Journal: BMC Medical Genomics

Article Title: The identification of circular RNAs from peripheral blood mononuclear cells in systemic lupus erythematosus

doi: 10.1186/s12920-021-00919-w

Figure Lengend Snippet: Detailed Annotation for circRNA-miRNA interactions. Representative notation example is showing the complementary situation of has_circRNA_100236, has_circRNA_102489, has_circRNA_101413, and their target miRNAs and also the predicted sponge site

Article Snippet: The Arraystar miRNA target prediction software (TargetScan & Miranda) was usd to predict the circRNA/miRNA interactions, and the circRNAs/miRNA interaction information was annotated in detail.

Techniques:

Journal: Nature ecology & evolution

Article Title: Massive gene amplification on a recently formed Drosophila Y-chromosome

doi: 10.1038/s41559-019-1009-9

Figure Lengend Snippet: Karyotype and gene content evolution on the neo-sex chromosomes of D. miranda . Shown are the karyotype of D. miranda , and its close relative D. pseudoobscura , from which it diverged about 2MY ago. In D. miranda , the fusion of an autosome (chr3) with the Y-chromosome created the neo-sex chromosomes, about 1.5 MY ago. Shown along the tree are numbers of gene amplifications (in green) and gene losses (in red) of genes ancestrally present on chr3, on the neo-X and neo-Y-chromosomes, assuming parsimony. X chromosomes are shown in red, Y-chromosomes in blue, and autosomes in black. B . Schematic representation of gene content of the D. miranda neo-Y/Y-chromosome. The D. miranda neo-Y/Y harbors different types of genes: our annotation contains 1736 ancestral single-copy genes; 1697 multi-copy Y genes (derived from 363 distinct proteins), and 2036 genes (derived from 94 distinct proteins) that co-amplified on both the X/neo-X and Y/neo-Y. Most ampliconic Y genes were ancestrally present on the autosome that formed the neo-sex chromosome (that is, they are located on chr3 of D. pseudoobscura ). “Others” refers to genes not present or mapping to an unknown location in D. pseudoobscura (446 genes), or genes with complex mapping (513 genes; see Methods). C. Pie charts show the assignment of genes on the neo-Y/Y or neo-X to these different categories (using the same color scheme as in panel B), with the size of the pie scaled by the number of genes on the neo-Y/Y or neo-X. D. Co-amplified X/Y genes typically exist as tandem repeats on the X and the Y-chromosomes. Shown is a subset of 18 co-amplified X/Y gene families with meiosis and siRNA functions.

Article Snippet: Intriguingly, however, for 457 unique single-copy D. pseudoobscura protein-coding genes, we find multiple copies in our neo-Y-chromosome annotation of D. miranda (which were all verified by manual inspection of BLAST and nucmer alignments and also confirmed by Illumina read-depth analysis, ).

Techniques: Derivative Assay, Amplification

Journal: Nature ecology & evolution

Article Title: Massive gene amplification on a recently formed Drosophila Y-chromosome

doi: 10.1038/s41559-019-1009-9

Figure Lengend Snippet: . The 94 co-amplified X/Y gene families are sorted by copy number on the Y in panels A-E. A. Copy numbers on the Y and X chromosomes for co-amplified gene families in D. miranda . B. Tissue expression patterns for co-amplified X and Y genes in D. miranda male tissues. Co-amplified X/Y genes are highly expressed in testis. C. Tissue expression patterns of homologos of co-amplified X/Y genes in D. pseudoobscura. Homologs of co-amplified X/Y genes are highly expressed in testis and ovaries, suggesting an ancestral function in gametogenesis. D. Sense- and anti-sense transcription of total RNA for co-amplified X and Y genes in D. miranda testis. E. Sense- and anti-sense counts of small RNA for co-amplified X and Y genes in D. miranda testis. F. Fraction of sense and anti-sense transcripts produced for different categories of genes on the X/neo-X and Y/neo-Y-chromosome (i.e. ancestral single-copy Y and X genes; multi-copy Y/neo-Y genes and their neo-X gametologs; genes co-amplified on the Y/neo-Y and X/neo-X). G. Enrichment of small RNAs mapping to co-amplified X and Y genes. Shown are testis small RNA counts (normalized by total gene length for all copies of a gene family) for different categories of genes on the X/neo-X and Y/neo-Y-chromosome (as in panel F). The Wilcoxon test p-value significance is denoted by asterisks. The upper whisker and lower whisker in the boxplots show the 75th percentile + 1.5 times the interquartile range and the 25th percentile - 1.5 times the inter-quartile range, respectively. The Z-Scores are calculated by scaling the rows to have 0 mean and standard deviation 1. The data shown are presented in – .

Article Snippet: Intriguingly, however, for 457 unique single-copy D. pseudoobscura protein-coding genes, we find multiple copies in our neo-Y-chromosome annotation of D. miranda (which were all verified by manual inspection of BLAST and nucmer alignments and also confirmed by Illumina read-depth analysis, ).

Techniques: Amplification, Expressing, Produced, Whisker Assay, Standard Deviation