Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Jeff...

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Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Jeff Vierstra, Eric Rynes, Richard Sandstrom, Miaohua Zhang, Theresa Canfield, R. Scott Hansen, Sandra Stehling-Sun, Peter J. Sabo, Rachel Byron, Richard Humbert, Robert E. Thurman, Audra K. Johnson, Shinny Vong, Kristen Lee, Daniel Bates, Fidencio Neri, Morgan Diegel, Erika Giste, Eric Haugen, Douglas Dunn, Matthew S. Wilken, Steven Josefowicz, Robert Samstein, Kai-Hsin Chang, Evan E. Eichler, Marella De Bruijn, Thomas A. Reh, Arthur Skoultchi, Alexander Rudensky, Stuart H. Orkin, Thalia Papayannopoulou, Piper M. Treuting, Licia Selleri, Rajinder Kaul, Mark Groudine, M. A. Bender, and John A. Stamatoyannopoulos Science Volume ():1246426 November 19, 2014 Published by AAAS

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Fig. 2 Cell and tissue lineage encoding within shared regulatory elements.(A) k-means clustering of DHSs by accessibility at each of the 475,701 mouse DHSs shared with human. Jeff Vierstra et al. Science 2014;science Published by AAAS

Transcript of Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Jeff...

Page 1: Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Jeff Vierstra, Eric Rynes, Richard Sandstrom, Miaohua Zhang, Theresa.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

by Jeff Vierstra, Eric Rynes, Richard Sandstrom, Miaohua Zhang, Theresa Canfield, R. Scott Hansen, Sandra Stehling-Sun, Peter J. Sabo, Rachel Byron, Richard

Humbert, Robert E. Thurman, Audra K. Johnson, Shinny Vong, Kristen Lee, Daniel Bates, Fidencio Neri, Morgan Diegel, Erika Giste, Eric Haugen, Douglas Dunn,

Matthew S. Wilken, Steven Josefowicz, Robert Samstein, Kai-Hsin Chang, Evan E. Eichler, Marella De Bruijn, Thomas A. Reh, Arthur Skoultchi, Alexander Rudensky, Stuart H. Orkin, Thalia Papayannopoulou, Piper M. Treuting, Licia Selleri, Rajinder

Kaul, Mark Groudine, M. A. Bender, and John A. Stamatoyannopoulos

ScienceVolume ():1246426November 19, 2014

Published by AAAS

Page 2: Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Jeff Vierstra, Eric Rynes, Richard Sandstrom, Miaohua Zhang, Theresa.

Fig. 1 Conservation of mouse regulatory DNA in humans.(A) The accessible landscape of the mouse was derived from 45 tissues and cell types.

Jeff Vierstra et al. Science 2014;science.1246426

Published by AAAS

Page 3: Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Jeff Vierstra, Eric Rynes, Richard Sandstrom, Miaohua Zhang, Theresa.

Fig. 2 Cell and tissue lineage encoding within shared regulatory elements.(A) k-means clustering of DHSs by accessibility at each of the 475,701 mouse DHSs shared with human.

Jeff Vierstra et al. Science 2014;science.1246426

Published by AAAS

Page 4: Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Jeff Vierstra, Eric Rynes, Richard Sandstrom, Miaohua Zhang, Theresa.

Fig. 3 Conservation and repurposing of regulatory DNA activity.(A) Pairwise comparison (median Jaccard distance) of shared DHS landscape usage between all mouse (rows) and human

(columns) tissues largely mirrors their conserved morphological and embryological origins.

Jeff Vierstra et al. Science 2014;science.1246426

Published by AAAS

Page 5: Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Jeff Vierstra, Eric Rynes, Richard Sandstrom, Miaohua Zhang, Theresa.

Fig. 4 Evolutionary dynamics of transcription factor recognition sequences within regulatory DNA.(A) Conservation of TF recognition sequences within shared DHSs. (B) Conserved TF

recognition sequences (both positional and operational conservation) are enriched within DHSs that have conserved tissue activity patterns.

Jeff Vierstra et al. Science 2014;science.1246426

Published by AAAS

Page 6: Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Jeff Vierstra, Eric Rynes, Richard Sandstrom, Miaohua Zhang, Theresa.

Fig. 5 Conservation of global cis-regulatory content predominates that of individual regulatory elements.(A) Density of individual TF recognition sequences in human (x axis) and mouse (y

axis) regulatory T cells.

Jeff Vierstra et al. Science 2014;science.1246426

Published by AAAS


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