Joshi Dheeraj Chandra, Kadam Aakanksha, Sachidanandan Chetana, Pillai Beena
CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
Bioinform Adv. 2025 Jun 12;5(1):vbaf139. doi: 10.1093/bioadv/vbaf139. eCollection 2025.
Inherited non-coding RNAs can be the third major component of epigenetic information transfer from one generation to the next. Here, we present a comprehensive resource of lncRNAs and circular RNAs that are inherited, compiled from meta-analysis of zebrafish transcriptomics data and comparative genomics with mouse and human. Maternal and paternal inheritance of mRNA into the zygote is accepted to be an important regulator of embryonic development as well as adult characteristics. Although inheritance of certain specific miRNAs is known, other non-coding RNA inheritance remains less explored.
We performed a comprehensive analysis of the inherited lncRNAs and circRNAs in zebrafish. We discovered that nearly 20% of all known lncRNA and 7% of circRNAs are inherited. Many of these lncRNAs are conserved in mammals, and are expressed widely in adult tissues of zebrafish. The male and female gametes carry a highly similar pool of inherited lncRNAs, with only a few sperm/oocyte specific transcripts. The majority of inherited circRNAs originate from genes important for fertilization and can potentially regulate translational processes. Contrary to general belief, the inherited lncRNAs and circRNAs do not undergo degradation en masse coincidental to zygotic genomic activation, suggesting that these RNAs may have more sustained roles in development.
遗传性非编码RNA可能是表观遗传信息从一代传递到下一代的第三个主要组成部分。在此，我们展示了一份全面的遗传性长链非编码RNA（lncRNA）和环状RNA资源，这些资源是通过对斑马鱼转录组学数据的荟萃分析以及与小鼠和人类的比较基因组学汇编而成的。母体和父体的mRNA传递到受精卵中被认为是胚胎发育以及成年特征的重要调节因子。尽管某些特定微小RNA（miRNA）的遗传性是已知的，但其他非编码RNA的遗传性仍有待深入研究。
我们对斑马鱼中遗传性lncRNA和环状RNA进行了全面分析。我们发现，所有已知lncRNA中近20%以及环状RNA中7%是可遗传的。这些lncRNA中有许多在哺乳动物中是保守的，并且在斑马鱼的成年组织中广泛表达。雄性和雌性配子携带的遗传性lncRNA库高度相似，只有少数精子/卵母细胞特异性转录本。大多数遗传性环状RNA起源于对受精重要的基因，并可能潜在地调节翻译过程。与普遍看法相反，遗传性lncRNA和环状RNA在合子基因组激活时并不会同时大量降解，这表明这些RNA可能在发育过程中发挥更持久的作用。
