Legends to Supplementary Information

Supplementary Table 1

TCR signaling induces a global change of histone H3 acetylation. To compare the acetylation level between resting and activated T cell, the average detection frequency was calculated by normalizing the total number of tags to the number of NlaIII sites in a 3kb-window. The fold of change was calculated by dividing the average detection frequency of activated T cell by that of resting T cell. The chromatin regions with a change of more than 3-fold are listed in the excel file. The first page shows a summary of all chromosomes. Each chromosome is shown in one page.

Supplementary Figure 1

  1. The distribution of all the GMAT tags. A 20 kb region of 21,355 genes was aligned relative to their transcription initiation sites (x-axis). The y-axis shows the total number of tag counts in a 50bp-window.
  2. The distribution of the repetitive GMAT tags. The x-axis is same with in Panel A. The y-axis shows the tag counts of repetitive sequences in a 50bp-window.

Supplementary Figure 2

CpG islands are highly concentrated in a 1 kb-region surrounding the transcription initiation site. The 27,058 CpG island sequences were mapped to their genomic sites and were aligned relative to the transcription initiation site of the genes.

Supplementary Figure 3

The integrated acetylation map of the human genome in T cells. The detection frequency was derived from normalizing the tag counts detected in the GMAT library prepared from the ChIP DNA with the K9/K14 diacetylated histone H3 antibody to the number of the tag sequence that appears in the human genome. It (y-axis) was plotted against the chromosome coordinate (x-axis).

Supplementary Figure 4

The highest H3 acetylation is detected in gene-rich regions. The detection frequency was derived from normalizing the tag counts detected in the GMAT library prepared from the ChIP DNA with the K9/K14 diacetylated histone H3 antibody to the number of the tag sequence that appears in the human genome. It (y-axis) was plotted against the chromosome coordinate (x-axis) in the upper panel. The lower panel shows the number of genes in a 200kbp-window on the same chromosome (chr12).

Supplementary Figure 5

  1. IL2RA locus. The acetylation data and vista sequence analysis are shown. The positions of the four positive regulatory regions (PRR) and CD28 response element (CD28rE) are indicated above the gene. IL2R is an essential component of the trimeric high-affinity receptor for IL-2 that is a critical growth factor for antigen-activated lymphocytes (Lin and Leonard 1997). Extensive studies demonstrate that the gene is regulated transcriptionally by at least five positive regulatory regions (PRRs) that are widely spread (John et al. 1996; Kim et al. 2001; Yeh et al. 2001). PRRI and PRRII are proximal promoter elements, which are highly acetylated (#9 in Figure 5C). PRRIV is an intronic region that mediates the activity of both IL-2 signaling and TCR signaling (Kim et al. 2001; Kim and Leonard 2002). Interestingly, an acetylation island colocalized with PRRIV (#8). The CD28rE, which is required for mitogenic stimulation of the gene (Yeh et al. 2001), is also correlated with an acetylation island (#12). Since the PRRIII sequence does not contain NlaIII sites, we could not determine if there is an acetylation island in the region by the GMAT analysis (#10 in blue). However, PCR analysis of the ChIP DNA indicates that the region was indeed highly acetylated (data not shown). Interestingly, we also detected nine other acetylation islands (highlighted in green) in the region, suggesting that the gene may be controlled by more cis regulatory elements.
  1. BCL3 locus. The acetylation data and vista sequence analysis are shown as in Panel A. The four DNase hypersensitive sites identified in the region are indicated above the gene (HS1 to HS4). BCL3 is a member of the IB family of proteins, which is involved in inflammation and innate and adaptive immune responses by regulating the NF-B family of transcription factors (Ohno et al. 1990). Transcription of BCL3 is regulated by a conserved intronic enhancer, which is correlated with strong DNase hypersensitive sites (HS3 and HS4) (Ge et al. 2003). As shown in Figure, HS3 and HS4 as well as HS1 and HS2 were indeed correlated with high levels of acetylation, which were confirmed by PCR analysis of the ChIP DNA (data not shown).

Supplementary Figure 6

Genome-wide changes of acetylation induced by TCR signaling. The average tag density was derived by normalizing the total number of detected tags to the number of NlaIII site in a 3kb-window. The average tag densities from resting and activated T cells were compared directly to obtain the fold change. Changes of  three-fold between activated and resting T cells were plotted along the chromosome coordinates.

References

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John, S., C.M. Robbins, and W.J. Leonard. 1996. An IL-2 response element in the human IL-2 receptor alpha chain promoter is a composite element that binds Stat5, Elf-1, HMG-I(Y) and a GATA family protein. Embo J15: 5627-35.

Kim, H.P., J. Kelly, and W.J. Leonard. 2001. The basis for IL-2-induced IL-2 receptor alpha chain gene regulation: importance of two widely separated IL-2 response elements. Immunity15: 159-72.

Kim, H.P. and W.J. Leonard. 2002. The basis for TCR-mediated regulation of the IL-2 receptor alpha chain gene: role of widely separated regulatory elements. Embo J21: 3051-9.

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