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Research: Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants
- Ya-Ru Li and
- Ming-Jung Liu
Genome Res. October 2020 30: 1418-1433; Published in Advance September 24, 2020, doi:10.1101/gr.261834.120
.... (B) The median translation initiation efficiency (TE) of TISs at AUG and individual near-cognate codons identified in tomato (orange) and humans (blue) (Methods). (C) The correlation between TIS codon enrichment and tRNA abundance in tomato. (r) Pearson correlation coefficient.We also found...
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Research: A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization
- Amit Blumberg,
- Charles G. Danko,
- Anshul Kundaje,
- and Dan Mishmar
Genome Res. August 2018 28: 1158-1168; Published in Advance July 12, 2018, doi:10.1101/gr.230409.117
...mRNAs encoding protein subunits of the OXPHOS, 14 tRNAs, and two ribosomal RNA genes are encoded by the heavy strand; the mtDNA light strand encodes for a single mRNA (the ND6 subunit of OXPHOS complex I) and eight tRNA molecules. The polycistronic transcripts of both strands are cleaved, in turn...
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Research: Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)
- Sünje J. Pamp,
- Eoghan D. Harrington,
- Stephen R. Quake,
- David A. Relman,
- and Paul C. Blainey
Genome Res. June 2012 22: 1107-1119; Published in Advance March 20, 2012, doi:10.1101/gr.131482.111
...clostridia (Supplemental Fig. S4); and (5) number of tRNAs compared with other clostridia (Supplemental Material; Supplemental Fig. S3).We recovered 98.7% of the sequence using the five SFB filaments, when compared with the of SFB-mouse-Yit (1.586 Mb) (Prakash et al. 2011). ThemeanGC content was 27...
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LETTER: Draft Sequencing and Comparative Genomics of Xylella fastidiosa Strains Reveal Novel Biological Insights
- Anamitra Bhattacharyya,
- Stephanie Stilwagen,
- Gary Reznik,
- Helene Feil,
- William S. Feil,
- Iain Anderson,
- Axel Bernal,
- Mark D'Souza,
- Natalia Ivanova,
- Vinayak Kapatral,
- Niels Larsen,
- Tamara Los,
- Athanasios Lykidis,
- Eugene Selkov, Jr.,
- Theresa L. Walunas,
- Alexander Purcell,
- Rob A. Edwards,
- Trevor Hawkins,
- Robert Haselkorn,
- Ross Overbeek,
- Nikos C. Kyrpides,
- and Paul F. Predki
Genome Res. October 1, 2002 12: 1556-1563; Published in Advance September 13, 2002, doi:10.1101/gr.370702
...Potential Host-Specific Functions During our comparative analysis of the three Xylella s, we noticed that the XFA contains two tRNA genes (encoding glycine and threonine, at 1,638,644 and 1,707,587 bp) that flank a region marked by the presence of prophage genes absent from the XFX and XFY s. This region...
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LETTER: Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens
- Garry S.A. Myers,
- David A. Rasko,
- Jackie K. Cheung,
- Jacques Ravel,
- Rekha Seshadri,
- Robert T. DeBoy,
- Qinghu Ren,
- John Varga,
- Milena M. Awad,
- Lauren M. Brinkac,
- Sean C. Daugherty,
- Daniel H. Haft,
- Robert J. Dodson,
- Ramana Madupu,
- William C. Nelson,
- M.J. Rosovitz,
- Steven A. Sullivan,
- Hoda Khouri,
- George I. Dimitrov,
- Kisha L. Watkins,
- Stephanie Mulligan,
- Jonathan Benton,
- Diana Radune,
- Derek J. Fisher,
- Helen S. Atkins,
- Tom Hiscox,
- B. Helen Jost,
- Stephen J. Billington,
- J. Glenn Songer,
- Bruce A. McClane,
- Richard W. Titball,
- Julian I. Rood,
- Stephen B. Melville,
- and Ian T. Paulsen
Genome Res. August 2006 16: 1031-1040; Published in Advance July 6, 2006, doi:10.1101/gr.5238106
...structures. Strain 13 possesses one large capsular cluster, encoding 49 genes. This cluster is flanked on the 3′ end by a tRNA (tRNA–Met-7), suggesting that it may have been acquired and inserted into this genomic location, as is typical of pathogenicity islands ( Morschhauser et al. 2000 ). Within...
