Retro-miRs: novel and functional miRNAs originating from mRNA retrotransposition.

BACKGROUND: Reverse-transcribed gene copies (retrocopies) have emerged as major sources of evolutionary novelty. MicroRNAs (miRNAs) are small and highly conserved RNA molecules that serve as key post-transcriptional regulators of gene expression. The origin and subsequent evolution of miRNAs have been addressed but not fully elucidated. RESULTS: In this study, we performed a comprehensive investigation of miRNA origination through retroduplicated mRNA sequences (retro-miRs). We identified 17 retro-miRs that emerged from the mRNA retrocopies. Four of these retro-miRs had de novo origins within retrocopied sequences, while 13 retro-miRNAs were located within exon regions and duplicated along with their host mRNAs. We found that retro-miRs were primate-specific, including five retro-miRs conserved among all primates and two human-specific retro-miRs. All retro-miRs were expressed, with predicted and experimentally validated target genes except miR-10527. Notably, the target genes of retro-miRs are involved in key biological processes such as metabolic processes, cell signaling, and regulation of neurotransmitters in the central nervous system. Additionally, we found that these retro-miRs play a potential oncogenic role in cancer by targeting key cancer genes and are overexpressed in several cancer types, including liver hepatocellular carcinoma and stomach adenocarcinoma. CONCLUSIONS: Our findings demonstrated that mRNA retrotransposition is a key mechanism for the generation of novel miRNAs (retro-miRs) in primates. These retro-miRs are expressed, conserved, have target genes with important cellular functions, and play important roles in cancer.

Associations between neighborhood-level factors and opioid-related mortality: A multi-level analysis using death certificate data.

AIM: To identify associations between opioid-related mortality and neighborhood-level risk factors. DESIGN: Cross-sectional study. SETTING: Massachusetts, USA. PARTICIPANTS: Using 2011-14 Massachusetts death certificate data, we identified opioid-related (n = 3089) and non-opioid-related premature deaths (n = 8729). MEASUREMENTS: The independent variables consisted of four sets of neighborhood-level factors: (1) psychosocial, (2) economic, (3) built environment and (4) health-related. At the individual level we included the following compositional factors: age at death, sex, race/ethnicity, marital status, education, veteran status and nativity. The primary outcome of interest was opioid-related mortality. FINDINGS: Multi-level models identified number of social associations per 10 000 [odds ratio (OR) = 0.84, P = 0.002, 95% confidence interval (CI) = 0.75-0.94] and number of hospital beds per 10 000 (OR = 0.78, P < 0.001, 95% CI = 0.68-0.88) to be inversely associated with opioid-related mortality, whereas the percentage living in poverty (OR = 1.01, P = 0.008, 95% CI = 1.00-1.01), food insecurity rate (OR = 1.21, P = 0.002, 95% CI = 1.07-1.37), number of federally qualified health centers (OR = 1.02, P = 0.028, 95% CI = 1.02-1.08) and per-capita morphine milligram equivalents of hydromorphone (OR = 1.05, P = 0.003, 95% CI = 1.01-1.08) were positively associated with opioid-related mortality. CONCLUSIONS: Opioid-related deaths between 2011 and 2014 in the state of Massachusetts appear to be positively associated with the percentage living in poverty, food insecurity rate, number of federally qualified health centers and per-capita morphine milligram equivalents of hydromorphone, but inversely associated with number of social associations per 10 000 and number of hospital beds per 10 000.

An investigation of Y chromosome incorporations in 400 species of Drosophila and related genera.

Y chromosomes are widely believed to evolve from a normal autosome through a process of massive gene loss (with preservation of some male genes), shaped by sex-antagonistic selection and complemented by occasional gains of male-related genes. The net result of these processes is a male-specialized chromosome. This might be expected to be an irreversible process, but it was found in 2005 that the Drosophila pseudoobscura Y chromosome was incorporated into an autosome. Y chromosome incorporations have important consequences: a formerly male-restricted chromosome reverts to autosomal inheritance, and the species may shift from an XY/XX to X0/XX sex-chromosome system. In order to assess the frequency and causes of this phenomenon we searched for Y chromosome incorporations in 400 species from Drosophila and related genera. We found one additional large scale event of Y chromosome incorporation, affecting the whole montium subgroup (40 species in our sample); overall 13% of the sampled species (52/400) have Y incorporations. While previous data indicated that after the Y incorporation the ancestral Y disappeared as a free chromosome, the much larger data set analyzed here indicates that a copy of the Y survived as a free chromosome both in montium and pseudoobscura species, and that the current Y of the pseudoobscura lineage results from a fusion between this free Y and the neoY. The 400 species sample also showed that the previously suggested causal connection between X-autosome fusions and Y incorporations is, at best, weak: the new case of Y incorporation (montium) does not have X-autosome fusion, whereas nine independent cases of X-autosome fusions were not followed by Y incorporations. Y incorporation is an underappreciated mechanism affecting Y chromosome evolution; our results show that at least in Drosophila it plays a relevant role and highlight the need of similar studies in other groups.

Improved assembly of noisy long reads by k-mer validation.

Genome assembly depends critically on read length. Two recent technologies, from Pacific Biosciences (PacBio) and Oxford Nanopore, produce read lengths >20 kb, which yield de novo genome assemblies with vastly greater contiguity than those based on Sanger, Illumina, or other technologies. However, the very high error rates of these two new technologies (∼15% per base) makes assembly imprecise at repeats longer than the read length and computationally expensive. Here we show that the contiguity and quality of the assembly of these noisy long reads can be significantly improved at a minimal cost, by leveraging on the low error rate and low cost of Illumina short reads. Namely, k-mers from the PacBio raw reads that are not present in Illumina reads (which account for ∼95% of the distinct k-mers) are deemed sequencing errors and ignored at the seed alignment step. By focusing on the ∼5% of k-mers that are error free, read overlap sensitivity is dramatically increased. Of equal importance, the validation procedure can be extended to exclude repetitive k-mers, which prevents read miscorrection at repeats and further improves the resulting assemblies. We tested the k-mer validation procedure using one long-read technology (PacBio) and one assembler (MHAP/Celera Assembler), but it is very likely to yield analogous improvements with alternative long-read technologies and assemblers, such as Oxford Nanopore and BLASR/DALIGNER/Falcon, respectively.