Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells

Sherstyuk, Vladimir V.; Medvedev, S. P.; Elisaphenko, Eugeny A.; Vaskova, Evgeniya; Ri, Maxim; Vyatkin, Yuri; Saik, Olga V.; Shtokalo, Dmitry; Pokushalov, E. A.; Zakian, Suren M.

doi:10.1038/s41598-017-02632-0

Cited by 15 publications

(13 citation statements)

References 66 publications

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“…For v22 miRBase Anopheles sequences, we found 103 miRNAs represented in our libraries and removed 26 v22 miRBase Anopheles sequences due to their genome multi-mapping properties. Removing multi-mapping small RNAs is a common practice in miRNA transcriptomic studies (Sherstyuk et al 2017; Wen et al 2014; Biryukova et al 2014; Fu et al 2017) (Dataset S2). For Ae.…”

Section: Resultsmentioning

confidence: 99%

“…aegypti orthologs, our libraries contained both previously reported miRNAs miR-71 , miR-252 , miR-999 , and miR-2940 (Biryukova et al 2014) and miRNAs discovered in this current study, miR -193, miR-316 , miR-2765 , and miR-2942 (Dataset S1). For previously reported 41 novel miRNAs (Fu et al 2017; Biryukova et al 2014), our libraries possessed 21 of these miRNAs (Dataset S1) and 20 of these novel miRNAs (Fu et al 2017; Biryukova et al 2014) were removed due to (i) genome multi-mapping properties or (ii) redundant miRNA naming (Sherstyuk et al 2017; Wen et al 2014; Biryukova et al 2014; Fu et al 2017) (Dataset S2). For candidate miRNAs in this study, unannotated mapped reads were further interrogated by miRDeep2 (Friedländer et al 2012) where output yielded (1) a predicted hairpin, (2) miRNA -star and -mature sequences, (3) number of reads for candidate miRNA, (4) and number of mismatch reads for candidate miRNA.…”

Section: Resultsmentioning

confidence: 99%

“…A curious part of our mosquito tissue small RNA-Seq data are the substantial number of multi-mapping small RNAs. While common in small RNA-Seq studies (Sherstyuk et al 2017; Wen et al 2014; Johnson et al 2016; Biryukova et al 2014; Fu et al 2017), the current practice is to remove multi-mapping reads from miRNA analysis (Sherstyuk et al 2017; Wen et al 2014). Indeed, here we removed many Anopheles v22 miRBase and previously reported miRNAs (Fu et al 2017; Biryukova et al 2014) due to their multi-mapping nature.…”

Section: Discussionmentioning

confidence: 99%

“…As multi-mapping reads are repetitive in nature, only their percentage from the total reads was determined. Further, the multi-mapping reads were removed from further analysis, routine practice for miRNA transcriptomic studies (Sherstyuk et al 2017; Wen et al 2014). Unique reads were queried against miRBase v22 (Kozomara and Griffiths-Jones 2014) pre-miRNA sequences from An.…”

Section: Methodsmentioning

confidence: 99%

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Small RNA-Seq Analysis Reveals miRNA Expression Dynamics Across Tissues in the Malaria Vector, Anopheles gambiae

Bryant

Mills

Olson

et al. 2019

G3 Genes|Genomes|Genetics

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Malaria continues to be a major global health problem, where disease transmission is deeply linked to the repeated blood feeding nature of the anautogenous mosquito. Given the tight link between blood feeding and disease transmission, understanding basic biology behind mosquito physiology is a requirement for developing effective vector-borne disease control strategies. In the mosquito, numerous loss of function studies with notable phenotypes demonstrate microRNAs (miRNAs) play significant roles in mosquito physiology. While the field appreciates the importance of a handful of miRNAs, we still need global mosquito tissue miRNA transcriptome studies. To address this need, our goal was to determine the miRNA transcriptome for multiple tissues of the pre-vitellogenic mosquito. To this end, by using small RNA-Seq analysis, we determined miRNA transcriptomes in tissues critical for mosquito reproduction and immunity including (i) fat body-abdominal wall enriched tissues, (ii) midguts, (iii) ovaries, and (iv) remaining tissues comprised of the head and thorax. We found numerous examples of miRNAs exhibiting pan-tissue high- or low- expression, tissue exclusion, and tissue enrichment. We also updated and consolidated the miRNA catalog and provided a detailed genome architecture map for the malaria vector, Anopheles gambiae . This study aims to build a foundation for future research on how miRNAs and potentially other small RNAs regulate mosquito physiology as it relates to vector-borne disease transmission.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Small RNA-Seq Analysis Reveals miRNA Expression Dynamics Across Tissues in the Malaria Vector, Anopheles gambiae

