Roles of Intragenic and Intergenic L1s in Mouse and Human

<div><p>Long INterspersed Element-1 (LINE-1 or L1) is a retrotransposable element that has shaped the evolution of mammalian genomes. There is increasing evidence that transcriptionally active L1 could have been co-opted through evolution to play various roles including X-inactivation, homologous recombination and gene regulation. Here, we compare putatively active L1 distributions in the mouse with human. L1 density is higher in the mouse except for the Y-chromosome. L1 density is the highest in X-chromosome, implying an X-inactivation role. L1 is more common outside genes (intergenic) except for the Y-chromosome in both species. The structure of mouse L1 is distinguished from human L1 by the presence of a 200 bp repeat in the 5′ UTR of the former. We found that mouse intragenic L1 has significantly higher repeat copy numbers than intergenic L1, suggesting that this is important for control of L1 expression. Furthermore, a significant association between the presence of intragenic L1s and down-regulated genes in early embryogenesis was found in both species. In conclusion, the distribution of L1 in the mouse genome points to biological roles of L1 in mouse similar to human.</p></div

The comparison between intragenic and intergenic human L1s.

<p>(A) A bar graph shows 15 significant features passing the significance p-value 1.0E-03 (dashed line) from Mantel-Haenszel chi-square tests. The green and orange bars represent conserved and mutated features, respectively. These colored bars are aligned with L1 structure shown below the graphs. The bars marked with an asterisk (*) indicate the features calculated for the entire L1 sequence. (B) A bar graph shows non-categorical features whose significance p-value pass 1.0E-03 (dashed line). The blue columns indicate that more of these features appear in the intragenic L1s than that of intergenic ones. The red columns indicate that there are more of such features in the intergenic L1s than that of intragenic ones.</p

The comparison between intragenic and intergenic mouse L1s.

<p>(A) Bar graph of conserved (green columns) and mutated (orange columns) features from Mantel-Haenszel chi-square tests with cutoff of p-value <1.0E-03 (dashed line). The structure of mouse L1 is shown under the bar graph to indicate the relative location of the feature in L1 sequence. The bars marked with an asterisk (*) indicate the features calculated for the entire L1 sequence. (B) A bar graph shows significant non-categorical features with p-value <1.0E-03, using the Student's <i>t</i>-test. The blue columns indicate that more of these features appear in the intragenic L1s than that of intergenic ones. The red columns indicate that there are more of such features in the intergenic L1s than that of intragenic ones.</p

Distribution of mouse and human L1s over their genomes.

<p>(A) Graphical definition of intragenic and intergenic L1s. An intragenic L1 is represented by a blue box, while the intergenic one is represented in a red box. The black box represents a gene (intragenic region) and the black line represents an area outside (intergenic region) the gene bodies. (B) A bar graph shows the distribution of mouse (gray columns) and human (black columns) L1s residing on autosome, X, and Y-chromosomes. (C) Two side-by-side bar graphs comparing intragenic (blue columns) vs. intergenic (red columns) L1s on mouse and human genomes.</p

Intragenic L1s control gene expression in human early embryogenesis.

<p>Bold items indicate differential stages that pass the threshold (OR >1.0 and p-value <1.0E-03).</p><p>Intragenic L1s control gene expression in human early embryogenesis.</p

Additional file 1: Figure S1. of The association between Alu hypomethylation and severity of type 2 diabetes mellitus

Alu methylation patterns of COBRA-Alu assay. (A) The Alu amplicons are 133 bp and contain 2 CpG-dinucleotides. (B) A schematic representation of the COBRA-Alu assay shows the methylation patterns of Alu amplicons, including fully methylated loci (mCmC), unmethylated loci (uCuC) and two partially methylated forms (mCuC and uCmC). (C) For bisulfate treatment, methylated cytosine bases are not changed to uracil bases, whereas the unmethylated cytosine bases are converted to uracil bases. After the PCR products are digested with Taq1 restriction enzyme, the digested products are mCmC (43, 32 and 58 bp), uCuC ( 133 bp), mCuC ( 43 and 90 bp) and uCmC ( 75 and 58 bp). (TIFF 98 kb

Intragenic L1s control gene expression in mouse early embryogenesis.

