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Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast

Brian T Wilhelm12*, Samuel Marguerat1, Sofia Aligianni13, Sandra Codlin1, Stephen Watt14 and Jürg Bähler1

Author Affiliations

1 Department of Genetics, Evolution and Environment and UCL Cancer Institute, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK

2 Institut de Recherche en Immunologie et en Cancérologie (IRIC), 2900 boulevard Édouard-Montpetit, Montréal, H3C 3J7, Canada

3 Salk Institute for Biological Studies, San Diego, CA 92186-5800, USA

4 Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK

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Genome Biology 2011, 12:R82  doi:10.1186/gb-2011-12-8-r82

Published: 22 August 2011

Additional files

Additional file 1:

Single-gene examples of Pol II occupancy. (a-f) Affymetrix tiling array data for RNA Pol II is shown for three genes (SPAC13G7.11 (a), SPBC1773.01 (b), SPCC126.05c (c)) with low expression (ranked 2,447,1,666, and 2,310 out of 4,816, respectively, according to Affymetrix expression data) and three genes (SPBC4F6.18c (d), SPAC17G6.06 (e), SPCC24B10.09 (f)) with high expression (ranked 216, 90, and 56 out of 4,816, respectively, from data as above). Additional annotated features are shown (expression rankings are SPAC13G7.12c (3,307), SPBC1773.02c (2,764), SPCC126.04c (2,123), SPCC126.06 (2,591), SPBC4F6.17c (1,944), SPAC17G6.05c (4,227), SPAC17G6.07c (811), SPCC24B10.08c (3,300), SPCC24B10.10c (3,376)) and the range of absolute values of RNA Pol II signals (as previously calculated [7]) are shown on the left side of each panel. Introns within genes shown are indicated by red lines.

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Additional file 2:

Expression level of spliced genes is not biased by intron size. A scatterplot showing the size of each intron in the annotated S. pombe genome and the corresponding gene expression level (according to previously published Affymetrix microarray data [7]).

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Additional file 3:

Validation of Pol II occupancy in single genes by quantitative PCR.

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