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Research: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
- Wenli Xu,
- Chang Liu,
- Bing Deng,
- Penghui Lin,
- Zhenghua Sun,
- Anrui Liu,
- Jiajia Xuan,
- Yuying Li,
- Keren Zhou,
- Xiaoqin Zhang,
- Qiaojuan Huang,
- Hui Zhou,
- Qingyu He,
- Bin Li,
- Lianghu Qu,
- and Jianhua Yang
Genome Res. May 24, 2022 ; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
...to explore the possibility that lncRNAencoded peptides might constitute part of the TP53 network. For this purpose, we combined CRISPR-Cas9 technology with the DNA-damage responsive system to investigate the expression of TP53-regulated lncRNAs, following by ribosome profiles and mass spectrometry (MS...
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Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
- Isabel X. Wang,
- Christopher Grunseich,
- Youree G. Chung,
- Hojoong Kwak,
- Girish Ramrattan,
- Zhengwei Zhu,
- and Vivian G. Cheung
Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
...the control of a GAL1 promoter and induced their expression in yeast tup1 knockout strain. By Western blot, we showed that the protein level of the RNA form (V459) of Tup1 is higher than that of the DNA form (A459), Table 1. Examples of RDDs in genes that play a role in ribosome biogenesis RDD levels (%) Gene...
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LETTER: Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae
- Michaël Bekaert,
- Hugues Richard,
- Bernard Prum,
- and Jean-Pierre Rousset
Genome Res. October 2005 15: 1411-1420; doi:10.1101/gr.4258005
...of putative programmed -1 ribosomal frameshift signals in large DNA databases. Genome Res. 9 : 417 -427. ↵ Harrison, P., Kumar, A., Lan, N., Echols, N., Snyder, M., and Gerstein, M. 2002 . A small reservoir of disabled ORFs in the yeast and its implications for the dynamics of proteome evolution. J. Mol. Biol...
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LETTER: Identification of Mammalian microRNA Host Genes and Transcription Units
- Antony Rodriguez,
- Sam Griffiths-Jones,
- Jennifer L. Ashurst,
- and Allan Bradley
Genome Res. October 2004 14: 1902-1910; Published in Advance September 13, 2004, doi:10.1101/gr.2722704
.... Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res. 13 : 1301 -1306. ↵ Okazaki, Y.M., Furuno, T., Kasukawa, J., Adachi, H., Bono, S., Kondo, I., Nikaido, N., Osato, R., Saito, H., Suzuki, I. et al. 2002 . Analysis of the mouse transcriptome based on functional...
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LETTER: Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs
- Hanhui Kuang,
- Chellappan Padmanabhan,
- Feng Li,
- Ayako Kamei,
- Pudota B. Bhaskar,
- Shu Ouyang,
- Jiming Jiang,
- C. Robin Buell,
- and Barbara Baker
Genome Res. January 2009 19: 42-56; Published in Advance November 26, 2008, doi:10.1101/gr.078196.108
...genomic DNA (NCBI Nicotiana tabacum gss) databases and extrapolated the number of hits retrieved to estimate -wide copy numbers as described in Supplemental Table S1.2. An extended data set of N. tabacum MiS1 , MiS5 , and MiS17 sequences is provided in Supplemental Data S1.2. Several MiS families from...
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LETTER: Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22
- Paul M. Harrison,
- Hedi Hegyi,
- Suganthi Balasubramanian,
- Nicholas M. Luscombe,
- Paul Bertone,
- Nathaniel Echols,
- Ted Johnson,
- and Mark Gerstein
Genome Res. February 1, 2002 12: 272-280; doi:10.1101/gr.207102
...DNA using the FASTA program ( Pearson et al. 1997 ), expanded on either side by the length of the matching sequence (in nucleotides). From these alignments, we picked any matching sequences that had more than one disablement (either a frameshift or a premature stop codon) as a potential pseudogene...
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REPORT: Identification of Human Epidermal Differentiation Complex (EDC)-Encoded Genes by Subtractive Hybridization of Entire YACs to a Gridded Keratinocyte cDNA Library
- Ingo Marenholz,
- Maja Zirra,
- David F. Fischer,
- Claude Backendorf,
- Andreas Ziegler,
- and Dietmar Mischke
Genome Res. March 1, 2001 11: 341-355; doi:10.1101/gr.114801
...(i.e., detection of multiple restriction fragments of several YACs) or gave no signal at all. Therefore, all clones containing repetitive elements were excluded from further analyses. A second source of non-specific hybridization were cDNA clones containing ribosomal DNA that were detected by YAC 986...
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ARTICLES: Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1.
- T M Smith,
- M K Lee,
- C I Szabo,
- N Jerome,
- M McEuen,
- M Taylor,
- L Hood,
- and M C King
Genome Res. November 1996 6: 1029-1049; doi:10.1101/gr.6.11.1029
...of metaphase chromosome bands. Cell 53 : 391 – 400 . Kunkel, T. 1986 . Frameshift mutagenesis by eucaryotic DNA polymerases in vitro. J. Biol. Chem. 261 : 13581 – 13587 . La Mantia, G., Pengue, G. Maglione, D. Pannuti, A. Pascucci, A. and Lania. L. 1989 . Identification of new human repetitive sequences...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
..., multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
...raw signal to DNA reference, UNCALLED has a lighter computational footprint than DTW (Kovaka et al. 2021). Still, it requires abundant computational resources. The newly designed Readfish toolkit eliminates the need for complex signal mapping algorithms and exploits existing ONT tools to provide...

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