Lariat intronic RNAs in the cytoplasm of Xenopus tropicalis oocytes

Abstract

We previously demonstrated that the oocyte nucleus (germinal vesicle or GV) of Xenopus tropicalis contains a population of stable RNA molecules derived from the introns of most expressed genes. Here we show that similar stable intronic sequence (sis) RNAs occur in the oocyte cytoplasm. About 9000 cytoplasmic sisRNAs have been identified, all of which are resistant to the exonuclease RNase R. About half have been confirmed as lariat molecules and the rest are presumed to be lariats, whereas nuclear sisRNAs are a mixture of lariat and linear molecules. Cytoplasmic sisRNAs are more abundant on a molar basis than nuclear sisRNAs and are derived from short introns, mostly under 1 kb in length. Both nuclear and cytoplasmic sisRNAs are transmitted intact to the egg at GV breakdown and persist until at least the blastula stage of embryogenesis, when zygotic transcription begins. We compared cytoplasmic sisRNAs derived from orthologous genes of X. tropicalis and X. laevis, and found that the specific introns from which sisRNAs are derived are not conserved. The existence of sisRNAs in the cytoplasm of the oocyte, their transmission to the fertilized egg, and their persistence during early embryogenesis suggest that they might play a regulatory role in mRNA translation.

Zygotic Genome Activation in Vertebrates

“…Thus, intronic read levels from RNA-seq likely correlate with nascent embryonic transcription (Lee et al, 2013), and can be used to define zygotic gene timing. However, the recently discovered circular RNAs–which can contain unspliced introns–expressed in human oocytes and embryos (Dang et al, 2016) and stable intronic sequences (sisRNAs) in early frog embryos can be confounding factors (Talhouarne and Gall, 2014). …”

Circular RNA participates in the carcinogenesis and the malignant behavior of cancer

“…Investigators found that intronic circRNAs can be duplicated in plasma and directly passed on to off-spring via mitosis, which hinted at the potential roles of intronic circRNAs in epigenetics and RNA-mediated inheritance. 29 Given the fact that the introns in the linear form are engaged in the mechanism to minimize tissue-inappropriate gene expression, the biological function of intronic circRNAs is close to being discovered in the near future. 30 Beyond regulating microRNAs, circRNAs may bind to and sequester RNA-binding proteins (RBPs) via their conserved seed matches, resulting in the formation of large RNA-protein complexes.…”

Sequencing of lariat termini in S. cerevisiae reveals 5′ splice sites, branch points, and novel splicing events

“…Thus, the lariat intron product offers a faithful, efficient, and direct alternative to mRNA for studying splicing genome-wide. Importantly, capturing the full landscape of introns, or the intronome, can provide insight into the production of not only mRNAs but also intron-encoded ncRNAs, such as small nucleolar RNAs, microRNAs, and some intronic circRNAs (Zhang et al 2013;Hesselberth 2014;Talhouarne and Gall 2014).…”