Intronic enhancer region governs transcript-specific Bdnf expression in rodent neurons
Abstract
Brain-derived neurotrophic factor (BDNF) controls the survival, growth, and function of neurons both during the development and in the adult nervous system. Bdnf is transcribed from several distinct promoters generating transcripts with alternative 5' exons. Bdnf transcripts initiated at the first cluster of exons have been associated with the regulation of body weight and various aspects of social behavior, but the mechanisms driving the expression of these transcripts have remained poorly understood. Here, we identify an evolutionarily conserved intronic enhancer region inside the Bdnf gene that regulates both basal and stimulus-dependent expression of the Bdnf transcripts starting from the first cluster of 5' exons in mouse and rat neurons. We further uncover a functional E-box element in the enhancer region, linking the expression of Bdnf and various pro-neural basic helix-loop-helix transcription factors. Collectively, our results shed new light on the cell-type- and stimulus-specific regulation of the important neurotrophic factor BDNF.
Data availability
Mass-spectrometry results of the in vitro DNA pulldown experiment are provided in Supplementary Table 3.
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Widespread transcription at neuronal activity-regulated enhancersNCBI Gene Expression Omnibus, GSE21161.
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Rapid and Pervasive Changes in Genome-Wide Enhancer Usage During Mammalian DevelopmentNCBI Gene Expression Omnibus, GSE52386.
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Genome-wide identification and characterization of functional neuronal activity-dependent enhancersNCBI Gene Expression Omnibus, GSE60192.
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A protein interaction network of mental disorder factors in neural stem cellsNCBI Gene Expression Omnibus, GSE70872.
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Genome-wide maps of EGR1 binding in mouse frontal cortexNCBI Gene Expression Omnibus, GSE67482.
Article and author information
Author details
Funding
Estonian Research Council (IUT19-18)
- Jürgen Tuvikene
- Eli-Eelika Esvald
- Annika Rähni
- Kaie Uustalu
- Annela Avarlaid
- Tõnis Timmusk
Estonian Research Council (PRG805)
- Jürgen Tuvikene
- Eli-Eelika Esvald
- Annela Avarlaid
- Tõnis Timmusk
Norwegian Financial Mechanism (EMP128)
- Jürgen Tuvikene
- Eli-Eelika Esvald
- Annika Rähni
- Kaie Uustalu
- Tõnis Timmusk
European Regional Development Fund (2014-2020.4.01.15-0012)
- Jürgen Tuvikene
- Eli-Eelika Esvald
- Annika Rähni
- Kaie Uustalu
- Annela Avarlaid
- Tõnis Timmusk
H2020-MSCA-RISE-2016 (EU734791)
- Jürgen Tuvikene
- Eli-Eelika Esvald
- Anna Zhuravskaya
- Annela Avarlaid
- Eugene V Makeyev
- Tõnis Timmusk
Biotechnology and Biological Sciences Research Council (BB/M001199/1)
- Anna Zhuravskaya
- Eugene V Makeyev
Biotechnology and Biological Sciences Research Council (BB/M007103/1)
- Anna Zhuravskaya
- Eugene V Makeyev
Biotechnology and Biological Sciences Research Council (BB/R001049/1)
- Anna Zhuravskaya
- Eugene V Makeyev
European Regional Development Fund (ASTRA 2014-2020.4.01.16-0032)
- Jürgen Tuvikene
- Eli-Eelika Esvald
- Annela Avarlaid
- Tõnis Timmusk
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Tuvikene et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Further reading
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- Chromosomes and Gene Expression
- Evolutionary Biology
Gene regulation is essential for life and controlled by regulatory DNA. Mutations can modify the activity of regulatory DNA, and also create new regulatory DNA, a process called regulatory emergence. Non-regulatory and regulatory DNA contain motifs to which transcription factors may bind. In prokaryotes, gene expression requires a stretch of DNA called a promoter, which contains two motifs called –10 and –35 boxes. However, these motifs may occur in both promoters and non-promoter DNA in multiple copies. They have been implicated in some studies to improve promoter activity, and in others to repress it. Here, we ask whether the presence of such motifs in different genetic sequences influences promoter evolution and emergence. To understand whether and how promoter motifs influence promoter emergence and evolution, we start from 50 ‘promoter islands’, DNA sequences enriched with –10 and –35 boxes. We mutagenize these starting ‘parent’ sequences, and measure gene expression driven by 240,000 of the resulting mutants. We find that the probability that mutations create an active promoter varies more than 200-fold, and is not correlated with the number of promoter motifs. For parent sequences without promoter activity, mutations created over 1500 new –10 and –35 boxes at unique positions in the library, but only ~0.3% of these resulted in de-novo promoter activity. Only ~13% of all –10 and –35 boxes contribute to de-novo promoter activity. For parent sequences with promoter activity, mutations created new –10 and –35 boxes in 11 specific positions that partially overlap with preexisting ones to modulate expression. We also find that –10 and –35 boxes do not repress promoter activity. Overall, our work demonstrates how promoter motifs influence promoter emergence and evolution. It has implications for predicting and understanding regulatory evolution, de novo genes, and phenotypic evolution.
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- Chromosomes and Gene Expression
- Developmental Biology
The male-specific lethal complex (MSL), which consists of five proteins and two non-coding roX RNAs, is involved in the transcriptional enhancement of X-linked genes to compensate for the sex chromosome monosomy in Drosophila XY males compared with XX females. The MSL1 and MSL2 proteins form the heterotetrameric core of the MSL complex and are critical for the specific recruitment of the complex to the high-affinity ‘entry’ sites (HAS) on the X chromosome. In this study, we demonstrated that the N-terminal region of MSL1 is critical for stability and functions of MSL1. Amino acid deletions and substitutions in the N-terminal region of MSL1 strongly affect both the interaction with roX2 RNA and the MSL complex binding to HAS on the X chromosome. In particular, substitution of the conserved N-terminal amino-acids 3–7 in MSL1 (MSL1GS) affects male viability similar to the inactivation of genes encoding roX RNAs. In addition, MSL1GS binds to promoters such as MSL1WT but does not co-bind with MSL2 and MSL3 to X chromosomal HAS. However, overexpression of MSL2 partially restores the dosage compensation. Thus, the interaction of MSL1 with roX RNA is critical for the efficient assembly of the MSL complex on HAS of the male X chromosome.