1. Volume 10, Issue 6, Pages 1479-1487 (December 2002)
Promoter Activation by Enhancer-Dependent and -Independent Loading of Activator and Coactivator Complexes 
Salvatore Spicuglia, Sanjeev Kumar, Jung-Hua Yeh, Elodie Vachez, Lionel Chasson, Sophie Gorbatch, Julie Cautres, Pierre Ferrier 
Molecular Cell 
Volume 10, Issue 6, Pages (December 2002)
DOI: /S (02)

2. Figure 1 TF Binding to pDβ1 in Eβ+ versus Eβ− Thymocytes
(A) Schematic map of the ∼25 kb DNA region at the 3′ end of the mouse TCRβ locus (top line). The bottom line illustrates the ∼400 bp DNA sequence that encompasses the pDβ1 proximal promoter and demonstrates high (∼80%) human/mouse homology. Relevant TF binding motifs identified within this region are indicated, together with the Dβ1 gene segment, flanking RSs (open triangles), and major transcriptional starts (broken arrows).
(B) Soluble chromatin from formaldehyde-crosslinked Rag−/− (Eβ+), Rag−/−Eβ−/− (Eβ−) thymocytes, or NIH3T3 cells was immunoprecipitated using Abs against the indicated TFs. The amounts of pDβ1, Eα, Oct2, Eα, Vβ11, CD3e, or histone H4 (H4) gene regulatory DNA sequences in the ChIP-DNA fractions were estimated by radioactive PCR. Aliquots of immunoprecipitated chromatin using preimmune serum (control), and of total chromatin DNA before immunoprecipitation (input), were processed similarly. The diagram shows the relative enrichment (R.E.) of TF binding at pDβ1 in Eβ+ versus Eβ− thymocytes.
Molecular Cell  , DOI: ( /S (02) )

3. Figure 2 Loading of pDβ1 TF Binding Sites in Eβ+ versus Eβ− Thymocytes
Genomic DNA was prepared from DMS (A)- or KMnO4 (B)-treated thymocytes as indicated and analyzed for genomic footprints within pDβ1 by LM-PCR. Partial DMS-footprinting analyses are shown (complete results available as Supplemental Data at N, amplification patterns obtained using genomic DNA control. Filled or open circles on the right of the migrating lanes represent protected and hypersensitive sites, respectively. The numbers to the left of each panel represent the nucleotide position, commencing at the 3′ end of the Dβ1 gene segment.
Molecular Cell  , DOI: ( /S (02) )

4. Figure 3
Loading of Chromatin Remodeling Factors and the Basal Transcription Machinery to Distinct Regions of the TCRβ Locus in Eβ+ versus Eβ− Thymocytes
The legend for the autoradiograms shown in parts (A), (C), and (D) is as in Figure 1B, except that factor loading was analyzed at pDβ1 and Cβ1 in Eβ+ versus Eβ− thymocytes (A and C), or at Eβ and upstream (∼2.5 kb), or downstream (∼1.5 kb) Eβ regions (5′Eβ and 3′Eβ) in Eβ+ thymocytes (D); IP materials (from Eβ+ thymocytes) in (D) were the same as those used in parts (A) and (C). (B) Real-time PCR analysis of the relative enrichment in chromatin remodeling factors at pDβ1 and Cβ1 in Eβ+ versus Eβ− thymocytes. ND, not done. The diagram in (D) represents the relative enrichment of the indicated factors at Eβ versus pDβ1 in Eβ+ thymocytes.
Molecular Cell  , DOI: ( /S (02) )

5. Figure 4 Chromosomal Changes at pDβ1 in Eβ+ versus Eβ− Thymocytes
(A) Covalent modifications at histone N termini were investigated by ChIP using the indicated Abs; the CD25 gene promoter was used as a positive control for pS10-H3 analysis (analysis as in Figure 1B; except for the graphic representation of MeK9 results at pDβ1 where the Eβ− versus Eβ+ enrichment is shown).
(B) Determination of nucleosome occupancy at pDβ1 in Eβ+, Eβ−, and Eβ+ TCRβ thymocytes was performed by PCR mapping of mononucleosome-sized chromosomal DNA. GDNA, genomic DNA from Rag−/− thymocytes used as a reference control. The DNA fragments amplified by each primer pair used for PCR (left panels) are respresented below a schematic map of the pDβ1 region (legend as in Figure 1). The characteristics of the “-2bis,” “pIL12,” and “Eα” negative control fragments are described in the Experimental Procedures. A quantitative representation of the PCR results is shown; pDβ1 signals were normalized to the pIL12 signal in the same sample and are represented relative to those from gDNA.
Molecular Cell  , DOI: ( /S (02) )