Abstract
The vertebrate brain-derived neurotrophic factor (BDNF) gene produces a number of alternatively spliced transcripts only some of which generate the BDNF protein required for synaptic plasticity and learning. Many of the transcripts are uncharacterized and are of unknown biological significance. Previously, we described alternative splicing within the protein-coding sequence of the BDNF gene in the pond turtle (tBDNF) that generates a functionally distinct truncated protein isoform (trcBDNF) that is regulated during a neural correlate of eyeblink classical conditioning in ex vivo brainstem preparations. We hypothesized that trcBDNF has a dominant negative function because of its anticorrelated expression pattern compared to its full-length BDNF counterpart. The data presented here suggests that trcBDNF functions as a transcriptional repressor of a conditioning-inducible downstream tBDNF promoter that controls expression of full-length BDNF required for learning. First, expression of full-length transcripts is negatively correlated with trcBDNF; transcripts are inhibited when endogenous trcBDNF is ectopically induced and expressed when trcBDNF is inhibited. Second, ChIP-qPCR assays of a recombinant trcBDNF protein, RtrcBDNF, show strong binding to the downstream tBDNF exon III promoter that corresponds with inhibition of conditioning. Third, deletions of the C-terminus of RtrcBDNF result in inhibition of promoter binding and conditioning acquisition when a tropomyosin receptor kinase B (TrkB) binding site is accounted for. Finally, microinjection of RtrcBDNF directly into brainstem preparations inhibits conditioning. These data reveal a new mechanism of activity-dependent BDNF transcriptional regulation and suggest that BDNF is an autoregulatory gene. How generalizable this mechanism is across plasticity genes remains to be elucidated.
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References
Adelman K, Lis JT (2012) Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet 13:720–731
Aid T, Kazantseva A, Piirsoo M, Palm K, Timmusk T (2007) Mouse and rat BDNF gene structure and expression revisited. J Neurosci Res 85:525–535
Ambigapathy G, Zheng Z, Keifer J (2013) Identification of a functionally distinct truncated BDNF mRNA splice variant and protein in Trachemys scripta elegans. PLoS One 8:e67141
Ambigapathy G, Zheng Z, Keifer J (2014) Genomic organization and identification of promoter regions for the BDNF gene in the pond turtle Trachemys scripta elegans. J Mol Neurosci 53:626–636
Ambigapathy G, Zheng Z, Keifer J (2015) Regulation of BDNF chromatin status and promoter accessibility in a neural correlate of associative learning. Epigenetics 10:981–993
Cao X, Mahendran R, Guy GR, Tan YH (1993) Detection and characterization of cellular EGR-1 binding to its recognition site. J Biol Chem 268:16949–16957
Chen J, Tresenrider A, Chia M, McSwiggen DT, Spedale G, Jorgensen V, Liao H, van Werven FJ, Unal E (2017) Kinetochore inactivation by expression of a repressive mRNA. eLife 6:e27417
Chia M, Tresenrider A, Chen J, Spedale G, Jorgensen V, Unal E, van Werven FJ (2017) Transcription of a 5′ extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter. eLife 6:e27420
Flavell SW, Kim T-K, Gray JM, Harmin DA, Hemburg M, Hong EJ, Markenscoff-Papadimitriou E, Bear DM, Greenberg ME (2008) Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron 60:1022–1038
Heinrich G, Pagtakhan CJ (2004) Both 5′ and 3′ flanks regulate zebrafish brain-derived neurotrophic factor gene expression. BMC Neurosci 5:19
Ibanez CF, Ebendal T, Persson H (1991) Chimeric molecules with multiple neurotrophic activities reveal structural elements determining the specificities of NGF and BDNF. EMBO J 10:2105–2110
Ibanez CF, IIag LL, Murry-Rust J, Persson H (1993) An extended surface of binding to Trk tyrosine kinase receptors in NGF and BDNF allows the engineering of a multifunctional pan-neurotrophin. EMBO J 12:2281–2293
Keifer J (2017) Primetime for learning genes. Genes 8:e69
Keifer J, Zheng Z (2017) Cold block of in vitro eyeblink reflexes: evidence supporting the use of hypothermia as an anesthetic in pond turtles. J Exp Biol 220:4370–4373
Keifer J, Armstrong KE, Houk JC (1995) In vitro classical conditioning of abducens nerve discharge in turtles. J Neurosci 15:5036–5048
Keifer J, Sabirzhanov BE, Zheng Z, Li W, Clark TG (2009) Cleavage of proBDNF to BDNF by a tolloid-like metalloproteinase is required for acquisition of in vitro eyeblink classical conditioning. J Neurosci 29:14956–14964
Kidane AH, Heinrich G, Dirks RPH, de Ruyck BA, Lubsen NH, Roubos EW, Jenks BG (2009) Differential neuroendocrine expression of multiple brain-derived neurotrophic factor transcripts. Neuroendocrinol 150:1361–1368
Konieczny P, Stepniak-Konieczna E, Taylor K, Sznajder LJ, Sobczak K (2017) Autoregulation of MBNL1 function by exon 1 exclusion from MBNL1 transcript. Nucleic Acids Res 45:1760–1775
