 2013 23: 1928-1937; Published in Advance August 15, 2013, doi:10.1101/gr.157420.113
.... Twenty-one teams submitted results predicting the expression levels of 53 different promoters from yeast ribosomal protein genes. Analysis of participant predictions shows that accurate values for low-expressed andmutated promoters were difficult to obtain, although in the latter case, only when...
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Research: Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes
- Pierre Chymkowitch,
- Aurélie Nguéa P,
- Håvard Aanes,
- Christian J. Koehler,
- Bernd Thiede,
- Susanne Lorenz,
- Leonardo A. Meza-Zepeda,
- Arne Klungland,
- and Jorrit M. Enserink
Genome Res. June 2015 25: 897-906; Published in Advance March 23, 2015, doi:10.1101/gr.185793.114
...in translation, such as tRNA genes and ribosomal protein genes (RPGs). Genome-wide expression analysis showed that Sumo positively regulates their transcription. We also discovered that the Sumo consensus motif at RPG promoters is identical to the DNA binding motif of the transcription factor Rap1. We...
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Research: RNA–DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA
- Dan Bar-Yaacov,
- Gal Avital,
- Liron Levin,
- Allison L. Richards,
- Naomi Hachen,
- Boris Rebolledo Jaramillo,
- Anton Nekrutenko,
- Raz Zarivach,
- and Dan Mishmar
Genome Res. November 2013 23: 1789-1796; Published in Advance August 2, 2013, doi:10.1101/gr.161265.113
...without shearing (TechnionGenomeCenter). A total of 404,509 and 242,395 reads were generated for individual GM14447 and GM14381, respectively. The reads were mapped to the rCRS and analyzed using the MitoBamAnnotator according to the method described above. Ribosome structure visualization Six available...
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Research: Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
- Danny Zeevi,
- Shai Lubliner,
- Maya Lotan-Pompan,
- Eran Hodis,
- Rita Vesterman,
- Adina Weinberger,
- and Eran Segal
Genome Res. December 2014 24: 1991-1999; Published in Advance October 7, 2014, doi:10.1101/gr.179259.114
...Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters Danny Zeevi 1 , 2 , 3 , 4 , Shai Lubliner 1 , 4 , Maya Lotan-Pompan 1 , 2 , Eran Hodis 1 , 2...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...periodicity. (A) Metagene analysis by aligning all RFs mapped to the annotated start codon (AUG) can reveal the position of the P-site within ribosomes for each length of RFs. For Arabidopsis cytosolic and chloroplast RFs, the 13th nucleotide (offset by 12 nt from 5′) is typically the first nucleotide...
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