bims-micpro 2023-01-15 papers

Methods. 2023 Jan 05. pii: S1046-2023(22)00248-1. [Epub ahead of print]

Prediction of protein-coding small ORFs in multi-species using integrated sequence-derived features and the random forest model.

Jiafeng Yu, Wenwen Jiang, Sen-Bin Zhu, Zhen Liao, Xianghua Dou, Jian Liu, Feng-Biao Guo, Chuan Dong.

Proteins encoded by small open reading frames (sORFs) can serve as functional elements playing important roles in vivo. Such sORFs also constitute the potential pool for facilitating the de novo gene birth, driving evolutionary innovation and species diversity. Therefore, their theoretical and experimental identification has become a critical issue. Herein, we proposed a protein-coding sORFs prediction method merely based on integrative sequence-derived features. Our prediction performance is better or comparable compared with other nine prevalent methods, which shows that our method can provide a relatively reliable research tool for prediction of protein-coding sORFs. Our method allows users to estimate the potential expression of a queried sORF, which has been demonstrated by the correlation analysis between our possibility estimation and codon adaption index (CAI). Based on the features that we used, we demonstrated that the sequence features of the protein-coding sORFs in the two domains have significant differences implying that it might be a relatively hard task in terms of cross-domain prediction, hence domain-specific models were developed, which allowed users to predict protein-coding sORFs both in eukaryotes and prokaryotes. Finally, a web-server was developed and provided to boost and facilitate the study of the related field, which is freely available at http://guolab.whu.edu.cn/codingCapacity/index.html.

Keywords: Protein-coding sORFs; Random forest-based model; Sequence-derived features

DOI: https://doi.org/10.1016/j.ymeth.2022.12.003

Front Oncol. 2022 ;12 1081997

Advances in peptides encoded by non-coding RNAs: A cargo in exosome.

Jing Yang, Mengxiao Liu, Xidong Fang, Huiyun Zhang, Qian Ren, Ya Zheng, Yuping Wang, Yongning Zhou.

The metastasis of malignant tumors determines patient prognosis. This is the main reason for the poor prognosis of patients with cancer and the most challenging aspect of treating malignant tumors. Therefore, it is important to identify early tumor markers and molecules that can predict patient prognosis. However, there are currently no molecular markers with good clinical accuracy and specificity. Many non-coding RNA (ncRNAs)have been identified, which can regulate the process of tumor development at multiple levels. Interestingly, some ncRNAs are translated to produce functional peptides. Exosomes act as signal carriers, are encapsulated in nucleic acids and proteins, and play a messenger role in cell-to-cell communication. Recent studies have identified exosome peptides with potential diagnostic roles. This review aims to provide a theoretical basis for ncRNA-encoded peptides or proteins transported by exosomes and ultimately to provide ideas for further development of new diagnostic and prognostic cancer markers.

Keywords: cancer; exosome; non-coding RNA; peptide; translation

DOI: https://doi.org/10.3389/fonc.2022.1081997

Brief Bioinform. 2023 Jan 05. pii: bbac610. [Epub ahead of print]

slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences.

Bo Song, Hao Li, Mengyun Jiang, Zhongtian Gao, Suikang Wang, Lei Gao, Yunsheng Chen, Wujiao Li.

Trans-splicing of a spliced leader (SL) to the 5' ends of mRNAs is used to produce mature mRNAs in several phyla of great importance to human health and the marine ecosystem. One of the consequences of the addition of SL sequences is the change or disruption of the open reading frames (ORFs) in the recipient transcripts. Given that most SL sequences have one or more of the trinucleotide NUG, including AUG in flatworms, trans-splicing of SL sequences can potentially supply a start codon to create new ORFs, which we refer to as slORFs, in the recipient mRNAs. Due to the lack of a tool to precisely detect them, slORFs were usually neglected in previous studies. In this work, we present the tool slORFfinder, which automatically links the SL sequences to the recipient mRNAs at the trans-splicing sites identified from SL-containing reads of RNA-Seq and predicts slORFs according to the distribution of ribosome-protected footprints (RPFs) on the trans-spliced transcripts. By applying this tool to the analyses of nematodes, ascidians and euglena, whose RPFs are publicly available, we find wide existence of slORFs in these taxa. Furthermore, we find that slORFs are generally translated at higher levels than the annotated ORFs in the genomes, suggesting they might have important functions. Overall, this study provides a tool, slORFfinder (https://github.com/songbo446/slORFfinder), to identify slORFs, which can enhance our understanding of ORFs in taxa with SL machinery.

Keywords: open reading frames; ribosome footprints; spliced leader; trans-splicing

DOI: https://doi.org/10.1093/bib/bbac610