Single-cell RNA sequencing reveals dynamic changes in A-to-I RNA editome during early human embryogenesis

Qiu, Si; Li, Wenhui; Xiong, Heng; Bai, Yang; Wu, Kui; Zhang, Xiuqing; Yang, Huanming; Ma, Kun; Hou, Yong; Li, Bo

doi:10.1186/s12864-016-3115-2

Cited by 29 publications

(33 citation statements)

References 35 publications

(42 reference statements)

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“…RNA‐sequencing provides an unprecedented opportunity to identify RNA editing sites in yeast, fungi , humans, and plants (Bruno et al ., ; Peng et al ., ; Bentolila et al ., ; Eifler et al ., ; Qiu et al ., ). We identified 692 RNA editing sites in the mitochondrial genome of G. hirsutum , based on analysis of RNA‐seq datasets.…”

Section: Discussionmentioning

confidence: 97%

Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation

Xiao

Líu

et al. 2018

New Phytologist

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RNA editing is a post-transcriptional maturation process affecting organelle transcripts in land plants. However, the molecular functions and physiological roles of RNA editing are still poorly understood. Using high-throughput sequencing, we identified 692 RNA editing sites in the Gossypium hirsutum mitochondrial genome. A total of 422 editing sites were found in the coding regions and all the edits are cytidine (C) to uridine (U) conversions. Comparative analysis showed that two editing sites in Ghatp1, C1292 and C1415, had a prominent difference in editing efficiency between fiber and ovule. Biochemical and genetic analyses revealed that the two vital editing sites were important for the interaction between the α and β subunits of ATP synthase, which resulted in ATP accumulation and promoted cell growth in yeast. Ectopic expression of C1292, C1415, or doubly edited Ghatp1 in Arabidopsis caused a significant increase in the number of trichomes in leaves and root length. Our results indicate that editing at C1292 and C1415 sites in Ghatp1 is crucial for ATP synthase to produce sufficient ATP for cotton fiber cell elongation. This work extends our understanding of RNA editing in atp1 and ATP synthesis, and provides insights into the function of mitochondrial edited Atp1 protein in higher plants.

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Section: Discussionmentioning

confidence: 97%

Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation

Xiao

Líu

et al. 2018

New Phytologist

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“…Here, three transcript isoforms with TPM = 0 in 21 cells were dropped, and expression profiles of 6 transcript isoforms were analyzed (Figure 7B). Qiu et al (2016) constructed A-to-I RNA editome during early human embryogenesis and demonstrated Adar expression and A-to-I RNA editing level remained relatively stable until 4-cell stage, but dramatically decreased at 8-cell stage, continually decreased at morula stage. Similar to human embryogenesis, in mouse embryogenesis, we demonstrated Adar expression level was stable and remarkably elevated until 2-cell stage, but sharply decreased at 4-cell stage, continually decreased until blastocysts stage.…”

Section: The Identification Of Iss In Consecutive Stages Of Preimplanmentioning

confidence: 99%

Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development

Xing

Yang

Liu

et al. 2020

Front. Bioeng. Biotechnol.

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The mechanism of alternative pre-mRNA splicing (AS) during preimplantation development is largely unknown. In order to capture the dynamic changes of AS occurring during embryogenesis, we carried out bioinformatics analysis based on scRNA-seq data over the time-course preimplantation development in mouse. We detected numerous previously-unreported differentially expressed genes at specific developmental stages and investigated the nature of AS at both minor and major zygotic genome activation (ZGA). The AS and differential AS atlas over preimplantation development were established. The differentially alternatively spliced genes (DASGs) are likely to be key splicing factors (SFs) during preimplantation development. We also demonstrated that there is a regulatory cascade of AS events in which some key SFs are regulated by differentially AS of their own gene transcripts. Moreover, 212 isoform switches (ISs) during preimplantation development were detected, which may be critical for decoding the mechanism of early embryogenesis. Importantly, we uncovered that zygotic AS activation (ZASA) is in conformity with ZGA and revealed that AS is coupled with transcription during preimplantation development. Our results may provide a deeper insight into the regulation of early embryogenesis.

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“…Enzymes triggering RNA editing are essential for several processes requiring cell growth and adaptation (e.g., embryogenesis, proliferation, immunity and neural plasticity) [27][28][29]. In this respect, activity of editing enzymes can lead to various functional cellular outcomes depending on the RNA molecules being modified and of the type of modification.…”

Section: Editing Of Mirnamentioning

confidence: 99%

“…In early stages of human embryogenesis (eight cells to the morula stage), RNA editing activity was reported to be low [27], but whether this observation can be extrapolated to miRNA editing is unknown. Nevertheless, in murine E15 embryonic stage miRNA editing events were reported to be rare, but to increase with postnatal development [122].…”

Section: Developmentmentioning

confidence: 99%

Deciphering miRNAs’ Action through miRNA Editing

Sousa

Gjorgjieva

Dolicka

et al. 2019

IJMS

635

343

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MicroRNAs (miRNAs) are small non-coding RNAs with the capability of modulating gene expression at the post-transcriptional level either by inhibiting messenger RNA (mRNA) translation or by promoting mRNA degradation. The outcome of a myriad of physiological processes and pathologies, including cancer, cardiovascular and metabolic diseases, relies highly on miRNAs. However, deciphering the precise roles of specific miRNAs in these pathophysiological contexts is challenging due to the high levels of complexity of their actions. Indeed, regulation of mRNA expression by miRNAs is frequently cell/organ specific; highly dependent on the stress and metabolic status of the organism; and often poorly correlated with miRNA expression levels. Such biological features of miRNAs suggest that various regulatory mechanisms control not only their expression, but also their activity and/or bioavailability. Several mechanisms have been described to modulate miRNA action, including genetic polymorphisms, methylation of miRNA promoters, asymmetric miRNA strand selection, interactions with RNA-binding proteins (RBPs) or other coding/non-coding RNAs. Moreover, nucleotide modifications (A-to-I or C-to-U) within the miRNA sequences at different stages of their maturation are also critical for their functionality. This regulatory mechanism called "RNA editing" involves specific enzymes of the adenosine/cytidine deaminase family, which trigger single nucleotide changes in primary miRNAs. These nucleotide modifications greatly influence a miRNA's stability, maturation and activity by changing its specificity towards target mRNAs. Understanding how editing events impact miRNA's ability to regulate stress responses in cells and organs, or the development of specific pathologies, e.g., metabolic diseases or cancer, should not only deepen our knowledge of molecular mechanisms underlying complex diseases, but can also facilitate the design of new therapeutic approaches based on miRNA targeting. Herein, we will discuss the current knowledge on miRNA editing and how this mechanism regulates miRNA biogenesis and activity.

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Single-cell RNA sequencing reveals dynamic changes in A-to-I RNA editome during early human embryogenesis

Cited by 29 publications

References 35 publications

Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation

Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation

Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development

Deciphering miRNAs’ Action through miRNA Editing

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