Bryant

Mills

Olson

et al. 2019

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

show abstract

“…Mammalian cells express several classes of small ncRNA, including microRNA (miRNA) ( 11 ), small interfering RNAs (siRNA), small nucleolar RNAs (snoRNA) ( 12 ), small nuclear RNA (snRNA) ( 13 ), PIWI-interacting RNA (piRNA) ( 14 ), and tRNA-derived small RNAs (tRFs) ( 15 ), with some being shown to be expressed in a tissue- ( 16 ), cell type- ( 17 ), or even cell state-specific manner ( 18 ). Through their interactions with ribosomes and mRNA, these small noncoding molecules shape the dynamic molecular spectrum of tissues ( 4 , 17 ).…”

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confidence: 99%

A mouse tissue atlas of small noncoding RNA

Isakova

Fehlmann

Keller

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Small noncoding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (microRNA [miRNA], small nucleolar RNA [snoRNA], small nuclear RNA [snRNA], small Cajal body-specific RNA [scaRNA], and transfer RNA [tRNA] fragments) across 11 mouse tissues by deep sequencing. Using 14 biological replicates spanning both sexes, we identified that ∼30% of small ncRNAs are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. We found that some miRNAs are subject to “arm switching” between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of 11 profiled tissues, we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified in this study. Furthermore, by combining these findings with single-cell chromatin accessibility (scATAC-seq) data, we were able to connect identified brain-specific ncRNAs with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that these data will be a resource for the further identification of ncRNAs involved in tissue function in health and dysfunction in disease.

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Ultrastructural heterogeneity of the mitochondrial population in rat embryonic and induced pluripotent stem cells

Suldina

Sorokina

Morozova

2021

Cell Biology International

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Even though rats are popular model animals, the ultrastructure of their pluripotent cells, that is, embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), remains unexplored, although fine structure of pluripotent stem cells of mice and humans and its changes during differentiation have been investigated well. In the present study, we carried out ultrastructural and morphometric analyses of three lines of rat ESCs and two lines of rat iPSCs. The rat pluripotent stem cells were found to have the main typical morphological features of pluripotent cells: large nuclei of irregular or nearly round shape, scanty cytoplasm with few membrane organelles, and a poorly developed Golgi apparatus and endoplasmic reticulum. The cytoplasm of the rat pluripotent cells contains clusters of glycogen, previously described in human ESCs. To identify possible differences between rat ESCs and iPSCs, we performed a morphometric analysis of cell parameters. The mean area of cells and nuclei, the nuclear/cytoplasmic ratio, distributions of glycogen and diversity of mitochondria showed marked variations among the lines of rat pluripotent stem cells and were more pronounced than variations between rat ESCs and iPSCs as separate types of pluripotent stem cells. We noted morphological heterogeneity of the mitochondrial population in the rat pluripotent stem cells. The cells contained three types of mitochondria differing in the structure of cristae and in matrix density, and our morphometric analysis revealed differences in cristae structure.

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Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells

Cited by 15 publications

References 66 publications

Small RNA-Seq Analysis Reveals miRNA Expression Dynamics Across Tissues in the Malaria Vector, Anopheles gambiae

Small RNA-Seq Analysis Reveals miRNA Expression Dynamics Across Tissues in the Malaria Vector, Anopheles gambiae

A mouse tissue atlas of small noncoding RNA

Ultrastructural heterogeneity of the mitochondrial population in rat embryonic and induced pluripotent stem cells

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