Li W, Keifer J (2008) Coordinate action of pre- and postsynaptic brain-derived neurotrophic factor is required for AMPAR trafficking and acquisition of in vitro classical conditioning. Neuroscience 155:686–697
Lipovich L, Dachet F, Cai J, Bagla S, Balan K, Jia H, Loeb JA (2012) Activity-dependent human brain coding/noncoding gene regulatory networks. Genetics 192:1133–1148
Lister R, Mukamel EA (2015) Turning over DNA methylation in the mind. Front Neurosci 9:252
Liu Q-R, Walther D, Drgon T, Polesskaya O, Lesnick TG, Strain KJ, de Andrade M, Bower JH, Maragonore DM, Uhl GR (2005) Human brain derived neurotrophic factor (BDNF) genes, splicing pattern, and assessments of associations with substance abuse and Parkinson’s disease. Am J Med Genet Pt B 134B:93–103
Lyons MR, West AE (2011) Mechanisms of specificity in neuronal activity-regulated gene transcription. Prog Neurobiol 94:259–295
Magistri M, Faghihi MA, St. Laurent G III, Wahlestedt C (2012) Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts. Trends Genet 28:389–396
Manavella PA, Roqueiro G, Darling DS, Cabanillas AM (2007) The ZFHX1A gene is differentially autoregulated by its isoform. Biochem Biophys Res Commun 360:621–626
Martinez M, Hinojosa M, Trombly D, Morin V, Stein J, Stein G, Javed A, Gutierrez SE (2016) Transcriptional auto-regulation of RUNX1 P1 promoter. PLoS One 11:e0149119
Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, Brothers SP, van der Brug MP, Wahlestedt C (2012) Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol 30:453–459
Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA (2008) Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat Protoc 3:698–709
Niibori Y, Hayashi F, Hirai K, Matsui M, Inokuchi K (2007) Alternative poly(A) site-selection regulates the production of alternatively spliced vesl-1/homer1 isoforms that encode postsynaptic scaffolding proteins. Neurosci Res 57:399–410
Pruunsild P, Kazantseva A, Aid T, Palm K, Timmusk T (2007) Dissecting the human BDNF locus: bidirectional transcription, complex splicing, and multiple promoters. Genomics 90:397–406
Sakai N, Tolbert LM, Duman RS (1999) Identification and functional analysis of novel cAMP response element binding protein splice variants lacking the basic/leucine zipper domain. Mol Pharmacol 56:917–925
Sala C, Futai K, Yamamoto K, Worley PF, Hayashi Y, Sheng M (2003) Inhibition of dendritic spine morphogenesis and synaptic transmission by activity-inducible protein Homer1a. J Neurosci 23:6327–6337
Sassone-Corsi P, Sisson JC, Verma IM (1988) Transcriptional autoregulation of the proto-oncogene fos. Nature 334:314–319
Tognoli C, Rossi F, di Cola F, Baj G, Tongiorgi E, Terova G, Saroglia M, Bernardini G, Gornati R (2010) Acute stress alters transcript expression pattern and reduces processing of proBDNF to mature BDNF in Dicentrarchus labrax. BMC Neurosci 11:4
Van der Knaap JA, Kumar BRP, Moshkin YM, Langenberg K, Krijgsveld J, Heck AJR, Karch F, Verrijzer CP (2005) GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7. Mol Cell 17:695–707
West AE, Pruunsild P, Timmusk T (2014) Neurotrophins: transcription and translation. Handb Exp Pharmacol 220:67–100
Williamson L, Saponaro M, Boeing S, East P, Mitter R, Kantidakis T, Kelly GP, Lobley A, Walker J, Spencer-Dene B, Howell M, Stewart A, Svejstrup JQ (2017) UV irradiation induces a non-coding RNA that functionally opposes the protein encoded by the same gene. Cell 168:843–855
Yu Y, Zhang H, Byerly MS, Bacon LD, Porter TE, Liu GE, Song J (2009) Alternative splicing variants and DNA methylation status of BDNF in inbred chicken lines. Brain Res 1269:1–10
Zheng Z, Sabirzhanov B, Keifer J (2012) Two-stage AMPA receptor trafficking in classical conditioning and selective role for glutamate receptor subunit 4 (tGluA4) flop splice variant. J Neurophysiol 108:101–111
Zheng Z, Ambigapathy G, Keifer J (2017) MeCP2 regulates Tet1-catalyzed demethylation, CTCF binding, and learning-dependent alternative splicing of the BDNF gene in turtle. eLife 6:e25384
Acknowledgements
We thank Dr. Ganesh Ambigapathy for contributing to the data shown in Fig. 2.
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Supported by a Sanford School of Medicine Research Grant and internal departmental grant funds to J.K.
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Conceptualization and design: JK. Data curation and analysis: ZZ, JK. Supervision and Funding acquisition: JK. Writing review and editing: ZZ, JK.
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All experiments involving the use of animals were performed in accordance with the guidelines of the National Institutes of Health and were approved by the University of South Dakota Institutional Animal Care and Use Committee.
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Zheng, Z., Keifer, J. Learning-Dependent Transcriptional Regulation of BDNF by its Truncated Protein Isoform in Turtle. J Mol Neurosci 71, 999–1014 (2021). https://doi.org/10.1007/s12031-020-01722-5
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DOI: https://doi.org/10.1007/s12031-020-01722-5