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Chromatin conformation signatures of cellular differentiation

James Fraser1, Mathieu Rousseau2, Solomon Shenker1, Maria A Ferraiuolo1, Yoshihide Hayashizaki3, Mathieu Blanchette2 and Josée Dostie1*

Author Affiliations

1 Department of Biochemistry and McGill Cancer Center, McGill University, 3655 Promenade Sir-William-Osler, Montréal, H3G1Y6, Canada

2 McGill Centre for Bioinformatics, McGill University, 3775 University, Montréal, H3A 2B4, Canada

3 RIKEN Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, 230-0045, Japan

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Genome Biology 2009, 10:R37  doi:10.1186/gb-2009-10-4-r37

Published: 19 April 2009

Additional files

Additional data file 1:

Human primer sequences for quantitative RT-PCR analysis.

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Additional data file 2:

Human 3C primer sequences for HoxA and gene desert analysis of THP-1 libraries.

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Additional data file 3:

5C primer sequences generated with the 5Cprimer algorithm.

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Additional data file 4:

(a) Representative agarose gel resolution of amplified multiplex cellular and BAC 5C libraries. Libraries were generated by mixing 29 of each forward and reverse 5C primers with corresponding 3C libraries as described in Materials and methods. BAC 5C library products typically migrate more heterogeneously then cellular counterparts due to increased complexity. (b) Linear schematic representation of HoxA cluster region analyzed in (c). Cluster features are as described in Figure 2b. Predicted BglII restriction pattern below HoxA diagram is shown to scale and restriction fragment number is indicated below each line. Orange shading identifies 'fixed' 3C region and green boxes indicate position of interacting fragments. (c) Detection of individual 5C contacts in multiplex 5C libraries. Formation of four different 5C ligation products in cellular and BAC multiplex 5C libraries was measured with internal 5C primers (right). Interaction frequencies in undifferentiated and differentiated cells were expressed relative to neighboring 71 and 72 interaction, which was set at one. 5C internal priming results are compared to 3C results shown on the left. 3C data are from Figures 3 &4 except that interaction frequencies were expressed relative to contact neighboring fixed region as described above. Each histogram value represents the average of at least three PCR reactions and error bars correspond to standard error of the mean. 5C internal primer sequences are shown in Additional data file 4.

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Additional data file 5:

Human internal 5C primer sequences for quality control of 5C libraries.

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Additional data file 6:

(a) Diagram of the HoxA cluster region compared in (b, c). Features are as described in Figure 2b. Predicted BglII restriction pattern below HoxA schematic is shown to scale and restriction fragments are identified below each line. (b) 3C chromatin interaction profiles from four different fixed cluster regions. Fixed fragment is indicated above each graph. 3C data are from Figures 3 &4 except that interaction frequency in each cellular state is expressed relative to contact neighboring fixed region, which was set at one. Each histogram value represents the average of at least three PCR reactions and error bars correspond to standard error of the mean. (c) 5C chromatin interaction profiles from four different fixed cluster regions. 5C data are from Figures 5 &6 except that interaction frequency is presented as described in (b). Interaction frequencies are the average of at least three array technical repeats. Error bars represent standard error of the mean.

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Additional data file 7:

p-values of local chromatin densities around HoxA genes.

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