scholarly journals Small RNA-directed DNA elimination: the molecular mechanism and its potential for genome editing

RNA Biology ◽  
2021 ◽  
pp. 1-6
Author(s):  
Carolien Bastiaanssen ◽  
Chirlmin Joo
Keyword(s):  
Genome Editing ◽  
Molecular Mechanism ◽  
Small Rna ◽  
Dna Elimination

scholarly journals Small RNA-Mediated trans-Nuclear and trans-Element Communications in Tetrahymena DNA Elimination

2018 ◽  
Vol 28 (12) ◽  
pp. 1938-1949.e5 ◽  
Author(s):  
Tomoko Noto ◽  
Kazufumi Mochizuki
Keyword(s):  
Small Rna ◽  
Dna Elimination

scholarly journals Correction of RNA splicing defect in β654-thalassemia mice using CRISPR/Cas9 gene-editing technology

Haematologica ◽  
2021 ◽  
Author(s):  
Dan Lu ◽  
Xiuli Gong ◽  
Yudan Fang ◽  
Xinbing Guo ◽  
Yanwen Chen ◽  
...  
Keyword(s):  
Survival Rate ◽  
Genome Editing ◽  
Molecular Mechanism ◽  
Splice Site ◽  
Rna Splicing ◽  
Gene Editing ◽  
Clinical Symptoms ◽  
Rna Expression ◽  
Wild Type ◽  
Acceptor Splice Site

β654-thalassemia is a prominent Chinese subtype of β-thalassemia, representing 17% of total β-thalassemia cases in China. The molecular mechanism underlying this subtype involves the IVS-2-654 C→T mutation leading to aberrant β-globin RNA splicing. This results in an additional 73-nucleotide exon between exons 2 and 3 and leads to severe thalassemia syndrome. Herein, we explored a CRISPR/Cas9 genome editing approach to eliminate the additional 73-nt by targeting both the IVS-2-654 C→T and a cryptic acceptor splice site at IVS-2-579 in order to correct aberrant β-globin RNA splicing and ameliorate the clinical β-thalassemia syndrome in β654 mice. Gene-edited mice were generated by microinjection of sgRNAs and Cas9 mRNAs into 1-cell embryos of β654 or control mice. 83.3% of live-born mice were gene-edited, 70% of which produced correctly spliced RNA. No off-target events were observed. The clinical symptoms, including hematologic parameters and tissue pathology of all of the edited-β654 founders and their offspring, were significantly improved compared to the non-edited β654 mice, consistent with the restoration of wild-type β-globin RNA expression. Notably, the survival rate of gene-edited heterozygous β654 mice increased significantly, and live-born homozygous β654 mice were observed. Our study demonstrated a new and effective gene-editing approach that may provide a groundwork for the exploration of β654-thalassemia therapy in the future.

scholarly journals Diversification of small RNA amplification mechanisms for targeting transposon-related sequences in ciliates

2019 ◽  
Vol 116 (29) ◽  
pp. 14639-14644 ◽  
Author(s):  
Masatoshi Mutazono ◽  
Tomoko Noto ◽  
Kazufumi Mochizuki
Keyword(s):  
Transposable Elements ◽  
Small Rna ◽  
Signal Amplification ◽  
Small Rnas ◽  
Ciliated Protozoa ◽  
Rna Amplification ◽  
Somatic Nucleus ◽  
Dna Elimination ◽  
Internal Eliminated Sequences ◽  
Rna Biogenesis

The silencing of repetitive transposable elements (TEs) is ensured by signal amplification of the initial small RNA trigger, which occurs at distinct steps of TE silencing in different eukaryotes. How such a variety of secondary small RNA biogenesis mechanisms has evolved has not been thoroughly elucidated. Ciliated protozoa perform small RNA-directed programmed DNA elimination of thousands of TE-related internal eliminated sequences (IESs) in the newly developed somatic nucleus. In the ciliate Paramecium, secondary small RNAs are produced after the excision of IESs. In this study, we show that in another ciliate, Tetrahymena, secondary small RNAs accumulate at least a few hours before their derived IESs are excised. We also demonstrate that DNA excision is dispensable for their biogenesis in this ciliate. Therefore, unlike in Paramecium, small RNA amplification occurs before IES excision in Tetrahymena. This study reveals the remarkable diversity of secondary small RNA biogenesis mechanisms, even among ciliates with similar DNA elimination processes, and thus raises the possibility that the evolution of TE-targeting small RNA amplification can be traced by investigating the DNA elimination mechanisms of ciliates.

scholarly journals Whats, hows and whys of programmed DNA elimination in Tetrahymena

Open Biology ◽  
2017 ◽  
Vol 7 (10) ◽  
pp. 170172 ◽  
Author(s):  
Tomoko Noto ◽  
Kazufumi Mochizuki
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Feedback Loop ◽  
Tetrahymena Thermophila ◽  
Repetitive Sequences ◽  
Genome Comparison ◽  
High Similarity ◽  
Dna Elimination ◽  
Elimination Mechanism ◽  
Key Questions

Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between transposable elements (TEs) and host genomes. DNA elimination in Tetrahymena thermophila removes approximately 12 000 internal eliminated sequences (IESs), which correspond to one-third of the genome, when the somatic macronucleus (MAC) differentiates from the germline micronucleus (MIC). More than half of the IESs, many of which show high similarity to TEs, are targeted for elimination in cis by the small RNA-mediated genome comparison of the MIC to the MAC. Other IESs are targeted for elimination in trans by the same small RNAs through repetitive sequences. Furthermore, the small RNA–heterochromatin feedback loop ensures robust DNA elimination. Here, we review an updated picture of the DNA elimination mechanism, discuss the physiological and evolutionary roles of DNA elimination, and outline the key questions that remain unanswered.

scholarly journals Small-RNA-Mediated Genome-wide trans -Recognition Network in Tetrahymena DNA Elimination

2015 ◽  
Vol 59 (2) ◽  
pp. 229-242 ◽  
Author(s):  
Tomoko Noto ◽  
Kensuke Kataoka ◽  
Jan H. Suhren ◽  
Azusa Hayashi ◽  
Katrina J. Woolcock ◽  
...  
Keyword(s):  
Small Rna ◽  
Dna Elimination ◽  
Genome Wide

scholarly journals Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA

2017 ◽  
Vol 36 (8) ◽  
pp. 1029-1045 ◽  
Author(s):  
Alexandre Smirnov ◽  
Chuan Wang ◽  
Lisa L Drewry ◽  
Jörg Vogel
Keyword(s):  
Molecular Mechanism ◽  
Small Rna ◽  
In Trans

scholarly journals Genomics of the Parasitic Nematode Ascaris and Its Relatives

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 493
Author(s):  
Jianbin Wang
Keyword(s):  
Small Rna ◽  
Drug Targets ◽  
Sex Chromosome ◽  
Model Organisms ◽  
Parasitic Nematodes ◽  
Embryonic Cells ◽  
Genomic Resources ◽  
Dna Elimination ◽  
Parasite Relationship ◽  
Host Parasite

Nematodes of the genus Ascaris are important parasites of humans and swine, and the phylogenetically related genera (Parascaris, Toxocara, and Baylisascaris) infect mammals of veterinary interest. Over the last decade, considerable genomic resources have been established for Ascaris, including complete germline and somatic genomes, comprehensive mRNA and small RNA transcriptomes, as well as genome-wide histone and chromatin data. These datasets provide a major resource for studies on the basic biology of these parasites and the host–parasite relationship. Ascaris and its relatives undergo programmed DNA elimination, a highly regulated process where chromosomes are fragmented and portions of the genome are lost in embryonic cells destined to adopt a somatic fate, whereas the genome remains intact in germ cells. Unlike many model organisms, Ascaris transcription drives early development beginning prior to pronuclear fusion. Studies on Ascaris demonstrated a complex small RNA network even in the absence of a piRNA pathway. Comparative genomics of these ascarids has provided perspectives on nematode sex chromosome evolution, programmed DNA elimination, and host–parasite coevolution. The genomic resources enable comparison of proteins across diverse species, revealing many new potential drug targets that could be used to control these parasitic nematodes.

scholarly journals Study of an RNA helicase implicates small RNA-noncoding RNA interactions in programmed DNA elimination in Tetrahymena

2008 ◽  
Vol 22 (16) ◽  
pp. 2228-2241 ◽  
Author(s):  
L. Aronica ◽  
J. Bednenko ◽  
T. Noto ◽  
L. V. DeSouza ◽  
K.W. M. Siu ◽  
...  
Keyword(s):  
Small Rna ◽  
Noncoding Rna ◽  
Rna Helicase ◽  
Dna Elimination

scholarly journals Identification and analysis of functional associations among natural eukaryotic genome editing components

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1374 ◽  
Author(s):  
Estienne C. Swart ◽  
Cyril Denby Wilkes ◽  
Pamela Y. Sandoval ◽  
Cristina Hoehener ◽  
Aditi Singh ◽  
...  
Keyword(s):  
Genome Editing ◽  
Small Rnas ◽  
Rna Binding ◽  
Elongation Factor ◽  
Chromatin Remodelling ◽  
Eukaryotic Genome ◽  
Functional Relationships ◽  
Dna Elimination ◽  
Somatic Genome ◽  
Main Components

During development in the ciliate Paramecium, excess DNA interspersed throughout the germline genome is deleted to generate a new somatic genome. In this process, most of the intervening DNA is excised by a Piggybac-derived transposase, assisted by small RNAs (scnRNAs and iesRNAs) and chromatin remodelling. As the list of genes involved in DNA elimination has been growing, a need for a general approach to discover functional relationships among these genes now exists. We show that deep sequencing-based comparisons of experimentally-induced DNA retention provide a sensitive, quantitative approach to identify and analyze functional associations among genes involved in native genome editing. This reveals two functional molecular groups: (i) iesRNAs/scnRNAs, the putative Piwi- and RNA-binding Nowa1/2 proteins, and the transcription elongation factor TFIIS4; and (ii) PtCAF1 and Ezl1, two proteins involved in chromatin remodelling. Comparative analyses of silencing effects upon the largely unstudied regions comprising most developmentally eliminated DNA in Paramecium suggests a continuum between precise and imprecise DNA elimination. These findings show there is now a way forward to systematically elucidate the main components of natural eukaryotic genome editing systems.

Sign in / Sign up

Export Citation Format

Share Document