The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes-2

<p><b>Copyright information:</b></p><p>Taken from "The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes"</p><p>http://www.biomedcentral.com/1471-2180/7/44</p><p>BMC Microbiology 2007;7():44-44.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1888695.</p><p></p>e schematics along the top edge of the extensions depict the sequence as it relates to the SL RNA gene map. Oligonucleotide C and C' were used to generate the results. The light gray and dark ovals represent total range of nucleosome protection along the sequence. Lane 1, MNase-digested chromatin; lane2, MNase-digested purified DNA; lane 3,HII digested or III-digested DNA, respectively; lane 4, Mock treated DNA. Arrowheads in lane 1 indicate bands resulting from nucleosome protection. The sequences below the extensions map the major 5' and 3' ends of the protected DNA. *: anomalous HII digestion product. B) Schematic of nucleosome organization on the SL RNA gene array. The genomic SL RNA gene array has a regular arrangement of nucleosomes confined to the non-transcribed spacer regions. The top schematic highlights the regular ~164-bp phasing between the major PE stops. Four potential positions of the nucleosome are presented relative to the DNA sequence of the spacer region. The bottom diagram depicts the conformation of the nucleosome in the SL RNA gene array. ~180 bp encompassing the upstream promoter sequences and the transcribed region are free of nucleosome binding

The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes-0

<p><b>Copyright information:</b></p><p>Taken from "The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes"</p><p>http://www.biomedcentral.com/1471-2180/7/44</p><p>BMC Microbiology 2007;7():44-44.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1888695.</p><p></p>ne array was visualized using a green Alexafluor 488-conjugated PCR fragment that corresponded to the entire SL RNA gene repeat. The genomic arrays reside in a single discrete location within the nucleus. B) Specificity control for the exon-tagged tSL RNA gene. The episome pX-tSL was visualized with an Alexafluor 488-labeled oligonucleotide, NSTAG, in transfected cells. No hybridization was observed to WT cells. C) Double staining for the SL RNA gene array and the episomal tSL RNA genes. The endogenous genes were visualized with an Alexafluor 488-conjugated PCR fragment, and the episome pX-tSL was visualized with a Tamara-labeled NSTAG oligonucleotide probe. There are examples of 1, 2, and three pX-tSL domains within the parasite nucleus

The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes-3

<p><b>Copyright information:</b></p><p>Taken from "The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes"</p><p>http://www.biomedcentral.com/1471-2180/7/44</p><p>BMC Microbiology 2007;7():44-44.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1888695.</p><p></p>he letter below each blot refers to the specific oligonucleotide hybridization probe, as listed in Table 1. The probe location is indicated by the lines above the schematic. The schematic shows the location of the SL RNA gene, the upstream promoter elements, and the borders of the cassette (thick black lines). The tag sequence is represented as a white box. The histogram represents the ratios of the genomic signal:monosome signal. Lane1, II digest of mock-treated DNA; lane 2, EII/I digest of the pX-tSL mock-treated DNA; lane 3, MNase-digested chromatin. B) Three hypothetical episomal nucleosome array conformations, to which only the first is able to bind the SL RNA gene pre-initiation complex. Assuming the periodicity of the nucleosomes on the drug-selectable marker-carrying episome are regular for , the tSL RNA gene promoter has at most a 26% chance of exposure to cognate transcription factors

The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes-4

<p><b>Copyright information:</b></p><p>Taken from "The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes"</p><p>http://www.biomedcentral.com/1471-2180/7/44</p><p>BMC Microbiology 2007;7():44-44.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1888695.</p><p></p> pX-tSL transfectants (U) and the derived clonal lines (1–6). Relative RNA levels were quantified by poisoned primer extension and relative DNA levels were quantified by Southern blotting. The ratio of the episomal tSL RNA transcript to the genomic SL RNA transcript is plotted by the gray bar and the corresponding episomal:chromosomal using the left hand scale. The DNA ratio is plotted by the black bar using the right hand scale. The white bar plots the RNA ratio divided by the DNA ratio using the left hand scale. Assuming factors influencing steady state levels of RNA are equivalent between the all the transfectants, the white bar gives an estimate of the pX-tSL episome transcription activity per gene copy. The pX-tSL clonal lines exhibit different expression rates

