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Research: Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer
- Marcos R.H. Estécio,
- Juan Gallegos,
- Céline Vallot,
- Ryan J. Castoro,
- Woonbok Chung,
- Shinji Maegawa,
- Yasuhiro Oki,
- Yutaka Kondo,
- Jaroslav Jelinek,
- Lanlan Shen,
- Helge Hartung,
- Peter D. Aplan,
- Bogdan A. Czerniak,
- Shoudan Liang,
- and Jean-Pierre J. Issa
Genome Res. October 2010 20: 1369-1382; Published in Advance August 17, 2010, doi:10.1101/gr.107318.110
...on retrotransposon frequency appear to be correlated but also complementary. In summary, our data indicate that retrotransposon elements, which are widespread in our genome, are strongly associated with gene promoter DNA methylation in cancer and may in fact play a role in influencing epigenetic regulation in normal...
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Chicken Special/Resources: Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
- Ivan Ovcharenko,
- Gabriela G. Loots,
- Belinda M. Giardine,
- Minmei Hou,
- Jian Ma,
- Ross C. Hardison,
- Lisa Stubbs,
- and Webb Miller
Genome Res. January 2005 15: 184-194; Published in Advance December 8, 2004, doi:10.1101/gr.3007205
...5 Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA Abstract Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements...
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ARTICLE: Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless
- Edwin J. Ostrin,
- Yumei Li,
- Kristi Hoffman,
- Jing Liu,
- Keqing Wang,
- Li Zhang,
- Graeme Mardon,
- and Rui Chen
Genome Res. April 2006 16: 466-476; Published in Advance March 13, 2006, doi:10.1101/gr.4673006
...proteins that function in multiple complexes, these genes form a genetic network that controls the specification and determination stages of retinal development ( Akimaru et al. 1997 ; Pignoni et al. 1997 ). At the top of this network are the two Pax6 homologs in Drosophila, toy and ey (Fig. 1A ). View...
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LETTER: Genome Duplication, a Trait Shared by 22,000 Species of Ray-Finned Fish
- John S. Taylor,
- Ingo Braasch,
- Tancred Frickey,
- Axel Meyer,
- and Yves Van de Peer
Genome Res. March 1, 2003 13: 382-390; doi:10.1101/gr.640303
...( National Biomedical Research Foundation , Washington D.C. ) 5, Suppl. 3 : 345 – 358 . ↵ Dulai K.S. , von Dornum M. , Mollon J.D. , Hunt D.M. ( 1999 ) The evolution of trichromatic colour vision by opsin gene duplication in New World and Old World primates. Genome Res. 9 : 629 – 638 . ↵ Elgar G. , Clark M...
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Research: Noncoding origins of anthropoid traits and a new null model of transposon functionalization
- Ricardo C.H. del Rosario,
- Nirmala Arul Rayan,
- and Shyam Prabhakar
Genome Res. September 2014 24: 1469-1484; Published in Advance July 20, 2014, doi:10.1101/gr.168963.113
...of studies that focus on transcribed genes (Enard et al. 2002;Varki et al. 2008; Tay et al. 2009; Pierron et al. 2012), very little is known about the DNA sequences that drove the emergence of anthropoid primates. The contribution of transposable elements (TEs) to species evolution is a topic of intense...
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Research: Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
- Chan-Shuo Wu,
- Chun-Ying Yu,
- Ching-Yu Chuang,
- Michael Hsiao,
- Cheng-Fu Kao,
- Hung-Chih Kuo,
- and Trees-Juen Chuang
Genome Res. January 2014 24: 25-36; Published in Advance October 16, 2013, doi:10.1101/gr.159483.113
...). Microarray-based global gene expression profiling further revealed that the expression levels of pluripotent genes, such as NANOG, POU5F1, SOX2, and TCF7L1, were significantly decreased in tsRMST knockdown hESCs, whereas key lineage-specific transcription factors, such as GATA6 (endoderm) and PAX6...
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LETTER: Generation and Analysis of 25 Mb of Genomic DNA from the Pufferfish Fugu rubripes by Sequence Scanning
- Greg Elgar,
- Melody S. Clark,
- Stephen Meek,
- Sarah Smith,
- Sarah Warner,
- Yvonne J.K. Edwards,
- Nassima Bouchireb,
- Amanda Cottage,
- Giles S.H. Yeo,
- Yagnesh Umrania,
- Gary Williams,
- and Sydney Brenner
Genome Res. October 1, 1999 9: 960-971; doi:10.1101/gr.9.10.960
...eliminated to prevent these repeats from forming families in subsequent gene clustering analysis. Identification and Characterization of Minisatellites in the Fugu Genome The aim was to identify the other two broad classes of repetitive elements (that is, the minisatellites and transposable elements...
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Research: Age-related epigenetic drift in the pathogenesis of MDS and AML
- Shinji Maegawa,
- Sheryl M. Gough,
- Naoko Watanabe-Okochi,
- Yue Lu,
- Nianxiang Zhang,
- Ryan J. Castoro,
- Marcos R.H. Estecio,
- Jaroslav Jelinek,
- Shoudan Liang,
- Toshio Kitamura,
- Peter D. Aplan,
- and Jean-Pierre J. Issa
Genome Res. April 2014 24: 580-591; Published in Advance January 10, 2014, doi:10.1101/gr.157529.113
...relevant genes such as Gata5, Pax6, Sfrp1, and Sox9 (Toyota et al. 1999; Suzuki et al. 2002; Akiyama et al. 2003; The Cancer Genome Atlas Network 2012). The names of the genes are shown in Supplemental Table S4. Functional pathways affected We examined the potential function of genes that showed common...
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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
...). Innovation and rapid evolution is also evident in thousands of gene regulatory sequences, which cover extended genomic regions and exhibit rapid turnover ( Smith et al. 2004 ; Fisher et al. 2006 ; Frith et al. 2006 ; Taylor et al. 2006 ). This includes the remarkable functional conservation of regulatory...
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Methods: A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles
- Li-Wei Chang,
- Rakesh Nagarajan,
- Jeffrey A. Magee,
- Jeffrey Milbrandt,
- and Gary D. Stormo
Genome Res. March 2006 16: 405-413; Published in Advance January 31, 2006, doi:10.1101/gr.4303406
...according to the user's input. Promoters were acquired and repetitive elements in the promoters were masked. Promoters of orthologous genes were aligned and transcription factor (TF) binding sites were identified and mapped. Probability scores of each promoter and each transcription factor were calculated...

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