International Journal of Molecular Sciences

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State-of-the-Art Molecular Genetics and Genomics in Poland: 3rd Edition

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Special Issue Editors

Special Issue Information

Dear Colleagues,

This is a continued series of the hot topic of State-of-the-Art Molecular Genetics and Genomics in Poland. We have already done 2 successful editions of this thematic issue that received interesting contributions and discussions.

This Special Issue aims to provide a comprehensive overview of recent advances in molecular genetics and genomes in Poland by inviting contributions from Polish research institutes/laboratories that consolidate our understanding of this area.

Research articles and reviews are sought that provide insight into any aspect of molecular genetics and genomes in Poland. Topics include but are not limited to:

Gene regulation, chromatin, and epigenetics;
Genome integrity, repair, and replication;
Genetic polymorphism;
Microbial genetics;
Plant genetic and genomic studies;
Sex differences;
Genes or genomes related to phenotypes and human physiopathology;
Cancer genetics and epigenetics;
Pharmacogenetics and pharmacogenomics;
Toxicogenomics, nutrigenomics and neurogenomics, etc.;
Technological and analytical developments of genomic data;
Functional genomics.

Dr. Ewa Fiedorowicz
Prof. Dr. Anna Cieślińska
Guest Editors

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Keywords

RNA
DNA
DNA structure, damage, and repair
post-translational modifications
autophagy
cell cycle
gene expression, functions and therapy
mutation
nuclear organization
polymerase
nucleic acid–protein interactions
molecular clone
sequencing analysis
epigenetics
transcriptomics
genetics of aging
genetic disorders, SNP, etc

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28 pages, 5081 KB

Open AccessArticle

Comprehensive Profiling of the miRNome and Degradome Reveals Regulatory Signatures of Seed Aging and Germination

by Marta Puchta-Jasińska, Paulina Bolc, Adrian Motor, Andreas Börner and Maja Boczkowska

Int. J. Mol. Sci. 2025, 26(19), 9292; https://doi.org/10.3390/ijms26199292 - 23 Sep 2025

Viewed by 208

Abstract

Small noncoding RNAs are recognized as crucial regulators of seed germination, but their role in seed aging remains unclear. To address this, we performed RNA sequencing (RNA-seq) on barley (Hordeum vulgare L.) seeds with varying viability levels after long-term storage in hermetically sealed containers since the 1972 harvest. This globally unique material, characterized by genetic homogeneity and contrasting germination capacities, enabled an in-depth analysis of microtranscriptomic changes during germination. We identified 62 known miRNAs from 11 families and 234 novel miRNAs, with miR159, miR168, and miR166 showing consistently high expression across all germination stages and viability groups. Differential expression analysis revealed 28 miRNAs whose abundance varied significantly with seed viability and germination phase. Functional predictions supported by quantitative reverse transcription PCR (qRT–PCR) and degradome-based target identification indicated that these miRNAs regulate key developmental and metabolic pathways. Several isomiRs exhibited sample-specific expression, suggesting the viability-dependent activation of distinct molecular mechanisms. Gene Ontology analysis highlighted processes related to nucleic acid binding, nuclear organization, and cytoplasmic metabolism as central during germination. We propose that miRNA profiles may reflect an “epigenetic inheritance”—a molecular memory of aging stored in seeds—rather than solely a response to current conditions. This concept may help explain aging-related phenotypes such as delayed germination and reduced vigor, warranting further investigation. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland: 3rd Edition)

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