Examples of co-localization between miRNAs and CIS retroviral integration sites in the mouse genome.

<p>Each panel represents 20 kb of genomic DNA. Blue triangles indicate retroviral integration sites, red ticks represent miRNAs, black boxes and lines show the position of spliced transcripts. (A) chr11:87,562,001–87,582,000. (B) chrX:48,977,001–48,997,000. (C) chr14:113,914,001–113,934,000. Genome assembly mm8.</p

Maintenance of transposon-free regions throughout vertebrate evolution-2

<p><b>Copyright information:</b></p><p>Taken from "Maintenance of transposon-free regions throughout vertebrate evolution"</p><p>http://www.biomedcentral.com/1471-2164/8/470</p><p>BMC Genomics 2007;8():470-470.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2241635.</p><p></p>ue describes the subset of TFRs that have an orthologous TFR in human larger than 10 kb, the area in red have an orthologous TFR in human larger than 5 kb. (B) Histogram of the GC content of human TFRs. Area indicated in blue describes the subset of TFRs that have an orthologous TFR in zebrafish larger than 10 kb, the area in red have an orthologous TFR in zebrafish larger than 5 kb. (C) Scatter plot of the GC content of orthologous pairs of zebrafish and human TFRs ≥ 10 kb in both species. Points in red indicate TFR pairs with a difference of absolute GC% greater than 20

Maintenance of transposon-free regions throughout vertebrate evolution-5

<p><b>Copyright information:</b></p><p>Taken from "Maintenance of transposon-free regions throughout vertebrate evolution"</p><p>http://www.biomedcentral.com/1471-2164/8/470</p><p>BMC Genomics 2007;8():470-470.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2241635.</p><p></p> the non-genic 13 kb TFR hs11.145 (red bar). Thick blue bars indicate blocks of sequence that are alignable to the orthologous zebrafish TFR dr25.92. Small purple bar indicates the position of the human miRNA mir-129-2. (B) A close up view of 130 bp around mir-129-2, thick purple bar indicates the mature miRNA, thin purple line indicates pre-miRNA hairpin. Blue conservation plot is based on the alignment of 17 vertebrate species and green plot based on pairwise alignment of human and zebrafish that shows a conservation profile consistent with the presence of a miRNA conserved in each species [38]. (C) Syntenic region of the zebrafish genome (20 kb chr25:31,421,001–31,441,000) including the TFR dr25.92. Thick blue bars indicate blocks of sequence that are alignable to the orthologous human TFR hs11.145. Although there are currently no genes annotated in this region, the conservation profile suggests that an ortholog of mir-129-2 resides within the TFR. All images are modified screen shots taken from the UCSC genome browser [31]

The number of miRNAs co-localized with retroviral integration sites.

<p>Blue diamonds represent the number of miRNAs located at the indicated distance or less from CIS inserts, and red diamonds correspond to miRNAs located at the indicated distance or less from non-CIS inserts. The trendline for miRNAs associated with non-CIS inserts is shown as red dotted line.</p

Maintenance of transposon-free regions throughout vertebrate evolution-3

<p><b>Copyright information:</b></p><p>Taken from "Maintenance of transposon-free regions throughout vertebrate evolution"</p><p>http://www.biomedcentral.com/1471-2164/8/470</p><p>BMC Genomics 2007;8():470-470.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2241635.</p><p></p>he UCSC genome browser. Horizontal red bars indicate TFRs and brown ticks indicate transposons. (A) Zebrafish (chr3:24,391-24,451 kb, March 2006) including the 25.9 kb TFR dr3.89. Human proteins mapped to the zebrafish genome by chained tBLASTn are indicated in blue. (B) Human (chr7:23,450-23,510 kb, March 2006) including the 13.7 kb TFR hs7.101. Human RefSeq genes are indicated in blue. (C) Mouse (chr6:49,114-49,174 kb, February 2006) including the 9.3 kb TFR mm6.309. Mouse RefSeq genes are indicated in blue. (D) Opossum (chr8:296,183-296,243 kb, January 2006) including the 16.4 kb TFR md8.376. Human RefSeq genes mapped to the opossum genome with BLAT are indicated in blue. (E) Frog (scaffold_56:3,208-3,268 kb, August 2005) including a 14 kb region that contains no transposons (red box). Human proteins mapped to the frog genome with tBLASTn are indicated in blue

Bootstrap analysis for co-localization between miRNAs and all non-CIS retroviral integration sites.

<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001133#pone-0001133-t002" target="_blank">Table 2</a> for description of the columns.</p

Bootstrap analysis for co-localization between miRNAs and CIS inserts.

a<p>Number of miRNA loci overlapping CIS inserts in the mouse genome.</p>b<p>Ratio between observed and bootstrap average.</p>c<p>Probability of obtaining at least the observed number of miRNA loci overlapping CIS inserts (upper line) or the probability of obtaining at least that number of CIS inserts overlapping miRNA loci (lower line) in bootstrap procedure.</p>d<p>Maximum number of miRNA loci overlapping with CIS inserts (upper line) or maximum number of CIS inserts overlapping miRNA loci (lower line) obtained in the bootstrap procedure.</p

Maintenance of transposon-free regions throughout vertebrate evolution-1

<p><b>Copyright information:</b></p><p>Taken from "Maintenance of transposon-free regions throughout vertebrate evolution"</p><p>http://www.biomedcentral.com/1471-2164/8/470</p><p>BMC Genomics 2007;8():470-470.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2241635.</p><p></p> the non-genic 13 kb TFR hs11.145 (red bar). Thick blue bars indicate blocks of sequence that are alignable to the orthologous zebrafish TFR dr25.92. Small purple bar indicates the position of the human miRNA mir-129-2. (B) A close up view of 130 bp around mir-129-2, thick purple bar indicates the mature miRNA, thin purple line indicates pre-miRNA hairpin. Blue conservation plot is based on the alignment of 17 vertebrate species and green plot based on pairwise alignment of human and zebrafish that shows a conservation profile consistent with the presence of a miRNA conserved in each species [38]. (C) Syntenic region of the zebrafish genome (20 kb chr25:31,421,001–31,441,000) including the TFR dr25.92. Thick blue bars indicate blocks of sequence that are alignable to the orthologous human TFR hs11.145. Although there are currently no genes annotated in this region, the conservation profile suggests that an ortholog of mir-129-2 resides within the TFR. All images are modified screen shots taken from the UCSC genome browser [31]

Retroviral CIS insertions within 10 kb of murine miRNAs.

a<p>Not all RISs are shown.</p>b<p>Reference in brackets, * less than 5 kb between insert and miRNA loci.</p>c<p>N/D – not determined, BM – bone marrow, HS – histiocytic sarcoma.</p

Bootstrap analysis for co-localization between non-CIS inserts separated by more than 3 kb and miRNAs.

<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001133#pone-0001133-t002" target="_blank">Table 2</a> for description of the columns.</p