TY - JOUR

T1 - Mapping rat lncRNA Bdnf-as

AU - Shaburova, Elizaveta V.

AU - Marchenko, Sergey A.

AU - Dneprovskaya, Veronika B.

AU - Sborschikova, Anna V.

AU - Lanshakov, Dmitriy A.

N1 - The studies were funded through the Russian Science Foundation grant No. 24-25-00154 SAM, DAL, VBD and AVS wage were funded through FWNR-2025-0022.

PY - 2025/7/28

Y1 - 2025/7/28

N2 - Background: Long noncoding RNAs (lncRNAs) are increasingly recognized for their roles in regulating gene expression, yet they remain poorly understood, especially in non-human species. This study investigates the lncRNA Bdnf-as in rats, which modulates the transcription of the Bdnf gene through interactions with chromatin remodelers. Methods: In this study, we employed a variety of methodologies to identify novel antisense transcripts of Bdnf-as in the rat genome. These methodologies included step-out rapid amplification of cDNA ends, lentivirus infusion in the neonatal rat prefrontal cortex (PFC), TET-on construct expression induction with doxycycline, de novo transcriptome assembly, and bioinformatics analysis. Our findings, derived from these rigorous methods, have led to the identification of two novel antisense transcripts of Bdnf-as in the rat genome. Results: These transcripts, located downstream of the Bdnf coding region, exhibit splicing and appear to be influenced by overexpression of proBDNF. The application of reverse transcription from gene-specific primers in conjunction with quantitative polymerase chain reaction (qPCR) analysis revealed that Bdnf-as exhibited augmented expression exclusively following proBDNF expression induction from a lentiviral construct, and not in the presence of a mutated form. A bioinformatic analysis revealed the potential binding of the following proteins to this site: E2F1, VDR, SP3, ZNF354C, YY2, SPI1, RUNX1, and TBX3. A comparative genomic analysis revealed limited evolutionary conservation of Bdnf-as between rats, humans, and mice, reflecting the rapid divergence of lncRNAs. The analysis of RNAseq data indicates that Bdnf-as is expressed at low levels and is likely unstable, a factor that could contribute to its detection challenges. Conclusions: The present findings offer the initial characterization of rat Bdnf-as, its differential expression depending on expression construct, thus establishing the foundation for future studies to explore its regulatory functions and protein interactions in neurobiological processes.

AB - Background: Long noncoding RNAs (lncRNAs) are increasingly recognized for their roles in regulating gene expression, yet they remain poorly understood, especially in non-human species. This study investigates the lncRNA Bdnf-as in rats, which modulates the transcription of the Bdnf gene through interactions with chromatin remodelers. Methods: In this study, we employed a variety of methodologies to identify novel antisense transcripts of Bdnf-as in the rat genome. These methodologies included step-out rapid amplification of cDNA ends, lentivirus infusion in the neonatal rat prefrontal cortex (PFC), TET-on construct expression induction with doxycycline, de novo transcriptome assembly, and bioinformatics analysis. Our findings, derived from these rigorous methods, have led to the identification of two novel antisense transcripts of Bdnf-as in the rat genome. Results: These transcripts, located downstream of the Bdnf coding region, exhibit splicing and appear to be influenced by overexpression of proBDNF. The application of reverse transcription from gene-specific primers in conjunction with quantitative polymerase chain reaction (qPCR) analysis revealed that Bdnf-as exhibited augmented expression exclusively following proBDNF expression induction from a lentiviral construct, and not in the presence of a mutated form. A bioinformatic analysis revealed the potential binding of the following proteins to this site: E2F1, VDR, SP3, ZNF354C, YY2, SPI1, RUNX1, and TBX3. A comparative genomic analysis revealed limited evolutionary conservation of Bdnf-as between rats, humans, and mice, reflecting the rapid divergence of lncRNAs. The analysis of RNAseq data indicates that Bdnf-as is expressed at low levels and is likely unstable, a factor that could contribute to its detection challenges. Conclusions: The present findings offer the initial characterization of rat Bdnf-as, its differential expression depending on expression construct, thus establishing the foundation for future studies to explore its regulatory functions and protein interactions in neurobiological processes.

KW - Bdnf-as

KW - Brain

KW - lncRNA

KW - Gene Expression Profiling/methods

KW - Humans

KW - Rats

KW - Prefrontal Cortex/metabolism

KW - Brain-Derived Neurotrophic Factor/genetics

KW - Computational Biology/methods

KW - Transcriptome/genetics

KW - Rats, Sprague-Dawley

KW - RNA, Long Noncoding/genetics

KW - Animals

KW - RNA, Antisense/genetics

KW - Gene Expression Regulation/genetics

UR - https://www.scopus.com/pages/publications/105011858212

UR - https://www.mendeley.com/catalogue/42ae520f-2887-3b32-b037-459e12f155be/

U2 - 10.1007/s11033-025-10871-y

DO - 10.1007/s11033-025-10871-y

M3 - Article

C2 - 40721686

VL - 52

SP - 764

JO - Molecular Biology Reports

JF - Molecular Biology Reports

SN - 0301-4851

IS - 1

M1 - 764

ER -