scholarly journals Spatiotemporal Expression and Molecular Characterization ofmiR-344bandmiR-344cin the Developing Mouse Brain

2016 ◽  
Vol 2016 ◽  
pp. 1-16 ◽  
Author(s):  
Jia-Wen Leong ◽  
Syahril Abdullah ◽  
King-Hwa Ling ◽  
Pike-See Cheah
Keyword(s):  
Mouse Brain ◽  
Noncoding Rna ◽  
Granular Layer ◽  
Developmental Stages ◽  
Adult Brain ◽  
Stem Loop ◽  
Small Noncoding Rna ◽  
Spatiotemporal Expression ◽  
Developing Mouse Brain

MicroRNAs (miRNAs) are small noncoding RNA known to regulate brain development. The expression of two novel miRNAs, namely,miR-344bandmiR-344c, was characterized during mouse brain developmental stages in this study.In situhybridization analysis showed thatmiR-344bandmiR-344cwere expressed in the germinal layer during embryonic brain developmental stages. In contrast,miR-344bwas not detectable in the adult brain whilemiR-344cwas expressed exclusively in the adult olfactory bulb and cerebellar granular layer. Stem-loop RT-qPCR analysis of whole brain RNAs showed that expression of themiR-344bandmiR-344cwas increased as brain developed throughout the embryonic stage and maintained at adulthood. Further investigation showed that these miRNAs were expressed in adult organs, wheremiR-344bandmiR-344cwere highly expressed in pancreas and brain, respectively. Bioinformatics analysis suggestedmiR-344bandmiR-344ctargetedOlig2andOtx2mRNAs, respectively. However, luciferase experiments demonstrated that these miRNAs did not targetOlig2andOtx2mRNAs. Further investigation on the locality ofmiR-344bandmiR-344cshowed that both miRNAs were localized in nuclei of immature neurons. In conclusion,miR-344bandmiR-344cwere expressed spatiotemporally during mouse brain developmental stages.

scholarly journals Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
David M Young ◽  
Siavash Fazel Darbandi ◽  
Grace Schwartz ◽  
Zachary Bonzell ◽  
Deniz Yuruk ◽  
...  
Keyword(s):  
Mouse Brain ◽  
3D Imaging ◽  
Developmental Stages ◽  
Brain Atlas ◽  
Imaging Data ◽  
Qualitative And Quantitative ◽  
Atlas Construction ◽  
Manual Curation ◽  
Developing Mouse Brain ◽  
2D Data

3D imaging data necessitate 3D reference atlases for accurate quantitative interpretation. Existing computational methods to generate 3D atlases from 2D-derived atlases result in extensive artifacts, while manual curation approaches are labor-intensive. We present a computational approach for 3D atlas construction that substantially reduces artifacts by identifying anatomical boundaries in the underlying imaging data and using these to guide 3D transformation. Anatomical boundaries also allow extension of atlases to complete edge regions. Applying these methods to the eight developmental stages in the Allen Developing Mouse Brain Atlas (ADMBA) led to more comprehensive and accurate atlases. We generated imaging data from 15 whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries). We provide the pipeline as the MagellanMapper software and the eight 3D reconstructed ADMBA atlases. These resources facilitate whole-organ quantitative analysis between samples and across development.

scholarly journals RNA Structures Required for Production of Subgenomic Flavivirus RNA

2010 ◽  
Vol 84 (21) ◽  
pp. 11407-11417 ◽  
Author(s):  
Anneke Funk ◽  
Katherine Truong ◽  
Tomoko Nagasaki ◽  
Shessy Torres ◽  
Nadia Floden ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Noncoding Rna ◽  
Secondary Structures ◽  
Vital Role ◽  
Rna Structures ◽  
Stem Loop ◽  
Small Noncoding Rna ◽  
Positive Sense ◽  
Cell Host Microbe ◽  
Nuclease Degradation

