Mouse and rat BDNF gene structure and expression revisited
Open accessAbstract
Brain‐derived neurotrophic factor (BDNF) has important functions in the development of the nervous system and in brain plasticity‐related processes such as memory, learning, and drug addiction. Despite the fact that the function and regulation of rodent BDNF gene expression have received close attention during the last decade, knowledge of the structural organization of mouse and rat BDNF gene has remained incomplete. We have identified and characterized several mouse and rat BDNF transcripts containing novel 5′ untranslated exons and introduced a new numbering system for mouse and rat BDNF exons. According to our results both mouse and rat BDNF gene consist of eight 5′ untranslated exons and one protein coding 3′ exon. Transcription of the gene results in BDNF transcripts containing one of the eight 5′ exons spliced to the protein coding exon and in a transcript containing only 5′ extended protein coding exon. We also report the distinct tissue‐specific expression profiles of each of the mouse and rat 5′ exon‐specific transcripts in different brain regions and nonneural tissues. In addition, we show that kainic acid‐induced seizures that lead to changes in cellular Ca 2+ levels as well as inhibition of DNA methylation and histone deacetylation contribute to the differential regulation of the expression of BDNF transcripts. Finally, we confirm that mouse and rat BDNF gene loci do not encode antisense mRNA transcripts, suggesting that mechanisms of regulation for rodent and human BDNF genes differ substantially. © 2006 Wiley‐Liss, Inc.
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The coding sequence of BDNF is located in exon IX in both human and rodents.
“Despite this complexity, the coding sequence is located in exon IX in both human and rodents.”
From Neurotrophic Factor BDNF, Physiological Functions and Therapeutic Potential in Depression, Neurodegeneration and Brain Cancer (2020) · cites this paper as [32]
The Discussion and Fig. 1 caption identify exon IX as the protein-coding exon in mouse and rat. The passages comparing human and rodent exons do not establish that the human coding sequence is also in an exon numbered IX. (LLM, conf=0.85)
Experimental — accuracy not yet measuredBDNF has a complex gene structure with 11 different exons in humans, nine different exons in rodents, and nine alternative promoters for both groups.
“Further studies, published in 2007, clarified that BDNF has a complex gene structure with 11 different exons in humans, nine different exons in rodents, and nine alternative promoters for both groups [32,33].”
From Neurotrophic Factor BDNF, Physiological Functions and Therapeutic Potential in Depression, Neurodegeneration and Brain Cancer (2020) · cites this paper as [32]
The Results (New Nomenclature for Mouse and Rat BDNF Gene) report eight 5′ exons and one coding exon in mice and rats, supporting the nine-exon rodent count. The Results (Identification of the Transcription Start Sites) suggest separate promoters for eight 5′ exon transcripts and the IXA transcript. The paper does not establish the claimed count of 11 human exons or nine human promoters. (LLM, conf=0.87)
Experimental — accuracy not yet measuredExon IX includes the common sequence that encodes for the proBDNF protein.
“The latter includes the common sequence that encodes for the proBDNF protein.”
From Neurotrophic Factor BDNF, Physiological Functions and Therapeutic Potential in Depression, Neurodegeneration and Brain Cancer (2020) · cites this paper as [32]
Exon IX is present in all BDNF mRNA isoforms.
“Exon IX is present in all BDNF mRNA isoforms.”
From Neurotrophic Factor BDNF, Physiological Functions and Therapeutic Potential in Depression, Neurodegeneration and Brain Cancer (2020) · cites this paper as [32]
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- Authors
- Aid, T., Kazantseva, A., Piirsoo, M., Palm, K., & Timmusk, T.
- Affiliations
- Tallinn University of Technology (EE)
- Corresponding author
- Timmusk, Tõnis
- Venue
- Journal of Neuroscience Research
- Publisher
- Wiley
- Published
- 2006-12-05
- Volume
- 85
- Issue
- 3
- Pages
- 525-535
- ISSN
- 0360-4012 (ISSN-L)
- 1097-4547
- PMC
- PMC1878509
- OpenAlex
- W2002637584
- Cited by
- 943
- References
- 8
- Citations by year
- 2026: 22 · 2025: 24 · 2024: 23 · 2023: 24 · 2022: 39 · 2021: 38 · 2020: 82 · 2019: 45 · 2018: 53 · 2017: 62 · 2016: 59 · 2015: 59 · 2014: 80 · 2013: 69 · 2012: 61
- FWCI
- 11.89
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Neuroscience Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (067952)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Nerve injury and regeneration
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- brain-derived neurotrophic factor, alternative splicing, tissue-specific gene expression, kainic acid-induced seizures, DNA methylation, histone deacetylation, calcium signaling, antisense transcripts, mice, rats
- MeSH terms
- Animals, Base Sequence, Brain, Exons, Gene Expression Regulation, Humans, Molecular Sequence Data, RNA, Messenger, Transcription, Genetic, DNA Methylation, Brain-Derived Neurotrophic Factor, Mice, Rats
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