Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner.

Recently developed long-read RNA sequencing technologies promise to provide a more accurate and comprehensive view of transcriptomes compared to short-read sequencers, primarily due to their capability to achieve full-length sequencing of transcripts. However, realizing this potential requires computational tools tailored to process long reads, which exhibit a higher error rate than short reads. Existing methods for assembling and quantifying long-read data often disagree on expressed transcripts and their abundance levels, leading researchers to lack confidence in the transcriptomes produced using this data. One approach to address the uncertainties in transcriptome assembly and quantification is by assigning the long reads to transcripts, enabling a more detailed characterization of transcript support at the read level. Here, we introduce TranSigner, a versatile tool that assigns long reads to any input transcriptome. TranSigner consists of three consecutive modules performing: read alignment to the given transcripts, computation of read-to-transcript compatibility based on alignment scores and positions, and execution of an expectation-maximization algorithm to probabilistically assign reads to transcripts and estimate transcript abundances. Using simulated data and experimental datasets from three well-studied organisms - Homo sapiens, Arabidopsis thaliana, and Mus musculus - we demonstrate that TranSigner achieves accurate read assignments, obtaining higher accuracy in transcript abundance estimation compared to existing tools.

Upstream open reading frames may contain hundreds of novel human exons.

Several recent studies have presented evidence that the human gene catalogue should be expanded to include thousands of short open reading frames (ORFs) appearing upstream or downstream of existing protein-coding genes, each of which would comprise an additional bicistronic transcript in humans. Here we explore an alternative hypothesis that would explain the translational and evolutionary evidence for these upstream ORFs without the need to create novel genes or bicistronic transcripts. We examined 2,199 upstream ORFs that have been proposed as high-quality candidates for novel genes, to determine if they could instead represent protein-coding exons that can be added to existing genes. We checked for the conservation of these ORFs in four recently sequenced, high-quality human genomes, and found a large majority (87.8%) to be conserved in all four as expected. We then looked for splicing evidence that would connect each upstream ORF to the downstream protein-coding gene at the same locus, thus creating a novel splicing variant using the upstream ORF as its first exon. These protein coding exon candidates were further evaluated using protein structure predictions of the protein sequences that included the proposed new exons. We determined that 582 out of 2,199 upstream ORFs have strong evidence that they can form protein coding exons that are part of an existing gene, and that the resulting protein is predicted to have similar or better structural quality than the currently annotated isoform.

EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes.

Accurate alignment of transcribed RNA to reference genomes is a critical step in the analysis of gene expression, which in turn has broad applications in biomedical research and in the basic sciences. We reveal that widely used splice-aware aligners, such as STAR and HISAT2, can introduce erroneous spliced alignments between repeated sequences, leading to the inclusion of falsely spliced transcripts in RNA-seq experiments. In some cases, the 'phantom' introns resulting from these errors make their way into widely-used genome annotation databases. To address this issue, we present EASTR (Emending Alignments of Spliced Transcript Reads), a software tool that detects and removes falsely spliced alignments or transcripts from alignment and annotation files. EASTR improves the accuracy of spliced alignments across diverse species, including human, maize, and Arabidopsis thaliana, by detecting sequence similarity between intron-flanking regions. We demonstrate that applying EASTR before transcript assembly substantially reduces false positive introns, exons, and transcripts, improving the overall accuracy of assembled transcripts. Additionally, we show that EASTR's application to reference annotation databases can detect and correct likely cases of mis-annotated transcripts.

IL-4 Induces CD4+CD25+ Regulatory T Cells from CD4+CD25- T Cells in Peripheral Blood / 대한류마티스학회지

OBJECTIVE: The CD4+CD25+ regulatory T cells (Treg) can be induced by TGFbeta and IL-10 in the periphery, and understanding the biological function of cytokine-induced Treg is critically important for the control of autoimmune diseases. We investigated the IL-4-induced CD4+CD25+ regulatory T cells in human PBMCs, which were derived from the CD4+CD25- T cells. METHODS: The CD4+CD25- T cells from human PBMC were isolated by MACS and cultured in the presence of IL-4 or absence of IL-4. The presence and phenotype of induced CD4+CD25+ T cells were determined by flow cytometry. Supressive activity of induced CD4+CD25+ T cells were assessed by culturing CD4+CD25- and CD4+CD25+ T cells with anti-CD3 monoclonal antibodies and antigen-presenting cells, followed by proliferation RESULTS: After 5 days, significant amount of CD4+CD25+ T cells were generated from the CD4+CD25- T cells cultured with anti-CD3 antibody in the presence of IL-4. These IL-4 induced CD4+CD25+ T cells presented with similar phenotype to natural occurred Treg cells, including CD45RO(hi), CD45RA(lo), CTLA-4(hi), OX40(hi), CD62L(hi) and HLA-DR(hi), and also exhibited high expression of Foxp3 molecule. In addition, the IL-4 induced CD4+CD25+ T cells can suppress the proliferative responses against anti-CD3. The regulatory property of IL-4 induced CD4+CD25+ T cell was partially abrogated after treatment with anti-IL-10 and anti-TGFbeta antibodies. CONCLUSION: These data indicate that IL-4 induced CD4+CD25+ Treg cells can be generated from the CD4+CD25- T cells in the peripheral blood, and may contribute to the important immunoregulatory function in human.