ABSTRACT Flaviviruses are a group of single-stranded, positive-sense RNA viruses causing ∼100 million infections per year. We have recently shown that flaviviruses produce a unique, small, noncoding RNA (∼0.5 kb) derived from the 3′ untranslated region (UTR) of the genomic RNA (gRNA), which is required for flavivirus-induced cytopathicity and pathogenicity (G. P. Pijlman et al., Cell Host Microbe, 4: 579-591, 2008). This RNA (subgenomic flavivirus RNA [sfRNA]) is a product of incomplete degradation of gRNA presumably by the cellular 5′-3′ exoribonuclease XRN1, which stalls on the rigid secondary structure stem-loop II (SL-II) located at the beginning of the 3′ UTR. Mutations or deletions of various secondary structures in the 3′ UTR resulted in the loss of full-length sfRNA (sfRNA1) and production of smaller and less abundant sfRNAs (sfRNA2 and sfRNA3). Here, we investigated in detail the importance of West Nile virus Kunjin (WNVKUN) 3′ UTR secondary structures as well as tertiary interactions for sfRNA formation. We show that secondary structures SL-IV and dumbbell 1 (DB1) downstream of SL-II are able to prevent further degradation of gRNA when the SL-II structure is deleted, leading to production of sfRNA2 and sfRNA3, respectively. We also show that a number of pseudoknot (PK) interactions, in particular PK1 stabilizing SL-II and PK3 stabilizing DB1, are required for protection of gRNA from nuclease degradation and production of sfRNA. Our results show that PK interactions play a vital role in the production of nuclease-resistant sfRNA, which is essential for viral cytopathicity in cells and pathogenicity in mice.

scholarly journals Constructing and Optimizing 3D Atlases From 2D Data With Application to the Developing Mouse Brain

2020 ◽  
Author(s):  
David M Young ◽  
Siavash Fazel Darbandi ◽  
Grace Schwartz ◽  
Zachary Bonzell ◽  
Deniz Yuruk ◽  
...  
Keyword(s):  
Mouse Brain ◽  
3D Imaging ◽  
Developmental Stages ◽  
Brain Atlas ◽  
Imaging Data ◽  
Qualitative And Quantitative ◽  
Atlas Construction ◽  
Manual Curation ◽  
Developing Mouse Brain ◽  
2D Data

Abstract3D imaging data necessitate 3D reference atlases for accurate quantitative interpretation. Existing computational methods to generate 3D atlases from 2D-derived atlases result in extensive artifacts, while manual curation approaches are labor-intensive. We present a computational approach for 3D atlas construction that substantially reduces artifacts by identifying anatomical boundaries in the underlying imaging data and using these to guide 3D transformation. Anatomical boundaries also allow extension of atlases to complete edge regions. Applying these methods to the eight developmental stages in the Allen Developing Mouse Brain Atlas (ADMBA) led to more comprehensive and accurate atlases. We generated imaging data from fifteen whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries). We provide the methods as the MagellanMapper software and the eight 3D reconstructed ADMBA atlases. These resources facilitate whole-organ quantitative analysis between samples and across development.

scholarly journals Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Elin Lundin ◽  
Chenglin Wu ◽  
Albin Widmark ◽  
Mikaela Behm ◽  
Jens Hjerling-Leffler ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Editing ◽  
Mouse Brain ◽  
Developmental Stages ◽  
Cell Types ◽  
Specific Cell ◽  
Cell Type ◽  
Cell Type Specific ◽  
Specific Regulation

Abstract Background Adenosine-to-inosine (A-to-I) RNA editing is a process that contributes to the diversification of proteins that has been shown to be essential for neurotransmission and other neuronal functions. However, the spatiotemporal and diversification properties of RNA editing in the brain are largely unknown. Here, we applied in situ sequencing to distinguish between edited and unedited transcripts in distinct regions of the mouse brain at four developmental stages, and investigate the diversity of the RNA landscape. Results We analyzed RNA editing at codon-altering sites using in situ sequencing at single-cell resolution, in combination with the detection of individual ADAR enzymes and specific cell type marker transcripts. This approach revealed cell-type-specific regulation of RNA editing of a set of transcripts, and developmental and regional variation in editing levels for many of the targeted sites. We found increasing editing diversity throughout development, which arises through regional- and cell type-specific regulation of ADAR enzymes and target transcripts. Conclusions Our single-cell in situ sequencing method has proved useful to study the complex landscape of RNA editing and our results indicate that this complexity arises due to distinct mechanisms of regulating individual RNA editing sites, acting both regionally and in specific cell types.

scholarly journals In vivo Chemical Reprogramming of Astrocytes into Functional Neurons

