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LETTER: Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- Deyou Zheng,
- Adam Frankish,
- Robert Baertsch,
- Philipp Kapranov,
- Alexandre Reymond,
- Siew Woh Choo,
- Yontao Lu,
- France Denoeud,
- Stylianos E. Antonarakis,
- Michael Snyder,
- Yijun Ruan,
- Chia-Lin Wei,
- Thomas R. Gingeras,
- Roderic Guigó,
- Jennifer Harrow,
- and Mark B. Gerstein
Genome Res. June 2007 17: 839-851; doi:10.1101/gr.5586307
..., pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome’s structure and function. However, no consensus...
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Research: Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
- David E. Symer,
- Keiko Akagi,
- Heather M. Geiger,
- Yang Song,
- Gaiyun Li,
- Anne-Katrin Emde,
- Weihong Xiao,
- Bo Jiang,
- André Corvelo,
- Nora C. Toussaint,
- Jingfeng Li,
- Amit Agrawal,
- Enver Ozer,
- Adel K. El-Naggar,
- Zoe Du,
- Jitesh B. Shewale,
- Birgit Stache-Crain,
- Mark Zucker,
- Nicolas Robine,
- Kevin R. Coombes,
- and Maura L. Gillison
Genome Res. January 2022 32: 55-70; Published in Advance December 13, 2021, doi:10.1101/gr.275911.121
...kb of integrants. Across 95% of tumors with integration, host gene transcription is disrupted via intragenic integrants, chimeric transcription, outlier expression, gene breaking, and/or de novo expression of noncoding or imprinted genes. We conclude that virus integration can contribute...
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Research: Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
- Jingfeng Li,
- Keiko Akagi,
- Yongjun Hu,
- Anna L. Trivett,
- Christopher J.W. Hlynialuk,
- Deborah A. Swing,
- Natalia Volfovsky,
- Tamara C. Morgan,
- Yelena Golubeva,
- Robert M. Stephens,
- David E. Smith,
- and David E. Symer
Genome Res. May 2012 22: 870-884; Published in Advance February 23, 2012, doi:10.1101/gr.130740.111
...mapped thousands of endogenous retrovirus (ERV) germline integrants in highly divergent, previously unsequenced mouse lineages, facilitating a comparison of gene expression in the presence or absence of local insertions. Polymorphic ERVs occur relatively infrequently in gene introns and are particularly...
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Research: Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability
- Keiko Akagi,
- Jingfeng Li,
- Tatevik R. Broutian,
- Hesed Padilla-Nash,
- Weihong Xiao,
- Bo Jiang,
- James W. Rocco,
- Theodoros N. Teknos,
- Bhavna Kumar,
- Danny Wangsa,
- Dandan He,
- Thomas Ried,
- David E. Symer,
- and Maura L. Gillison
Genome Res. February 2014 24: 185-199; Published in Advance November 7, 2013, doi:10.1101/gr.164806.113
...(Narlik-Grassow et al. 2013) in UPCI:SCC090 cells, resulting fromHPV-associated looped structures.We also found ‘‘gene breaking’’ (Wheelan et al. 2005) by an HPV integrant in SLC47A2, a solute carrier, in UM-SCC-104 cells, caused by premature termination of transcripts at theHPV E5 polyadenylation site...
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PERSPECTIVE: Raising the estimate of functional human sequences
- Michael Pheasant and
- John S. Mattick
Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
...to underestimation of the neutral rate of evolution. Finally, we show that experimentally validated gene regulatory sequences and functional noncoding RNAs are evolving at quite variable rates, often relatively quickly compared to sequences encoding proteins, presumably reflecting different structure...
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Letter: Mobile elements create structural variation: Analysis of a complete human genome
- Jinchuan Xing,
- Yuhua Zhang,
- Kyudong Han,
- Abdel Halim Salem,
- Shurjo K. Sen,
- Chad D. Huff,
- Qiong Zhou,
- Ewen F. Kirkness,
- Samuel Levy,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. September 2009 19: 1516-1526; Published in Advance May 13, 2009, doi:10.1101/gr.091827.109
...insertions occurred in exons of three human genes. Based on the number of insertions and the estimated time to the most recent common ancestor of HuRef and the HGP reference genome, we estimated the Alu , L1, and SVA retrotransposition rates to be one in 21 births, 212 births, and 916 births, respectively...
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LETTER: Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
- Keiko Akagi,
- Jingfeng Li,
- Robert M. Stephens,
- Natalia Volfovsky,
- and David E. Symer
Genome Res. June 2008 18: 869-880; Published in Advance April 1, 2008, doi:10.1101/gr.075770.107
...from the C57BL/6J reference. Approximately 85% of such variants are due to recent mobilization of endogenous retrotransposons, predominantly L1 elements, greatly exceeding that reported in humans. Many genes’ structures and expression are altered directly by polymorphic L1 retrotransposons, including...
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REVIEW: Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
- Victoria P. Belancio,
- Dale J. Hedges,
- and Prescott Deininger
Genome Res. March 2008 18: 343-358; Published in Advance February 6, 2008, doi:10.1101/gr.5558208
...al. 2007 ), overturning the long-held perception that these elements were completely extinguished during early mammalian evolution. The diverse composition and activity of TEs both across and within taxa manifests itself in their differential contribution to mutagenesis and disease. The fraction...
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