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Methods: Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
- Gemma C. Langridge,
- Minh-Duy Phan,
- Daniel J. Turner,
- Timothy T. Perkins,
- Leopold Parts,
- Jana Haase,
- Ian Charles,
- Duncan J. Maskell,
- Sarah E. Peters,
- Gordon Dougan,
- John Wain,
- Julian Parkhill,
- and A. Keith Turner
Genome Res. December 2009 19: 2308-2316; Published in Advance October 13, 2009, doi:10.1101/gr.097097.109
...; circle 8, %(G + C) content. Simultaneous assay of every S. Typhi gene Genome Research 2311 www..org and energy metabolism genes in particular. This is unsurprising as these classes include the genes encoding essential proteins, such as ribosomal subunits, RNA/DNA polymerases, and tRNA synthetases. After...
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LETTER: Protein Coding Palindromes Are a Unique but Recurrent Feature in Rickettsia
- Hiroyuki Ogata,
- Stéphane Audic,
- Chantal Abergel,
- Pierre-Edouard Fournier,
- and Jean-Michel Claverie
Genome Res. May 1, 2002 12: 808-816; Published in Advance April 12, 2002, doi:10.1101/gr.227602
...to bacteriophage attachment site ( att ) ( Kirby et al. 1994 ). The homologous sites of the other tmRNA genes and tRNA genes have been known to harbor bacteriophages, retron phages, and pathogenicity islands in other bacteria ( Billington et al. 1999 ; Haring et al. 1995 ; Inouye et al. 1991 ; Julio et al. 2000...
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LETTER: Comparing Genomes within the Species Mycobacterium tuberculosis
- Midori Kato-Maeda,
- Jeanne T. Rhee,
- Thomas R. Gingeras,
- Hugh Salamon,
- Jorg Drenkow,
- Nat Smittipat,
- and Peter M. Small
Genome Res. April 1, 2001 11: 547-554; doi:10.1101/gr166401
...) were targeted to every ORF and intergenic region, and in total, the chip contained 118,180 probe pairs. Seventeen probe pairs were excluded from analysis because they failed to hybridize reliably with genomic DNA from H37Rv. In addition, hybridization was not expected to be informative from rRNA, and tRNA...
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LETTER: Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea
- Odile Lecompte,
- Raymond Ripp,
- Valérie Puzos-Barbe,
- Simone Duprat,
- Roland Heilig,
- Jacques Dietrich,
- Jean-Claude Thierry,
- and Olivier Poch
Genome Res. June 1, 2001 11: 981-993; Published in Advance May 8, 2001, doi:10.1101/gr.165301
...and the Euryarchaea. In Eubacteria, some tRNA genes can constitute the integration site of plasmids and phages ( Reiter et al. 1989 ; Dupont et al. 1995 ) and may also be the target site of recombination of pathogenicity islands ( Hou 1999 ). Thus, the involvement of tRNA genes in site-specific recombination appears...
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LETTER: Distribution of Hammerhead and Hammerhead-like RNA Motifs Through the GenBank
- Gerardo Ferbeyre,
- Véronique Bourdeau,
- Marie Pageau,
- Pedro Miramontes,
- and Robert Cedergren
Genome Res. July 1, 2000 10: 1011-1019; doi:10.1101/gr.10.7.1011
...of a virusoid and a structural model for the active sites. Cell 49 : 211 – 220 . ↵ Gautheret D. , Major F. , Cedergren R. ( 1990 ) Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA. Comput. Appl. Biosci. 6 : 325 – 331 . ↵ Hertel K.J. , Pardi A. , Uhlenbeck O...

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