2018 ◽  
Author(s):  
Yantao Ma ◽  
Handan Xie ◽  
Xiaomin Du ◽  
Lipeng Wang ◽  
Xueqin Jin ◽  
...  
Keyword(s):  
Cell Fate ◽  
Mouse Brain ◽  
Adult Brain ◽  
Specific Marker ◽  
Electrophysiological Properties ◽  
Chemically Induced ◽  
Chemical Reprogramming ◽  
Induced Neurons

AbstractMammals lack robust regenerative abilities. Lost cells in impaired tissue could potentially be compensated by converting nearby cells in situ through in vivo reprogramming. Small molecule-induced reprogramming is a spatiotemporally flexible and non-integrative strategy for altering cell fate, which is, in principle, favorable for the in vivo reprogramming in organs with poor regenerative abilities, such as the brain. Here, we demonstrate that in the adult mouse brain, small molecules can reprogram resident astrocytes into functional neurons. The in situ chemically induced neurons (CiNs) resemble endogenous neurons in terms of neuron-specific marker expression and electrophysiological properties. Importantly, these CiNs can integrate into the mouse brain. Our study, for the first time, demonstrates in vivo chemical reprogramming in the adult brain, which could be a novel path for generating desired cells in situ for regenerative medicine.

Cell-Type-Specific Spatiotemporal Expression of Creatine Biosynthetic Enzyme S-adenosylmethionine:guanidinoacetate N-methyltransferase in Developing Mouse Brain

2017 ◽  
Vol 43 (2) ◽  
pp. 500-510 ◽  
Author(s):  
Masanori Tachikawa ◽  
Masahiko Watanabe ◽  
Masahiro Fukaya ◽  
Kazuhisa Sakai ◽  
Tetsuya Terasaki ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Biosynthetic Enzyme ◽  
Cell Type ◽  
Spatiotemporal Expression ◽  
Cell Type Specific ◽  
Developing Mouse Brain

scholarly journals CrfA, a Small Noncoding RNA Regulator of Adaptation to Carbon Starvation in Caulobacter crescentus

2010 ◽  
Vol 192 (18) ◽  
pp. 4763-4775 ◽  
Author(s):  
Stephen G. Landt ◽  
Joseph A. Lesley ◽  
Leticia Britos ◽  
Lucy Shapiro
Keyword(s):  
Posttranscriptional Regulation ◽  
Noncoding Rna ◽  
Target Genes ◽  
Caulobacter Crescentus ◽  
Gene Activation ◽  
Carbon Starvation ◽  
Base Substitution ◽  
Complementary Sequence ◽  
Stem Loop ◽  
Small Noncoding Rna

ABSTRACT Small noncoding regulatory RNAs (sRNAs) play a key role in the posttranscriptional regulation of many bacterial genes. The genome of Caulobacter crescentus encodes at least 31 sRNAs, and 27 of these sRNAs are of unknown function. An overexpression screen for sRNA-induced growth inhibition along with sequence conservation in a related Caulobacter species led to the identification of a novel sRNA, CrfA, that is specifically induced upon carbon starvation. Twenty-seven genes were found to be strongly activated by CrfA accumulation. One-third of these target genes encode putative TonB-dependent receptors, suggesting CrfA plays a role in the surface modification of C. crescentus, facilitating the uptake of nutrients during periods of carbon starvation. The mechanism of CrfA-mediated gene activation was investigated for one of the genes predicted to encode a TonB-dependent receptor, CC3461. CrfA functions to stabilize the CC3461 transcript. Complementarity between a region of CrfA and the terminal region of the CC3461 5′-untranslated region (5′-UTR) and also the behavior of a deletion of this region and a site-specific base substitution and a 3-base deletion in the CrfA complementary sequence suggest that CrfA binds to a stem-loop structure upstream of the CC3461 Shine-Dalgarno sequence and stabilizes the transcript.

In situ self imine-crosslinked nanocomplexes loaded with small noncoding RNA for efficient osteoarthritis attenuation

2020 ◽  
pp. 127631
Author(s):  
Yu Zhu ◽  
Yanmao Wang ◽  
Yi Sun ◽  
Junjie Shen ◽  
Jia Xu ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Small Noncoding Rna
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