A Large Scale Genetic Analysis of c-Myc-regulated Gene Expression Patterns

The nervous system is highly sensitive to experience during early postnatal life, but this phase of heightened plasticity decreases with age. Recent studies have demonstrated that developmental-like plasticity can be reactivated in the visual cortex of adult animals through environmental or pharmacological manipulations. These findings provide a unique opportunity to study the cellular and molecular mechanisms of adult plasticity. Here we used the monocular deprivation paradigm to investigate large-scale gene expression patterns underlying the reinstatement of plasticity produced by fluoxetine in the adult rat visual cortex. We found changes, confirmed with RT-PCRs, in gene expression in different biological themes, such as chromatin structure remodelling, transcription factors, molecules involved in synaptic plasticity, extracellular matrix, and excitatory and inhibitory neurotransmission. Our findings reveal a key role for several molecules such as the metalloproteases Mmp2 and Mmp9 or the glycoprotein Reelin and open up new insights into the mechanisms underlying the reopening of the critical periods in the adult brain.

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Evolution of gene expression across species and specialized zooids in Siphonophora

10.1101/2021.07.30.454354 ◽

2021 ◽

Author(s):

Catriona Munro ◽

Felipe Zapata ◽

Mark Howison ◽

Stefan Siebert ◽

Casey W Dunn

Keyword(s):

Gene Expression ◽

Large Scale ◽

Developmental Stages ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Gene Trees ◽

Species Trees ◽

Examine Gene Expression ◽

Specialized Tissue ◽

Species Specific

Background: Siphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework. Results: Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Conclusions: Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

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Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags

The Plant Journal ◽

10.1046/j.1365-313x.2003.01687.x ◽

2003 ◽

Vol 33 (6) ◽

pp. 1001-1011 ◽

Cited By ~ 64

Author(s):

Yasunari Ogihara ◽

Keiichi Mochida ◽

Yasue Nemoto ◽

Koji Murai ◽

Yukiko Yamazaki ◽

...

Keyword(s):

Gene Expression ◽

Life Cycle ◽

Expressed Sequence Tags ◽

Large Scale ◽

Expression Patterns ◽

Statistical Analyses ◽

Gene Expression Patterns ◽

Virtual Display ◽

Expressed Sequence

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Losing maternal care: Neotenic gene expression in the preoptic area of avian brood parasites

10.1101/349118 ◽

2018 ◽

Author(s):

Kathleen S. Lynch ◽

Lauren A. O’Connell ◽

Matthew I. M. Louder ◽

Anthony Pellicano ◽

Annmarie Gaglio ◽

...

Keyword(s):

Gene Expression ◽

Parental Care ◽

Maternal Behavior ◽

Brood Parasitism ◽

Large Scale ◽

Preoptic Area ◽

Expression Patterns ◽

Critical Role ◽

Gene Expression Patterns ◽

Brood Parasites

AbstractParental care for is critical for offspring survival in many species. However, parental behaviors have been lost in roughly 1% of avian species known as the obligate brood parasites. To shed light on molecular and neurobiological mechanisms mediating brood parasitic behavior, brain gene expression patterns between two brood parasitic species and one closely related non-parasitic Icterid (blackbird) species were compared. Our analyses focused on gene expression changes specifically in the preoptic area (POA), a brain region known to play a critical role in maternal behavior across vertebrates. Using comparative transcriptomic approaches, we identified gene expression patterns associated with brood parasitism and evaluated two alternative explanations for the evolution of brood parasitism: reduced expression of parental-related genes in the POA versus retention of juvenile (neotenic) gene expression. While we did not find evidence for large scale gene downregulation, expression patterns did reflect substantial evidence for neotenic POA gene expression in parasitic birds. Differentially expressed genes with previously established roles in parental care were identified. Targeted examination of these selected candidate genes in additional hypothalamic regions revealed species differences in gene expression patterns is not POA-specific. Together, these results provide new insights into neurogenomics underlying maternal behavior loss in avian brood parasites.

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