1. Volume 11, Issue 5, Pages 1291-1299 (May 2003)
Transcription of Leishmania major Friedlin Chromosome 1 Initiates in Both Directions within a Single Region 
Santiago Martı́nez-Calvillo, Shaofeng Yan, Dan Nguyen, Mark Fox, Kenneth Stuart, Peter J Myler 
Molecular Cell 
Volume 11, Issue 5, Pages (May 2003)
DOI: /S (03)

2. Figure 1 Summary of Results from Nuclear Run-On Assays on LmjF Chr1
(A) Run-on RNA was radiolabeled by 6 min incubation of nuclei isolated from logarithmic phase promastigotes, extracted, and hybridized to dot blots of single-stranded M13 DNAs (1 μg) that contain inserts which are complementary to the top (T) or bottom (B) strand of most of the genes on chr1 (genes 2–79, as indicated) (see Supplemental Table S1 at Control DNAs include: 24 S, LSUα rRNA; tub, α-tubulin; SL, spliced-leader from L. donovani; SLs, spliced-leader spacer from L. donovani; 5′, 5′ end of chr3; 3′, 3′ end of chr3; G, BT1 from L. donovani; C, ORFC from the L. donovani LD1 locus; and M13, M13mp18 vector.
(B) The results from three separate experiments performed as above (blue dots) or three experiments with nuclei isolated from logarithmic phase promastigotes irradiated with 6 kJ/m2 UV light (magenta dots) were averaged and plotted against the position of each gene on chr1 (Myler et al., 1999). Signal from probes on the top strand are shown above the maps, while those from the bottom strand are shown below. Representative gene numbers are shown on the plots. The x axis scale indicates distance in kilobases. The y axis represents relative signal intensity (in arbitrary units × 103). The average signal for the M13 negative control was 625. The red and green arrowheads located at the right end of the chr1 cartoon represent subtelomeric repeats, and the blue arrowheads at both ends represent telomeric hexamer/octamer repeat regions.
Molecular Cell  , DOI: ( /S (03) )

3. Figure 2 Nuclear Run-On Assays Performed with Different UV Doses
Dot blots of single-stranded DNAs from several fragments around the strand-switch area on chr1 were hybridized to radiolabeled nascent RNA isolated from nuclei after an irradiation dose of 0, 1.25, 2.5, and 5 kJ/m2, as indicated below each panel. Fragments from the rRNA unit from LmjF, R-1 to R-4, were used as controls. The average distance of these fragments to the transcription start site in the rRNA unit is 104, 1543, 5383, and 8803 bp, respectively (Martinez-Calvillo et al., 2001). Illustrated below the four panels is a map of the strand-switch area on chr1, indicating the position of fragments AC, C, D, DE, and 30′ (which corresponds to the intergenic region between genes 30 and 31).
Molecular Cell  , DOI: ( /S (03) )

4. Figure 3 Relative Rates of Transcription as a Function of UV Dose
The results shown in Figure 2 were quantified, and the signal intensities relative to the nonirradiated control for each clone were plotted versus UV dose in (A)–(C). The average slope (K) of the curves from each fragment was calculated using the equation K = (ln R0/R)/d, where R0 = nascent RNA synthesis in nuclei made from nonirradiated cells, and R = nascent RNA synthesis at UV dose d (Johnson et al., 1987). In (D)–(F), K is plotted against the distance (in kilobases) from the putative promoter to the midpoint of each fragment. (A and D) Fragments AC and C and genes 26–29; (B and E) fragments D and DE and genes 30–33; (C and F) rRNA fragments R-1 to R-4.
Molecular Cell  , DOI: ( /S (03) )

5. Figure 4
Localization of Transcription Start Sites on Chr1 by 5′ RACE Analysis
The sequence shown is part of the intergenic region between XPP and PAXP. The putative transcription start sites (TSSs) are indicated with the arrows. The splice leader addition sites for XPP (CT at position 183) and PAXP (AG at position 915) are also indicated (SL). The region between the most distal TSS for each transcription unit is highlighted. The approximate location of fragments C, D, and E is shown on the right side of the figure.
Molecular Cell  , DOI: ( /S (03) )

6. Figure 5
Promoter Activity of the Chr1 Strand-Switch Area in Leishmania
(A) LmjF promastigotes were stably transfected with pFAB-Δ or pFAB-prom1. The results shown originated from 8 clones obtained with pFAB-Δ and 11 clones obtained with pFAB-prom1.
(B) L. donovani promastigotes were transfected with pFH-Δ, pFH-prom1, and pFH-prom2. Eight clones obtained with each vector were analyzed. For both panels, 2 × 107 cells were tested for luciferase activity. Each dot represents the average of three independent measurements. In L. donovani, a t test revealed statistically significant (p < 0.05) differences between the luciferase levels obtained with both pFH-prom1 and pFH-prom2 clones and the control (pFH-Δ).
Molecular Cell  , DOI: ( /S (03) )