<p>Bold items indicate differential stages that pass the threshold (OR >1.0 and p-value <1.0E-03).</p><p>Intragenic L1s control gene expression in mouse early embryogenesis.</p

Presentation_1_Identification and validation of a novel ferroptosis-related gene signature for prognosis and potential therapeutic target prediction in cholangiocarcinoma.pptx

Cholangiocarcinoma (CCA) is a highly heterogeneous and aggressive malignancy of the bile ducts with a poor prognosis and high mortality rate. Effective targeted therapy and accurate prognostic biomarkers are still lacking. Ferroptosis is a form of regulated cell death implicated in cancer progression and has emerged as a potential therapeutic target in various cancers. However, a comprehensive analysis of ferroptosis-related genes (FRGs) for predicting CCA prognosis and therapeutic targets and determining the role of ferroptosis in CCA remain to be performed. Here, we developed a prognostic FRG signature using a least absolute shrinkage and selection operator Cox regression analysis in a training cohort. We then validated it using four independent public datasets. The six-FRG signature was developed to predict CCA patient survival, stratifying them into low-risk and high-risk groups based on survival time. Significantly, the high-risk CCA patients had shorter overall survival. A receiver operating characteristic curve analysis further confirmed the prognostic FRG signature’s strong predictive ability, indicating that it was an independent prognostic indicator for CCA patients. Furthermore, the high-risk group was associated with fluke infection and high clinical stages. Cancer-associated fibroblast (CAF) score and CAF markers were significantly higher in the high-risk group than the low-risk group. Moreover, our FRG signature could predict immune checkpoint markers for immunotherapy and drug sensitivity. The mRNA expression levels of the six-FRG signature was validated in 10 CCA cell lines and dividing them into low-risk and high-risk groups using the FRG signature. We further showed that high-risk CCA cell lines were more resistant to ferroptosis inducers, including erastin and RSL3, than the low-risk CCA cell lines. Our study constructed a novel FRG signature model to predict CCA prognoses which might provide prognostic biomarkers and potential therapeutic targets for CCA patients. Ferroptosis sensitivity in high-risk and low-risk CCA cell lines suggests that ferroptosis resistance is associated with high-risk group CCA. Therefore, ferroptosis could be a promising therapeutic target for precision therapy in CCA patients.</p

The down-regulated gene sets at differential gene expression stages in early embryogenesis that pass the chi-square tests.

<p>(A) Intersection of 4 gene sets in mouse genome. Each gene set is represented by a colored oval. The numbers in green, pink, yellow and blue ovals indicate the numbers of associated mouse genes in “2-cell vs. 1-cell”, “4-cell vs. 1-cell”, “8-cell vs. 1-cell”, and “morula vs. 1-cell” differential expressions stages, respectively. (B) Intersection of 3 gene sets in human genome. A colored circle represents each gene set. The numbers in yellow, blue, and red circles indicate the numbers of associated human genes in “8-cell vs. 1-cell”, “morula vs. 1-cell”, and “blastocyst vs. 1-cell” differential expression stages, respectively. (C) Name listing of mouse-human orthologous genes found in both mouse and human intersection gene sets. Each orthologous gene pair indicates the mouse gene name followed by the human gene name. The numbers in parentheses present the corresponding gene ids.</p

The possible direction of LINE-1 methylation pattern changes.

<p>^mC^uC, ^uC^mC, ^mC^mC and ^uC^uC, represented %^mC^uC, %^uC^mC, %^mC^mC and %^uC^uC, respectively. The graphs were plotted for the percentages of either ^mC^uC or ^uC^mC on the X-axis and either ^mC^mC or ^uC^uC on the Y-axis. The vertical and horizontal lines indicate the mean percentages of each axis. The graph is divided into 4 quadrants. The numbers of NS and CS who fell in the upper left quadrant were counted and compared to the remainder of the group using the chi-squared test. The results are shown in the tables below the graphs.</p