Searching journal content for articles similar to Margulies et al. 13 (12): 2507.

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  1. Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
    • Liangxi Wang,
    • Tiegh Taylor,
    • Kumaragurubaran Rathnakumar,
    • Nadiya Khyzha,
    • Minggao Liang,
    • Azad Alizada,
    • Laura F. Campitelli,
    • Sara E. Pour,
    • Zain M. Patel,
    • Lina Antounians,
    • Ian C. Tobias,
    • Huayun Hou,
    • Timothy R. Hughes,
    • Sushmita Roy,
    • Jennifer A. Mitchell,
    • Jason E. Fish,
    • and Michael D. Wilson
    Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
    ...and inflammation. The extent to which TEs have contributed to NF-kB responses during mammalian evolution is not well established. Here, we perform a multi-species analysis of TEs bound by the NF-kB subunit RELA in response to the proinflammatory cytokine TNF. By comparing RELA ChIP-seq data from TNF...
  2. Method: Genome-wide identification of conserved regulatory function in diverged sequences
    • Leila Taher,
    • David M. McGaughey,
    • Samantha Maragh,
    • Ivy Aneas,
    • Seneca L. Bessling,
    • Webb Miller,
    • Marcelo A. Nobrega,
    • Andrew S. McCallion,
    • and Ivan Ovcharenko
    Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
    ...Genome-wide identification of conserved regulatory function in diverged sequences Leila Taher 1 , David M. McGaughey 2 , Samantha Maragh 2 , 3 , Ivy Aneas 4 , Seneca L. Bessling 2 , Webb Miller 5 , Marcelo A. Nobrega 4...
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  3. LETTER: Evolutionary constraints in conserved nongenic sequences of mammals
    • Peter D. Keightley,
    • Gregory V. Kryukov,
    • Shamil Sunyaev,
    • Daniel L. Halligan,
    • and Daniel J. Gaffney
    Genome Res. October 2005 15: 1373-1378; doi:10.1101/gr.3942005
    ...by clustering of genes of comparable expression profile. Genome Res. 14 : 1002 -1013. ↵ Margulies, E.H., Blanchette, M., Haussler, D., and Green, E.D. 2003 . Identification and characterization of multi-species conserved sequences. Genome Res. 13 : 2507 -2518. ↵ Matassi, G., Sharp, P.M., and Gautier, C. 1999...
  4. Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
    • Andrew L. Hufton,
    • Susanne Mathia,
    • Helene Braun,
    • Udo Georgi,
    • Hans Lehrach,
    • Martin Vingron,
    • Albert J. Poustka,
    • and Georgia Panopoulou
    Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
    ...Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention Andrew L. Hufton , Susanne Mathia , Helene Braun , Udo Georgi , Hans Lehrach , Martin Vingron , Albert J. Poustka...
  5. LETTER: Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation
    • Natalia Martin,
    • Satyakam Patel,
    • and Julia A. Segre
    Genome Res. December 2004 14: 2430-2438; doi:10.1101/gr.2709404
    ...and characterization of multi-species conserved sequences. Genome Res. 13 : 2507 -2518. ↵ Michel, S., Schmidt, R., Robinson, S.M., Shroot, B., and Reichert, U. 1987 . Identification and subcellular distribution of cornified envelope precursor proteins in the transformed human keratinocyte line SV-K14. J. Invest...
  6. 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
    .../or have acquired lineage-specific functions. Indeed, many regulatory sequences and known functional noncoding RNAs, including many microRNAs, are not conserved over significant evolutionary distances, and recent evidence from the ENCODE project suggests that many functional elements show no detectable...
  7. LETTER: Noncoding Sequences Conserved in a Limited Number of Mammals in the SIM2 Interval are Frequently Functional
    • Kelly A. Frazer,
    • Heng Tao,
    • Kazutoyo Osoegawa,
    • Pieter J. de Jong,
    • Xiyin Chen,
    • Mark F. Doherty,
    • and David R. Cox
    Genome Res. March 2004 14: 367-372; Published in Advance February 12, 2004, doi:10.1101/gr.1961204
    ...is difficult. Here, we analyze the 365-kb SIM2 interval to test the utility of using multispecies sequence conservation for prioritization of conserved noncoding sequences for functional characterization. RESULTS AND DISCUSSION Isolation of Syntenic BAC Sequences When performing cross-species DNA comparisons...
  8. LETTER: Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment
    • Emmanouil T. Dermitzakis,
    • Ewen Kirkness,
    • Scott Schwarz,
    • Ewan Birney,
    • Alexandre Reymond,
    • and Stylianos E. Antonarakis
    Genome Res. May 2004 14: 852-859; Published in Advance April 12, 2004, doi:10.1101/gr.1934904
    ..., USA 4 European Bioinformatics Institute, Hinxton CB10 1SD, UK Abstract The analysis of conservation between the human and mouse s resulted in the identification of a large number of conserved nongenic sequences (CNGs). The functional significance of this nongenic conservation remains unknown, however...
  9. Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
    • Wei-Jen Chung,
    • Phaedra Agius,
    • Jakub O. Westholm,
    • Michael Chen,
    • Katsutomo Okamura,
    • Nicolas Robine,
    • Christina S. Leslie,
    • and Eric C. Lai
    Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
    ..., whether an arbitrary hairpin is competent for processing by the miRNA generating machinery in vivo. Instead, the identification of newly evolved miRNAs has depended on small RNA sequencing, an approach revolutionized by recent technological advances. Many species-restricted genes 3These authors...
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  10. ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Adam Siepel,
    • Gill Bejerano,
    • Jakob S. Pedersen,
    • Angie S. Hinrichs,
    • Minmei Hou,
    • Kate Rosenbloom,
    • Hiram Clawson,
    • John Spieth,
    • LaDeana W. Hillier,
    • Stephen Richards,
    • George M. Weinstock,
    • Richard K. Wilson,
    • Richard A. Gibbs,
    • W. James Kent,
    • Webb Miller,
    • and David Haussler
    Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
    ...essential for regulation, then sequence conservation might result from selection against allelic divergence ( Lipman 1997 ). This possibility is of particular interest in light of the recent identification of a large number of apparent sense/antisense transcriptional units in eukaryotic s, many of which...
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