Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Distinct MicroRNAs Identified in Rabbit Blood Arising from Induced Diabetes and a Surgically Simulated Diabetic Ischemia Complication

BACKGROUND

Diabetic complications have been studied extensively in recent years. There are very few biomarkers in body fluids that can pinpoint a distinct diabetic complication due to insufficient known specific biomarkers for ischemia.

OBJECTIVE

Identifying microRNA in animal models for each complication could enable early diagnosis of a given complication if verified in humans. MicroRNA (miRNA) profiling has been done in rodent models for a number of diabetic complications, like diabetic glomerular injury, atherosclerosis, cognitive impairment, diabetic wound healing, angiopathy and other complications. Due to multiple differences between rodents and humans, the changes in rabbit skin, considered closer to humans than even pigs, may better simulate human diabetic complications of ischemia.

METHODS

To study the miRNA profile of rabbits in which diabetes was induced or ischemia was surgically generated, we studied whether diabetes or ischemia-induced specific miRNA could be detected. MicroRNA from the blood of diabetic rabbits and rabbits with local ischemia was collected in PAXgene Blood RNA tubes specifically designed for miRNA isolation and extracted using the PAX gene miRNA extraction kit. The isolated RNA was quality controlled using an RNA analyzer, and further, using RNA seq technology, it was analyzed for distinct miRNAs that were detected in diabetic and non-diabetic rabbits induced with ischemia.

RESULTS

A miRNA that was found to be expressed in diabetic rabbits and ischemic rabbits but not in untreated rabbits was miRNA-183. Several miRNAs were differentially expressed across comparison groups, and several upregulated miRNAs were identified being unique to each comparison. In rabbits with a potential diabetic complication of a long-term ischemic model, there was one distinct microRNA, which was highly significantly upregulated in ischemia rabbit (miRNA-133-3p). One miRNA that was highly significantly upregulated in diabetic rabbit but not in ischemic rabbits was miRNA-3074-5p. Only statistically significant results have been considered and analyzed.

CONCLUSION

These findings could lead to a precise and timely diagnosis of a potential single diabetic complication without invasive tissue biopsies and could be a novel tool in the management of diabetic patients developing complications due to the progression of diabetes.

Enhancement of gut barrier function by microbial metabolite, urolithin A via AhR-Nrf2 dependent pathways in IBD

Inflammatory bowel diseases (IBD) consisting of Crohn’s and ulcerative colitis are resultant of dysregulation of the immune system leading to intestinal inflammation and microbial dysbiosis. Numerous studies in recent years highlighted the pivotal role of gut microbiota and their metabolites in host physiological processes including in IBD. Urolithin A (UroA) is a microbial metabolite derived from polyphenolics (e.g., ellagitannins/ellagic acid) of pomegranate and berries. We also synthesized a potent structural analogue of UroA (UAS03) and tested their efficacies in preventing and treating colitis in pre-clinical models. Our studies showed that UroA/UAS03 significantly enhance gut barrier function in addition to blocking unwarranted inflammation. We demonstrate that UroA and UAS03 exert their barrier functions through activation of aryl hydrocarbon receptor (AhR)- nuclear factor erythroid 2–related factor 2 (Nrf2)-dependent pathways to upregulate epithelial tight junction proteins. In addition, treatment with these compounds attenuated colitis in pre-clinical models by remedying barrier dysfunction and blocking increased inflammatory mediators such as IL-6, TNF-α and IL-1β. UroA/UAS03 failed to induce tight junction proteins and protect against 2,4,6-Trinitrobenzenesulfonic acid (TNBS)-induced colitis in AhR−/− and Nrf2−/− mice suggesting an obligatory requirement of AhR and Nrf2 pathways for UroA/UAS03 mediated beneficial activities. Overall, the results highlight how microbial metabolites provide two-pronged beneficial activities at gut epithelium by enhancing barrier functions and reducing systemic and local inflammation to protect from colonic diseases.

SUN-009 N(6)-Methyladenosine Reader HNRNPA2B1 Regulates Tamoxifen-Sensitivity in Breast Cancer Cells

The RNA methylation reader Heterogeneous Nuclear Ribonucleoprotein A2/B1 (HNRNPA2B1) is a reader of the N(6)-methyladenosine (m6A) mark in mRNA and primary-miRNAs, HNRNPA2B1 interacts directly with DGCR8 in the DROSHA complex to promote processing of pri-miRNAs to precursor-miRNAs (pre-miRNAs). We report that HNRNPA2B1 expression is higher in tamoxifen-resistant, estrogen receptor α (ERα)+ LCC9 cells derived from tamoxifen-sensitive, ERα+ MCF-7 cells. To examine how increased expression of HNRNPA2B1 affects miRNA expression, we transiently overexpressed HNRNPA2B1 in MCF-7 cells for whole genome expression profiling (RNA seq). We identified 148 miRNAs upregulated and 88 downregulated 48 h after transfection and 177 miRNAs upregulated and 172 downregulated 72 h after transfection. MetaCore Gene Ontology was used to identify pathways downstream of miRNAs altered by HNRNPA2B1. Stable overexpression (~5.4-fold increase) of HNRNPA2B1 in MCF-7 cells (~5.4-fold increase) blocked growth inhibition by fulvestrant. siHNRNPA2B1 transfection enhanced tamoxifen and fulvestrant inhibition of MCF-7 cell viability. Results suggest a role for increased HNRNPA2B1 expression in tamoxifen-resistance.

