bims-micpro 2026-05-31 papers

J Biomol Struct Dyn. 2026 May 28. 1-16

mePTL: miRNA-encoded peptides identification using multi-source feature transformation and ensemble learning.

MicroRNA (miRNA) is a type of non-coding RNA and participates in the post-transcriptional control of genes to regulate the expression of target genes. Inspired by the discovery of small peptides translated from other ncRNAs, small open reading frames (sORFs) of plant primary miRNA (pri-miRNA) have been demonstrated to encode small peptides, known as miPEPs. So far, the number of identified functional miPEPs has gradually increased but still remains concentrated in plant. Although miPEPs are involved in a range of life activities in organisms, few methods have been developed to identify plant miPEPs. In this article, we present a novel computational method (mePTL) that uses multi-source feature transformation and ensemble learning to identify miPEPs. Multi-source features, rich in representation information and extracted from class-imbalanced miPEPs and sORFs data, are transformed by a feature representation learning framework. Ensemble learning is applied to fuse the outputs of different machine learning models trained on the transformation features to enhance generalization ability. Experimental results show that mePTL achieves better performance compared with the existing methods on multiple independent-test sets. mePTL shows good accuracy as well as generalization ability in identifying miPEPs, and we hope the method can provide some reference for research in related fields.

Keywords: Class-imbalanced data; ensemble learning; feature transformation; miPEPs; multi-source features; sORFs

DOI: https://doi.org/10.1080/07391102.2026.2677004

Planta. 2026 May 26. pii: 4. [Epub ahead of print]264(1):

Functional characterisation of the 5' UTR of two PEPCs in Suaeda aralocaspica, a halophyte with C4 photosynthesis pathway in a single polarised cell.

Zhimin Xu, Yanxia Liu, Mengyu Yan, Haiyan Lan.

MAIN CONCLUSION: The 5' UTRs of PEPCs in Suaeda aralocaspica repress gene expression via intron sequence and upstream ORFs, and contain candidate cis-acting elements that may be associated with differential transcriptional responses under ionic and osmotic stress conditions. The 5' untranslated region (5' UTR) plays a pivotal role in controlling gene expression during plant development and stress responses. It contains regulatory elements such as internal ribosome entry sites, upstream open reading frames (uORF), introns, and secondary structures, which collectively enable precisely translational control. Variations in these elements can give rise to multiple mRNA isoforms, thereby influencing gene expression levels. In this study, we analysed the 5' UTR of two key photosynthetic enzyme genes, PEPC1 and PEPC2, from Suaeda aralocaspica, a halophyte with C4 photosynthesis pathway in a single polarised cell. GUS and dual-luciferase reporter assays examined the effects of mutation in the 5' UTR, in particular its intron and uORFs on reporter gene expression. Both 5' UTRs significantly repressed PEPC gene expression, with the SaPEPC2 5' UTR exhibiting a stronger effect. Further dissection revealed that the SaPEPC2 5' UTR harbours greater sequence and structural complexity, including one intron and four uORFs critical for its repressive function. Moreover, transgenic Arabidopsis carrying these 5' UTRs showed differential reporter activity under NaCl and mannitol treatments, suggesting that candidate cis-acting elements within the 5' UTR may be involved in abiotic stress-related regulation. These findings indicate the 5' UTR as an important regulatory element for PEPC expression in heterologous reporter systems and provide a foundation for investigating its physiological role in halophytes.

Keywords: Suaeda aralocaspica ; 5′ UTR; Intron; Promoter; uORF

DOI: https://doi.org/10.1007/s00425-026-05028-5

J Anim Sci Biotechnol. 2026 May 29. pii: 103. [Epub ahead of print]17(1):

Integrative analysis of RNA-seq and Ribo-seq reveals that lncRNA regulates chicken myogenesis through encoding peptide.

Yufang Niu, Liyang He, Zhiyuan An, Meng Yuan, Haigang Ji, Wei Wang, Chengjie Wei, Ruili Han, Weihua Tian, Yadong Tian, Xiaojun Liu, Xiangtao Kang, Zhuanjian Li.

BACKGROUND: Long noncoding RNAs (lncRNAs) participate in various critical regulatory steps during myogenesis. LncRNAs can encode small peptides, which can regulate gene expression through multiple mechanisms, thereby participating in key biological processes.
RESULTS: The lncRNAs were screened between proliferating and differentiating myoblast in chicken through RNA-seq and Ribo-seq. As a result, 178 DE-lncRNAs were identified in RNA-seq, and three of them were identified as differentially translated lncRNAs by Ribo-seq. Among them, lncMPD, which showed coding potential, was highly expressed in proliferating myoblast. It encoded a small peptide containing 74 amino acids, which was named MPD-74aa. MPD-74aa was validated via WB and mass spectrometry. We subsequently confirmed that MPD-74aa promotes myoblast proliferation and inhibits its differentiation. Co-IP revealed that MPD-74aa interacts with the protein CDK1. Moreover, MPD-74aa positively regulated the expression of CDK1.
CONCLUSION: This study confirms that the lncMPD plays a crucial regulatory role in the chicken myogenesis by encoding the small peptide MPD-74aa. Mechanistically, MPD-74aa exerts its regulatory function through interaction with CDK1, a key protein marker of cell proliferation. These findings provide new insight into the molecular mechanisms about the coding capacity of lncRNA regulating chicken muscle development.

Keywords: Differentiation; LncRNA; MPD-74aa; Myoblasts; Proliferation

DOI: https://doi.org/10.1186/s40104-026-01421-y