Searching journal content for articles similar to Versteeg, et al. 13 (9): 1998.

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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
...repeat length of ∼151 bp, among the smallest periodicities reported. Our analysis has revealed that introns are frequently associated with inter-nucleosomal DNA, pointing to an evolutionary constraint favoring introns at the AT-rich nucleosome edge sequences. Using accurate splicing efficiency data from...
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Resource: Improved definition of the mouse transcriptome via targeted RNA sequencing
- Giovanni Bussotti,
- Tommaso Leonardi,
- Michael B. Clark,
- Tim R. Mercer,
- Joanna Crawford,
- Lorenzo Malquori,
- Cedric Notredame,
- Marcel E. Dinger,
- John S. Mattick,
- and Anton J. Enright
Genome Res. May 2016 26: 705-716; doi:10.1101/gr.199760.115
..., and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open...
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LETTER: Characterization of intron loss events in mammals
- Jasmin Coulombe-Huntington and
- Jacek Majewski
Genome Res. January 2007 17: 23-32; Published in Advance November 15, 2006, doi:10.1101/gr.5703406
...intron gain and loss dynamics in mammals. We utilize a gene mapping technique to map annotated reference human genes onto -wide, multispecies sequence alignments, allowing us to investigate the predicted intron-exon boundaries of 152,146 introns within 17,242 autosomal genes. A recent study...
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Research: Gene duplication and neofunctionalization: POLR3G and POLR3GL
- Marianne Renaud,
- Viviane Praz,
- Erwann Vieu,
- Laurence Florens,
- Michael P. Washburn,
- Philippe l'Hôte,
- and Nouria Hernandez
Genome Res. January 2014 24: 37-51; Published in Advance October 9, 2013, doi:10.1101/gr.161570.113
..., strongly suggesting that they arose from duplication. To examinewhether the duplication arose through an RNA- or DNA-based event, we compared the genomic structure of the human POLR3G and POLR3GL genes. Although the intron sequences are not conserved between the two genes, the division of the protein...
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Article: Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
- Timothy E. Reddy,
- Florencia Pauli,
- Rebekka O. Sprouse,
- Norma F. Neff,
- Kimberly M. Newberry,
- Michael J. Garabedian,
- and Richard M. Myers
Genome Res. December 2009 19: 2163-2171; Published in Advance October 2, 2009, doi:10.1101/gr.097022.109
...of GREs in identified high-confidence GR binding sites across the human . (D,E ) Example ChIP-seq data showing GR and Pol II (RNA Pol2) binding at GREs near the NFKBIA and PER1 genes. ChIP-seq data are plotted as the density of 25-bp tags mapping to the region. The density is separated to show reads...
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Resource: Massively parallel sequencing of the polyadenylated transcriptome of C. elegans
- LaDeana W. Hillier,
- Valerie Reinke,
- Philip Green,
- Martin Hirst,
- Marco A. Marra,
- and Robert H. Waterston
Genome Res. April 2009 19: 657-666; Published in Advance January 30, 2009, doi:10.1101/gr.088112.108
...with protein-coding genes, a small fraction falls in introns and intergenic regions. One notable region on the X chromosome encodes a noncoding transcript of &gt;10 kb localized to somatic nuclei. Footnotes ↵ 5 Corresponding author. ↵ E-mail waterston@gs.washington.edu ; fax (206) 685...
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LETTER: Widespread RNA Editing of Embedded Alu Elements in the Human Transcriptome
- Dennis D.Y. Kim,
- Thomas T.Y. Kim,
- Thomas Walsh,
- Yoshifumi Kobayashi,
- Tara C. Matise,
- Steven Buyske,
- and Abram Gabriel
Genome Res. September 2004 14: 1719-1725; doi:10.1101/gr.2855504
...Kampen, A.H. 2003 . The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res. 13 : 1998 -2004. ↵ Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R...
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LETTER: Domain-wide regulation of gene expression in the human genome
- Hinco J. Gierman,
- Mireille H.G. Indemans,
- Jan Koster,
- Sandra Goetze,
- Jurgen Seppen,
- Dirk Geerts,
- Roel van Driel,
- and Rogier Versteeg
Genome Res. September 2007 17: 1286-1295; Published in Advance August 10, 2007, doi:10.1101/gr.6276007
...). The highly expressed domains (called ridges) are gene dense, GC rich, and SINE repeat rich, and the genes have short introns, whereas the weakly expressed domains (called anti-ridges) show the opposite characteristics ( Lercher et al. 2003 ; Versteeg et al. 2003 ). Ridges were also described in the mouse...
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LETTER: Human gene organization driven by the coordination of replication and transcription
- Maxime Huvet,
- Samuel Nicolay,
- Marie Touchon,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Alain Arneodo,
- and Claude Thermes
Genome Res. September 2007 17: 1278-1285; Published in Advance August 3, 2007, doi:10.1101/gr.6533407
..., K. , Voute, P.A. , et al. ( 2001 ) The human transcriptome map: Clustering of highly expressed genes in chromosomal domains . Science 291 : 1289 – 1292 . ↵ Chakalova, L. , Debrand, E. , Mitchell, J.A. , Osborne, C.S. , Fraser, P. ( 2005 ) Replication and transcription: Shaping the landscape...
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LETTER: A highly divergent gene cluster in honey bees encodes a novel silk family
- Tara D. Sutherland,
- Peter M. Campbell,
- Sarah Weisman,
- Holly E. Trueman,
- Alagacone Sriskantha,
- Wolfgang J. Wanjura,
- and Victoria S. Haritos
Genome Res. November 2006 16: 1414-1421; Published in Advance October 25, 2006, doi:10.1101/gr.5052606
...scattering of silk ( Bombyx mori ) Int. J. Biol. Macromol. 24 : 127 – 138 . ↵ Versteeg, R. , van Schaik, B.D.C. , van Batenburg, M.F. , Roos, M. , Monajemi, R. , Caron, H. , Harmen, J. , Bussemaker, H.J. , van Kampen, A.H.C. ( 2003 ) The human transcriptome map reveals extremes in gene density, intron length...
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