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ARTICLE: Phylogenetic Analysis of Ribonuclease H Domains Suggests a Late, Chimeric Origin of LTR Retrotransposable Elements and Retroviruses
- Harmit S. Malik and
- Thomas H. Eickbush
Genome Res. July 1, 2001 11: 1187-1197; doi:10.1101/gr.185101
...transcription ( Crouch and Toulme 1998 ). There appear to be three broadly distributed lineages of RNH enzymes: RNase HI ( rnhA gene), HII ( rnhB ), and HIII ( rnhC ; Ohtani et al. 1999 ). Common evolutionary ancestry has been firmly established for rnhB and rnhC , whereas rnhA may represent a case...
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LETTER: Divergence of Spatial Gene Expression Profiles Following Species-Specific Gene Duplications in Human and Mouse
- Lukasz Huminiecki and
- Kenneth H. Wolfe
Genome Res. October 2004 14: 1870-1879; doi:10.1101/gr.2705204
...-derived neurotoxin), RNASE3 (eosinophil cationic protein; Hamann et al. 1990 ), and ECRP (GenBank X55989). Multiple mouse-specific duplications produced at least six genes ( Ear-1, Ear-2 , and mR-3 through mR-6 ; Batten et al. 1997 ). Zhang and co-workers have previously shown that the eosinophil...
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LETTER: Species-Specific Class I Gene Expansions Formed the Telomeric 1 Mb of the Mouse Major Histocompatibility Complex
- Toyoyuki Takada,
- Attila Kumánovics,
- Claire Amadou,
- Masayasu Yoshino,
- Elsy P. Jones,
- Maria Athanasiou,
- Glen A. Evans,
- and Kirsten Fischer Lindahl
Genome Res. April 1, 2003 13: 589-600; doi:10.1101/gr.975303
...by hybridization ( Johnson et al. 1992 ). We found a homolog of the human RPP21 subunit of the RNase P holoenzyme in this region, next to Trim39 (or Rnf23 ; Jarrous et al. 2001 ). View this table: In this window In a new window Table 1. Genes and Pseudogenes in the Mouse Telomeric Class I Region The H2-M region...
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LETTER: Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic Approach
- Eugene V. Koonin,
- Yuri I. Wolf,
- and L. Aravind
Genome Res. February 1, 2001 11: 240-252; doi:10.1101/gr.162001
...reported in eukaryotes. In a pattern of apparent gene loss complementary to that seen in Methanococcus and Halobacterium, Thermoplasma acidophilum lacks the RNase P subunits. Unexpectedly, the identified exosomal superoperon, in addition to the predicted exosome components, encodes the catalytic...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
.... 3B).View larger version: In this window In a new window Figure 3. Distribution of DNA methylation in Spirodela chromosomes and TEs. (A) Circos plot (Krzywinski et al. 2009) of -wide distribution of DNA methylation densities by chromosome in Spirodela. From outside to inside: gene density; TE density...
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ARTICLE: Structural Characterization of the Human Proteome
- Arne Müller,
- Robert M. MacCallum,
- and Michael J.E. Sternberg
Genome Res. November 1, 2002 12: 1625-1641; doi:10.1101/gr.221202
...branch-specific superfamilies. These functions are defense (e.g., immunity), transcriptional regulation, and hormone-related signaling. Gene Duplication The presence of multiple copies of any particular SCOP domains within the proteome is the result of domain duplication and divergence during evolution...
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ARTICLE: The Complete Genome and Proteome of Mycoplasma mobile
- Jacob D. Jaffe,
- Nicole Stange-Thomann,
- Cherylyn Smith,
- David DeCaprio,
- Sheila Fisher,
- Jonathan Butler,
- Sarah Calvo,
- Tim Elkins,
- Michael G. FitzGerald,
- Nabil Hafez,
- Chinnappa D. Kodira,
- John Major,
- Shunguang Wang,
- Jane Wilkinson,
- Robert Nicol,
- Chad Nusbaum,
- Bruce Birren,
- Howard C. Berg,
- and George M. Church
Genome Res. August 2004 14: 1447-1461; doi:10.1101/gr.2674004
...not detected. One copy of RNAse H II was not detected, but a second copy was, thus its functionality is clearly present. As well, M. mobile 's copy of ribosomal protein L36 ( rpmJ ) was not detected, but this particular gene has a suspicious phylogeny despite its conserved gene order with M. pulmonis and M...
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LETTER: Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions
- Tobias Doerks,
- Richard R. Copley,
- Jörg Schultz,
- Chris P. Ponting,
- and Peer Bork
Genome Res. January 1, 2002 12: 47-56; doi:10.1101/gr.203201
...-specific endoribonuclease activity ( Sidrauski and Walter 1997 ). This activity is consistent with the C-terminal location for RNase activity found in its homolog, 2‘-5′ oligo (A)-dependent ribonuclease ( Bork and Sander 1993 ). Consequently, we tentatively suggest the presence of divergent PUG domains in the C termini...
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LETTER: Reconstructing large regions of an ancestral mammalian genome in silico
- Mathieu Blanchette,
- Eric D. Green,
- Webb Miller,
- and David Haussler
Genome Res. December 2004 14: 2412-2423; doi:10.1101/gr.2800104
...a model of molecular evolution. On a smaller scale, such ancestral reconstructions have been performed for protein families including rhodopsin ( Chang et al. 2002 ), ultraviolet vision gene SWS1 ( Shi and Yokoyama 2003 ), ribonucleases ( Jermann et al. 1995 ; Zhang and Rosenberg 2002 ), Tu elongation...

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