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Local DNA topography correlates with functional noncoding regions of the human genome
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This is an interesting approach that assesses evolutionary conservation of DNA structure rather than DNA sequence and finds structural conservation of regulatory sequences.
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Parker S.C., Hansen L., Abaan H.O., Tullius T.D., and Margulies E.H. Local DNA topography correlates with functional noncoding regions of the human genome. Science 324 (2009) 389-392. This is an interesting approach that assesses evolutionary conservation of DNA structure rather than DNA sequence and finds structural conservation of regulatory sequences.
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The author reviews work on the evolution of cis-regulatory sequences and provides a model to explain morphological evolution by cis-regulatory changes.
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Carroll S.B. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134 (2008) 25-36. The author reviews work on the evolution of cis-regulatory sequences and provides a model to explain morphological evolution by cis-regulatory changes.
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Cell
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Carroll, S.B.1
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This paper coins the term 'shadow enhancers' for functionally overlapping or redundant enhancers of a specific gene and suggests that they might provide buffering activity during cis-regulatory evolution.
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Hong J.W., Hendrix D.A., and Levine M.S. Shadow enhancers as a source of evolutionary novelty. Science 321 (2008) 1314. This paper coins the term 'shadow enhancers' for functionally overlapping or redundant enhancers of a specific gene and suggests that they might provide buffering activity during cis-regulatory evolution.
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Science
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The authors show that different Ciona muscle enhancers can achieve the same function with widely different architectures, yet that functional architectures are often preserved in orthologous enhancers.
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Science
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This work examines ChIP data to show that transposable elements (TEs) are bound by TFs in vivo, suggesting that TE activity can rewire regulatory networks, as originally suggested 30 years ago.
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Bourque G., Leong B., Vega V.B., Chen X., Lee Y.L., Srinivasan K.G., Chew J.L., Ruan Y., Wei C.L., Ng H.H., et al. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 18 (2008) 1752-1762. This work examines ChIP data to show that transposable elements (TEs) are bound by TFs in vivo, suggesting that TE activity can rewire regulatory networks, as originally suggested 30 years ago.
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TRANSFAC: transcriptional regulation, from patterns to profiles
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Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., and Haussler D. The human genome browser at UCSC. Genome Res 12 (2002) 996-1006
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