Next generation sequencing analysis of soy glyceollins and 17-β estradiol: Effects on transcript abundance in the female mouse brain

Glyceollins (Glys) are produced by soy plants in response to stress and are known for their anti-estrogenic activity both in vivo and in vitro in cancer cell lines as well as peripheral tissues. Glys can also exhibit non-estrogen receptor (ER) mediated effects. The effects of Glys on gene expression in the brain are still unclear. For this study, 17-β estradiol (E2) or placebo slow-release pellets were implanted into ovariectomized CFW mice followed by 11 days of exposure to either Glys or vehicle i.p. injections. We then examined the female mouse brain transcriptome using paired-end RNA sequencing (RNA-Seq) on the Illumina GAIIx platform. The goal of this study was to compare and contrast the results obtained from RNA-Seq with the results from our previous whole brain microarray experiment, which indicated that Glys potentially act through both ER-mediated and non-ER-mediated mechanisms, exhibiting a gene expression profile distinct from E2-treated groups. Our results suggest that the transcripts regulated by both E2 and Glys alone or in combination annotated to similar pathway maps and networks in both microarray and RNA-Seq experiments. Additionally, unlike our microarray data analysis, RNA-Seq enabled the detection of treatment effects on low expression transcripts of interest (e.g., prolactin and growth hormone). Collectively, our results suggest that depending on the gene, Glys can regulate expression independently of E2 action, similarly to E2, or oppose E2's effects in the female mouse brain.

Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data

Background

In humans, copies of the Long Interspersed Nuclear Element 1 (LINE-1) retrotransposon comprise 21% of the reference genome, and have been shown to modulate expression and produce novel splice isoforms of transcripts from genes that span or neighbor the LINE-1 insertion site.

Results

In this work, newly released pilot data from the 1000 Genomes Project is analyzed to detect previously unreported full length insertions of the retrotransposon LINE-1. By direct analysis of the sequence data, we have identified 22 previously unreported LINE-1 insertion sites within the sequence data reported for a mother/father/daughter trio.

Conclusions

It is demonstrated here that next generation sequencing data, as well as emerging high quality datasets from individual genome projects allow us to assess the amount of heterogeneity with respect to the LINE-1 retrotransposon amongst humans, and provide us with a wealth of testable hypotheses as to the impact that this diversity may have on the health of individuals and populations.

Biological Sequence Mining Using Plausible Neural Network and its Application to Exon/intron Boundaries Prediction

Biological sequence usually contains yet to find knowledge, and mining biological sequences usually involves a huge dataset and long computation time. Common tasks for biological sequence mining are pattern discovery, classification and clustering. The newly developed model, Plausible Neural Network (PNN), provides an intuitive and unified architecture for such a large dataset analysis. This paper introduces the basic concepts of the PNN, and explains how it is applied to biological sequence mining. The specific task of biological sequence mining, exon/intron prediction, is implemented by using PNN. The experimental results show the capability of solving biological sequence mining tasks using PNN.

UTR reconstruction and analysis using genomically aligned EST sequences

Untranslated regions (UTR) play important roles in the posttranscriptional regulation of mRNA processing. There is a wealth of UTR-related information to be mined from the rapidly accumulating EST collections. A computational tool, UTR-extender, has been developed to infer UTR sequences from genomically aligned ESTs. It can completely and accurately reconstruct 72% of the 3' UTRs and 15% of the 5' UTRs when tested using 908 functionally cloned transcripts. In addition, it predicts extensions for 11% of the 5' UTRs and 28% of the 3' UTRs. These extension regions are validated by examining splicing frequencies and conservation levels. We also developed a method called polyadenylation site scan (PASS) to precisely map polyadenylation sites in human genomic sequences. A PASS analysis of 908 genic regions estimates that 40-50% of human genes undergo alternative polyadenylation. Using EST redundancy to assess expression levels, we also find that genes with short 3' UTRs tend to be highly expressed.

Identity by descent genome segmentation based on single nucleotide polymorphism distributions

In the course of our efforts to build extended regions of human genomic sequence by assembling individual BAC sequences, we have encountered several instances where a region of the genome has been sequenced independently using reagents derived from two different individuals. Comparing these sequences allows us to analyze the frequency and distribution of single nucleotide polymorphisms (SNPs) in the human genome. The observed transition/transversion frequencies are consistent with a biological origin for the sequence discrepancies, and this suggests that the data produced by large sequencing centers are accurate enough to be used as the basis for SNP analysis. The observed distribution of single nucleotide polymorphisms in the human genome is not uniform. An apparent duplication in the human genome extending over more than 130 kb between chromosomes 1p34 and 16p13 is reported. Independently derived sequences covering these regions are more than 99.9% identical, indicating that this duplication event must have occurred quite recently. FISH mapping results reported by the relevant laboratories indicate that the human population may be polymorphic for this duplication. We present a population genetic theory for the expected distribution of SNPs and derive an algorithm for probabilistically segmenting genomic sequence into regions that are identical by descent (IBD) between two individuals based on this theory and the observed locations of polymorphisms. Based on these methods and a random mating model for the human population, estimates are made for the mutation rate in the human genome.