Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development reveals spatiotemporal dynamics

Hsu, Chi-Lin; Chou, Chih-Hsuan; Huang, Shih-Chuan; Lin, Chia–Yi; Lin, Min; Tung, Chun-Che; Lin, Cheng; Lai, Ivan Pochou; Zou, Yan-Fang; Youngson, Neil A.; Lin, Shau-Ping; Yang, Chang-Hao; Chen, Shih‐Kuo; Gau, Susan Shur‐Fen; Huang, Hsiang‐Po

doi:10.1093/hmg/ddy023

Cited by 17 publications

(20 citation statements)

References 59 publications

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“…Subsequent work turned to genetic manipulations to identify the function of imprinted genes in mice. More recent, with the advent of genome wide approaches, investigators have generated large datasets from F1 individuals generated from the breeding of two inbred (homozygous) strains of mice [28]. An advantage of using mice to do this type of work is that most strains have been sequenced and all animals within a strain will have the same maternal and paternal DNA sequence.…”

Section: Resultsmentioning

confidence: 99%

Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model

Xie

Ferreira

et al. 2019

BMC Bioinformatics

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BackgroundHigh-throughput sequencing experiments, which can determine allele origins, have been used to assess genome-wide allele-specific expression. Despite the amount of data generated from high-throughput experiments, statistical methods are often too simplistic to understand the complexity of gene expression. Specifically, existing methods do not test allele-specific expression (ASE) of a gene as a whole and variation in ASE within a gene across exons separately and simultaneously.ResultsWe propose a generalized linear mixed model to close these gaps, incorporating variations due to genes, single nucleotide polymorphisms (SNPs), and biological replicates. To improve reliability of statistical inferences, we assign priors on each effect in the model so that information is shared across genes in the entire genome. We utilize Bayesian model selection to test the hypothesis of ASE for each gene and variations across SNPs within a gene. We apply our method to four tissue types in a bovine study to de novo detect ASE genes in the bovine genome, and uncover intriguing predictions of regulatory ASEs across gene exons and across tissue types. We compared our method to competing approaches through simulation studies that mimicked the real datasets. The R package, BLMRM, that implements our proposed algorithm, is publicly available for download at https://github.com/JingXieMIZZOU/BLMRM.ConclusionsWe will show that the proposed method exhibits improved control of the false discovery rate and improved power over existing methods when SNP variation and biological variation are present. Besides, our method also maintains low computational requirements that allows for whole genome analysis.

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Section: Resultsmentioning

confidence: 99%

Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model

Xie

Ferreira

et al. 2019

BMC Bioinformatics

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“…Eyeopening marks a step towards synapse maturation in the VC, with the appearance of visuallyevoked neuronal responses across the retinal-LGN-VC circuit (Espinosa and Stryker, 2012;Chen, 2006, 2020). Perturbing this process by methods of visual deprivation, such as dark rearing, delays both synaptic (Albanese et al, 1983;Desai et al, 2002;Freire, 1978;Funahashi et al, 2013;Hsu et al, 2018;Ishikawa et al, 2014;Ko et al, 2014;Majdan and Shatz, 2006;Tropea et al, 2006) and astrocyte maturation (Müller, 1990;Stogsdill et al, 2017). The VC's glutamatergic neurons are arranged in spatially defined layers, with distinct transcriptomic, functional, and connectivity profiles (Bannister, 2005;Douglas and Martin, 2004).…”

Section: Introductionmentioning

confidence: 99%

Activity-dependent modulation of synapse-regulating genes in astrocytes

Farhy-Tselnicker

Boisvert

Liu

et al. 2021

eLife

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Astrocytes regulate the formation and function of neuronal synapses via multiple signals, however, what controls regional and temporal expression of these signals during development is unknown. We determined the expression profile of astrocyte synapse-regulating genes in the developing mouse visual cortex, identifying astrocyte signals that show differential temporal and layer-enriched expression. These patterns are not intrinsic to astrocytes, but regulated by visually-evoked neuronal activity, as they are absent in mice lacking glutamate release from thalamocortical terminals. Consequently, synapses remain immature. Expression of synapse-regulating genes and synaptic development are also altered when astrocyte signaling is blunted by diminishing calcium release from astrocyte stores. Single nucleus RNA sequencing identified groups of astrocytic genes regulated by neuronal and astrocyte activity, and a cassette of genes that show layer-specific enrichment. Thus, the development of cortical circuits requires coordinated signaling between astrocytes and neurons, highlighting astrocytes as a target to manipulate in neurodevelopmental disorders.

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“…Detailed information about the mice, as well as genotyping and breeding strategies have been previously described for C57BL/6J (Mus musculus domesticus, B6) mice (stock number: 000664, JAX), CAST/EiJ (Mus musculus castaneus, CAST) mice (stock number: 000928, JAX), Camk2a-iCre mice (B6 background), 22 Gfap-Cre mice (stock number: 012886, JAX, B6 background), and Ai14 Cre-reporter mice (stock number: 007914, JAX, B6 background). 23,24 Genotyping information and breeding strategy have been detailed previously. 23,24 F1 initial cross (CASTB6F1 or F1i) was from a CAST mother × B6 father, and F1 reciprocal cross (B6CASTF1 or F1r) was from a B6 mother × CAST father.…”

Section: Micementioning

confidence: 99%

Mouse hybrid genome mediates diverse brain phenotypes with the specificity of reciprocal crosses

et al. 2022

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Genome hybridization serves as an evolutionary force for diversification, species modification, and adaption. 1 Genome hybridization contributes to novel patterns of gene expression through the interaction of two divergent genomes or transcriptional networks in plants and drosophila. 2 Genome hybridization in cichlid fish showed that phenotypic novelty was associated with increased genetic distance between species. 3 Gene expression in offspring is affected by parental origin through transgenerational epigenetic modification. Complex traits such as

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Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development reveals spatiotemporal dynamics

Cited by 17 publications

References 59 publications

Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model

Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model

Activity-dependent modulation of synapse-regulating genes in astrocytes

Mouse hybrid genome mediates diverse brain phenotypes with the specificity of reciprocal crosses

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