An 840 kb distant upstream enhancer is a crucial regulator of catecholamine‐dependent expression of the Bdnf gene in astrocytes

Abstract

Brain‐derived neurotrophic factor (BDNF) plays a fundamental role in the developing and adult nervous system, contributing to neuronal survival, differentiation, and synaptic plasticity. Dysregulation of BDNF synthesis, secretion or signaling has been associated with many neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Although the transcriptional regulation of the Bdnf gene has been extensively studied in neurons, less is known about the regulation and function of BDNF in non‐neuronal cells. The most abundant type of non‐neuronal cells in the brain, astrocytes, express BDNF in response to catecholamines. However, genetic elements responsible for this regulation have not been identified. Here, we investigated four potential Bdnf enhancer regions and based on reporter gene assays, CRISPR/Cas9 engineering and CAPTURE‐3C‐sequencing we conclude that a region 840 kb upstream of the Bdnf gene regulates catecholamine‐dependent expression of Bdnf in rodent astrocytes. We also provide evidence that this regulation is mediated by CREB and AP1 family transcription factors. This is the first report of an enhancer coordinating the transcription of Bdnf gene in non‐neuronal cells.

Runx3 and Brn3a interplay orchestrates the transcriptional program in the early stages of proprioceptive neuron development

“…The Runx3 HCT were DEGs that harbored Runx3_RBS peaks within their gene body and/or in the intergenic regions up to their nearest neighbors on both sides of the peak-bearing genes, acting as enhancers. However, it is known that enhancers of certain genes reside within the boundaries of their neighboring genes, such as the limb ZRS enhancer of Shh that resides within an intron of Lmbr1 [38,39] or even when separated from the regulated gene by other genes [40][41][42]. In fact, GREAT associated Runx3_RBS peaks to genes identi ed ~ 30 DEGs in which the Runx3_RBS peaks resided within introns of their neighboring non-DEGs.…”

An upstream enhancer and MEF2 transcription factors fine-tune the regulation of the Bdnf gene in cortical and hippocampal neurons

“…The gRNA targeting sequences ( Supporting information ) of the −4.8 kb enhancer were designed using Benchling CRISPR tool ( http://www.benchling.com ) as described previously in Avarlaid et al. 2024 ( 24 ), and cloned into the pRRL-U6-gRNA-hPGK-EGFP plasmid. Briefly, a total of 3 gRNAs targeting the ∼400 bp core region covering the −4.8 kb MRE sequence were used and the gRNA viruses were pooled for the CRISPR/dCas9 experiments.…”

“…In general, Bdnf transcripts of the first cluster (exon I, II, III) have a nervous system-specific expression pattern, whereas Bdnf exon IV- and VI-containing transcripts are expressed in both neural and non-neural tissues ( 18 , 19 , 20 ). The spatiotemporal expression of Bdnf gene is ensured by various transcription factors binding to its distinct promoters ( 16 , 21 , 22 , 23 ) and through the use of different enhancer regions ( 24 , 25 , 26 ).…”