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Widespread promoter-mediated coordination of transcription and mRNA degradation

Mally Dori-Bachash1, Ophir Shalem1, Yair S Manor1, Yitzhak Pilpel1* and Itay Tirosh12*

Author Affiliations

1 Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl Street, Rehovot 76100, Israel

2 Current address: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA

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Genome Biology 2012, 13:R114  doi:10.1186/gb-2012-13-12-r114

Published: 13 December 2012

Additional files

Additional file 1:

Table S1 and Figures S1 to 11. Table S1: genes examined by swapping of regulatory sequences. Figure S1: the effects of inserted selection markers on transcription and mRNA degradation. Figure S2: 5' RACE analysis. Figure S3: independent experiments reproduce the YLR326W expression differences between strains with swap segments of different lengths. Figure S4: correlation in different mRNA degradation measures between consecutive gene pairs with different genomic architectures. Figure S5: correlation of basal mRNA degradation rates for consecutive gene pairs. Figure S6: correlation of stress mRNA degradation rates for consecutive gene pairs. Figure S7: correlation of nascent transcription rates for consecutive gene pairs. Figure S8: similarity in mRNA degradation changes due to oxidative stress as a function of similarity in mRNA level changes in oxidative stress, for pairs of genes that share or do not share multiple promoter-associated regulators. Figure S9: the positive correlation between cell type-dependent differences (iPS cells versus HFFs) in mRNA levels and mRNA degradation is maintained in two control analyses. Figure S10: scatter plot of interspecies differences in total mRNA levels and in nascent mRNA levels. Figure S11: human-mouse comparison of non-orthologous genes reproduces the expected behavior of the Noise model (Model II in Figure 4)[39].

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