Special Issue "Advances of Brain Transcriptomics"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Neurogenomics".

Deadline for manuscript submissions: 20 November 2021.

Special Issue Editors

Dr. Vladimir Babenko
E-Mail Website
Guest Editor
FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
Interests: brain transcriptiomics; alternative splicing; evolution of exon–intron structure; population genomics; next generation sequencing (NGS) methodologies
Dr. Olga Redina
E-Mail Website
Guest Editor
Institute of Cytology and Genetics, Novosibirsk 630090, Russia
Interests: RNA-Seq; brain transcriptomics; hypertension animal models; stress induced arterial hypertension; qTLs (quantitative trait loci); molecular mechanisms of hypertension; behavior

Special Issue Information

Dear Colleagues,

Advancements in RNA-Seq technology in the last decade have underlined its power for elucidating the brain gene networks responsible for various stressful factors, as well as pathologies like Alzheimer and Parkinson, and other neurological diseases including schizophrenia and depressive disorders. Single cell RNA-seq (scRNA-seq) allows for ascertaining various neurons and glia cell identities by elucidating the specific marker genes within them. This technology underlinees multiple novel stable cell colonies in the course of scRNA-seq analysis. Associative networks between cell colonies have been provided over the course of cells’ maturation, rendering an exhaustive picture of cell population development dynamics.

As a separate relevant issue, RNA-Seq provides the basis for cell/tissue specific alternative splicing (AS) elucidation with a high resolution. As it is known, the brain maintains the most expanded AS-mediated proteome variability, as well as AS-mediated transcription regulation, via nonsense mediated decay. The research of Barres Lab reported a 10-fold expansion of transcript diversity analyzing mouse brain transcriptomes (Yan et al., 2015). Currently, it is reported that the AS-specific profile is more specific and robust in certain instances than gene expression for neuronal identity (Ha et al., 2021). Multiple databases like ASCOT and Genome (for elucidating the tissue/cell specific AS profiles for each gene) are arising, underlining the research of brain transcriptome structural and expression variability as a top priority.

Additionally, there is a genetic based vs. acquired trait paradigm, which would be represented by both genetic studies based on animal model strains/breeds (e.g., tame foxes, aggressive strains of rats, etc.), and those that acquired the trait within single generation upon administering certain stress-related protocols.

In this Issue, we hope to address the spectra of physiological studies, including, but not limited to, animal models of social stress response and various brain disease related data/models using the abovementioned approaches and methods.

Dr. Vladimir Babenko
Dr. Olga Redina
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • Brain transcriptome
  • Alternative splicing
  • Molecular basis of neurological diseases
  • Variability of brain proteome and plasticity
  • Brain disease marker genes/networks
  • Genetic basis of behavior
  • Marker gene networks in various brain regions based on RNA-Seq

Published Papers (1 paper)

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Reduced Expression of Slc Genes in the VTA and NAcc of Male Mice with Positive Fighting Experience
Genes 2021, 12(7), 1099; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12071099 - 20 Jul 2021
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A range of several psychiatric medications targeting the activity of solute carrier (SLC) transporters have proved effective for treatment. Therefore, further research is needed to elucidate the expression profiles of the Slc genes, which may serve as markers of altered brain metabolic processes [...] Read more.
A range of several psychiatric medications targeting the activity of solute carrier (SLC) transporters have proved effective for treatment. Therefore, further research is needed to elucidate the expression profiles of the Slc genes, which may serve as markers of altered brain metabolic processes and neurotransmitter activities in psychoneurological disorders. We studied the Slc differentially expressed genes (DEGs) using transcriptomic profiles in the ventral tegmental area (VTA), nucleus accumbens (NAcc), and prefrontal cortex (PFC) of control and aggressive male mice with psychosis-like behavior induced by repeated experience of aggression accompanied with wins in daily agonistic interactions. The majority of the Slc DEGs were shown to have brain region-specific expression profiles. Most of these genes in the VTA and NAcc (12 of 17 and 25 of 26, respectively) were downregulated, which was not the case in the PFC (6 and 5, up- and downregulated, respectively). In the VTA and NAcc, altered expression was observed for the genes encoding the transporters of neurotransmitters as well as inorganic and organic ions, amino acids, metals, glucose, etc. This indicates an alteration in transport functions for many substrates, which can lead to the downregulation or even disruption of cellular and neurotransmitter processes in the VTA and NAcc, which are attributable to chronic stimulation of the reward systems induced by positive fighting experience. There is not a single Slc DEG common to all three brain regions. Our findings show that in male mice with repeated experience of aggression, altered activity of neurotransmitter systems leads to a restructuring of metabolic and neurotransmitter processes in a way specific for each brain region. We assume that the scoring of Slc DEGs by the largest instances of significant expression co-variation with other genes may outline a candidate for new prognostic drug targets. Thus, we propose that the Slc genes set may be treated as a sensitive genes marker scaffold in brain RNA-Seq studies. Full article
(This article belongs to the Special Issue Advances of Brain Transcriptomics)
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