Laminar and Temporal Expression Dynamics of Coding and Noncoding RNAs in the Mouse Neocortex

Fertuzinhos, Sofia; Li, Mingfeng; Kawasawa, Yuka Imamura; Ivić, Vedrana; Franjic, Daniel; Singh, Darshani; Crair, Michael C.; Šestan, Nenad

doi:10.1016/j.celrep.2014.01.036

Cited by 67 publications

(65 citation statements)

References 64 publications

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“…While mRNA co-expression networks have been described as important in understanding the brain (Cabili et al 2011;Fertuzinhos et al 2014;Molyneaux et al 2015;Zeisel et al 2015), very few of them appear to reflect the complexity of brain architecture and function. We demonstrated how the data set can be used to profile trajectories of genes associated with specific neurobiological categories or disorders, many of which are not likely to be evident from transcriptomic profiles of commonly studied model systems.…”

Section: Discussionmentioning

confidence: 99%

Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain

Liu

Wang

Chen³

et al. 2017

Genome Res.

103

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Long noncoding RNAs (lncRNAs) mediate important epigenetic regulation in a wide range of biological processes and diseases. We applied comprehensive analyses of RNA-seq and CAGE-seq (cap analysis of gene expression and sequencing) to characterize the dynamic changes in lncRNA expression in rhesus macaque (Macaca mulatta) brain in four representative age groups. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age, and sex specificities. Spatiotemporal-and sex-biased changes in lncRNA expression were generally higher than those observed in mRNA expression. A negative correlation between lncRNA and mRNA expression in cerebral cortex was observed and functionally validated. Our findings offer a fresh insight into spatial-, age-, and sex-biased changes in lncRNA expression in macaque brain and suggest that the changes represent a previously unappreciated regulatory system that potentially contributes to brain development and aging.

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Section: Discussionmentioning

confidence: 99%

Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain

Liu

Wang

Chen³

et al. 2017

Genome Res.

103

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“…Next we surveyed available mouse RNA-seq data 21,22 to see whether the increasing A-to-I editing pattern in human brain development is conserved in mouse brain development. Among 742 A-to-I editing sites showing the increasing pattern in human brain, 95 sites were found to be conserved in the mouse genome (Supplementary Table 3 I II III II III II , third quartile (top box limit), median (center line), first quartile (bottom box limit) and minimum (bottom whisker).…”

Section: Developmental A-to-i Editing Patterns In Other Tissuesmentioning

confidence: 99%

Dynamic regulation of RNA editing in human brain development and disease

et al. 2016

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RNA editing is increasingly recognized as a molecular mechanism regulating RNA activity and recoding proteins. Here we surveyed the global landscape of RNA editing in human brain tissues and identified three unique patterns of A-to-I RNA editing rates during cortical development: stable high, stable low and increasing. RNA secondary structure and the temporal expression of adenosine deaminase acting on RNA (ADAR) contribute to cis- and trans-regulatory mechanisms of these RNA editing patterns, respectively. Interestingly, the increasing pattern was associated with neuronal maturation, correlated with mRNA abundance and potentially influenced miRNA binding energy. Gene ontology analyses implicated the increasing pattern in vesicle or organelle membrane-related genes and glutamate signaling pathways. We also found that the increasing pattern was selectively perturbed in spinal cord injury and glioblastoma. Our findings reveal global and dynamic aspects of RNA editing in brain, providing new insight into epitranscriptional regulation of sequence diversity.

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“…Total RNA was extracted as previously described with slight modification (22). Briefly, frozen muscle tissue was pulverized in liquid nitrogen with a mortar and pestle, followed by bead mill homogenization (Bullet Blender, Next Advance) using stainless steel beads (Next Advance, cat.…”

Section: Ethicsmentioning

confidence: 99%

Global deletion ofBCATmincreases expression of skeletal muscle genes associated with protein turnover

Lynch

Kimball

et al. 2015

Physiological Genomics

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Lynch CJ, Kimball SR, Xu Y, Salzberg AC, Kawasawa YI. Global deletion of BCATm increases expression of skeletal muscle genes associated with protein turnover. Physiol Genomics 47: 569-580, 2015. First published September 8, 2015 doi:10.1152/physiolgenomics.00055.2015.-Consumption of a protein-containing meal by a fasted animal promotes protein accretion in skeletal muscle, in part through leucine stimulation of protein synthesis and indirectly through repression of protein degradation mediated by its metabolite, ␣-ketoisocaproate. Mice lacking the mitochondrial branched-chain aminotransferase (BCATm/Bcat2), which interconverts leucine and ␣-ketoisocaproate, exhibit elevated protein turnover. Here, the transcriptomes of gastrocnemius muscle from BCATm knockout (KO) and wildtype mice were compared by next-generation RNA sequencing (RNA-Seq) to identify potential adaptations associated with their persistently altered nutrient signaling. Statistically significant changes in the abundance of 1,486/ϳ39,010 genes were identified. Bioinformatics analysis of the RNA-Seq data indicated that pathways involved in protein synthesis [eukaryotic initiation factor (eIF)-2, mammalian target of rapamycin, eIF4, and p70S6K pathways including 40S and 60S ribosomal proteins], protein breakdown (e.g., ubiquitin mediated), and muscle degeneration (apoptosis, atrophy, myopathy, and cell death) were upregulated. Also in agreement with our previous observations, the abundance of mRNAs associated with reduced body size, glycemia, plasma insulin, and lipid signaling pathways was altered in BCATm KO mice. Consistently, genes encoding anaerobic and/or oxidative metabolism of carbohydrate, fatty acids, and branched chain amino acids were modestly but systematically reduced. Although there was no indication that muscle fiber type was different between KO and wild-type mice, a difference in the abundance of mRNAs associated with a muscular dystrophy phenotype was observed, consistent with the published exercise intolerance of these mice. The results suggest transcriptional adaptations occur in BCATm KO mice that along with altered nutrient signaling may contribute to their previously reported protein turnover, metabolic and exercise phenotypes.

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Laminar and Temporal Expression Dynamics of Coding and Noncoding RNAs in the Mouse Neocortex

Cited by 67 publications

References 64 publications

Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain

Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain

Dynamic regulation of RNA editing in human brain development and disease

Global deletion ofBCATmincreases expression of skeletal muscle genes associated with protein turnover

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