The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes-1

<p><b>Copyright information:</b></p><p>Taken from "The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes"</p><p>http://www.biomedcentral.com/1471-2180/7/44</p><p>BMC Microbiology 2007;7():44-44.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1888695.</p><p></p>n of the chromatin produced a characteristic ladder of DNA fragments. M = 100-bp size marker; 0 = mock treated chromatin. Increasing units of MNase are indicated, ranging from 5 – 500 units/ml. The arrowhead indicates the monosome. B) Southern blot mapping reveals strong preferential protection of an intergenic region between the T tract and the Proximal Sequence Element (PSE). DNA size marker positions are indicated on the left. Lane1, II digest of the SL RNA gene in mock-treated DNA; lane 2, MNase digested chromatin. The blot was hybridized with P-labelled oligonucleotide probes. The letter below each blot refers to the specific oligonucleotide probe, as listed in Table 1. The probe location is indicated by the lines above the schematic. The histogram represents the ratios of the monosome signal: genomic signal

A population study of the minicircles in : predicting guide RNAs in the absence of empirical RNA editing-4

<p><b>Copyright information:</b></p><p>Taken from "A population study of the minicircles in : predicting guide RNAs in the absence of empirical RNA editing"</p><p>http://www.biomedcentral.com/1471-2164/8/133</p><p>BMC Genomics 2007;8():133-133.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1892023.</p><p></p>A sequence. Beside each putative gRNA is the WGS clone name or GenBank sequence identifier followed by the DTU strain designation for that sequence. Watson-Crick base pairs,

The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes-5

<p><b>Copyright information:</b></p><p>Taken from "The promoter and transcribed regions of the spliced leader RNA gene array are devoid of nucleosomes"</p><p>http://www.biomedcentral.com/1471-2180/7/44</p><p>BMC Microbiology 2007;7():44-44.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1888695.</p><p></p>7. B = HI; H = dIII; RI = RI; RV = RV. B. Diagram showing the formula used to calculate the bending angle from measured parameters [41,57]. L1 = length of DNA; L2 = end-to-end distance of bent RV-digested DNA. M= M2/M1 (Fig 1C) ≅ L2/L1 (Fig 1B). C. EMSA analysis of different pCY7 restriction fragments incubated with 30% ammonium sulphate cut of nuclear extract. M1 = mobility of RI digested DNA; M2 = mobility of RV digested DNA. W = wild type binding site; M = 10-bp transversion mutation of the binding site

A population study of the minicircles in : predicting guide RNAs in the absence of empirical RNA editing-6

<p><b>Copyright information:</b></p><p>Taken from "A population study of the minicircles in : predicting guide RNAs in the absence of empirical RNA editing"</p><p>http://www.biomedcentral.com/1471-2164/8/133</p><p>BMC Genomics 2007;8():133-133.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1892023.</p><p></p>pectrogram ('T'-red; 'A'-purple; 'C'-blue; 'G'-green) of aligned minicircle sequences. B) Ratios of nucleotide composition ('T'-red; 'A'-purple; 'C'-blue; 'G'-green) of aligned sequences by position

A population study of the minicircles in : predicting guide RNAs in the absence of empirical RNA editing-0

<p><b>Copyright information:</b></p><p>Taken from "A population study of the minicircles in : predicting guide RNAs in the absence of empirical RNA editing"</p><p>http://www.biomedcentral.com/1471-2164/8/133</p><p>BMC Genomics 2007;8():133-133.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1892023.</p><p></p>iability of the third. B) Weblogo diagrams show the high degree of intragenomic CSB conservation. At each position the height of the letter represents the proportion of sequences with the base represented by that lette

A population study of the minicircles in : predicting guide RNAs in the absence of empirical RNA editing-2

<p><b>Copyright information:</b></p><p>Taken from "A population study of the minicircles in : predicting guide RNAs in the absence of empirical RNA editing"</p><p>http://www.biomedcentral.com/1471-2164/8/133</p><p>BMC Genomics 2007;8():133-133.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1892023.</p><p></p>A sequences yielding a single best score. B) 1000 permutations and local alignment batteries were performed as a method of calculating the approximate probability of a given best score. C) The best hybridization scores for each minicircle sequence were ranked by cumulative probability from 0 to 1 (circles). All points to the left of the intersection with the false discovery rate threshold (heavy solid line) were deemed to represent scores from predicted gRNAs. D) Using false discovery rate to control for multiple testing, alignments with scores deemed significant were said to be predicted gRNAs