The accumulation of N6-methyl-2’-deoxyadenosine in DNA drives activity-induced gene expression and is required for the extinction of conditioned fear

Here we report that the recently discovered mammalian DNA modification N6-methyl-2’-deoxyadenosine (m6dA) is dynamically regulated in primary cortical neurons, and accumulates along promoters and coding sequences within the genome of activated prefrontal cortical neurons of adult C57/BI6 mice in response to fear extinction learning. The deposition of m6dA is generally associated with increased genome-wide occupancy of the mammalian m6dA methyltransferase, N6amt1, and this correlates with fear extinction learning-induced gene expression. Of particular relevance for fear extinction memory, the accumulation of m6dA is associated with an active chromatin state and the recruitment of transcriptional machinery to the brain-derived neurotrophic factor (Bdnf) P4 promoter, which is required for Bdnf exon IV mRNA expression and for the extinction of conditioned fear. These results expand the scope of DNA modifications in the adult brain and highlight changes in m6dA as a novel neuroepigenetic mechanism associated with activity-induced gene expression and the formation of fear extinction memory.

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SUN-235 Deficient Fear Extinction in PRKAR1A-Defective Mice

Journal of the Endocrine Society ◽

10.1210/jendso/bvaa046.1855 ◽

2020 ◽

Vol 4 (Supplement_1) ◽

Author(s):

Margaret Keil ◽

Enrica Paradiso ◽

Rita S Keil ◽

Maddalena Ugolini ◽

Evan Harris ◽

...

Keyword(s):

Gene Expression ◽

Fear Conditioning ◽

Conditioned Fear ◽

Critical Role ◽

Fear Memory ◽

Brain Regions ◽

Fear Extinction ◽

Carney Complex ◽

Bdnf Gene ◽

Extinction Learning

Abstract Background: The role of the cAMP/PKA signaling in molecular pathways involved in fear memory is well established: PKA is required for fear memory formation and is a constraint for fear extinction. Previously we reported that a Prkar1a heterozygote (HZ) mouse that was developed in our lab to investigate Carney complex (CNC), the disease caused by PRKAR1A mutations, showed brain region-specific increased PKA activity that was associated with anxiety-like behavioral phenotype and threat bias (Keil, 2010, 2013). We hypothesized that Prkar1a+/- (HZ) mice would have deficits in fear extinction behavior. Brain derived neurotrophic factor (BDNF) has a critical role in formation of fear memory and its transcription is regulated by PKA/CREB. A mouse model with down regulation of PKA provides an opportunity for the first time to investigate the effect of altered PKA signaling on fear conditioning and extinction. Method: Fear conditioning, fear extinction learning, and fear extinction recall were tested in adult male HZ and wild-type (WT) mice as follows: fear conditioning training followed 24hr later by extinction training (new context), then 24hr later by extinction recall training. Percentage of time freezing was used to assess conditioned fear response. We measured BDNF gene expression in brain regions after completion of extinction recall training. Results: As expected, fear conditioning (learning) behavior was similar in HZ and WT mice. However, HZ mice showed a significant deficit in the early phase of fear extinction learning compared to WT. There was no difference in extinction recall between genotypes. Alterations in BDNF gene expression in the prefrontal cortex and amygdala was associated with deficit in fear extinction. Conclusion: Mice with a downregulation of Prkar1a gene demonstrate intact fear conditioning but impaired fear extinction learning, consistent with prior studies that report that PKA inhibition is necessary to facilitate extinction learning. Prkar1a+/- mice provide a valuable model to investigate impaired fear extinction to identify mechanisms for therapeutic targets for anxiety and trauma-related disorders.

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The effects of transcutaneous vagus nerve stimulation on conditioned fear extinction in humans

10.31234/osf.io/8jsu9 ◽

2017 ◽

Author(s):

Andreas Michael Burger ◽

Bart Verkuil ◽

Ilse van Diest ◽

Willem van der Does ◽

Julian Thayer ◽

...

Keyword(s):

Vagus Nerve ◽

Nerve Stimulation ◽

Vagus Nerve Stimulation ◽

Conditioned Fear ◽

Fear Extinction ◽

Extinction Learning ◽

Transcutaneous Vagus Nerve Stimulation ◽

Extinction Memory ◽

Phase Retention ◽

To Receive

After fear conditioning participants were randomly assigned to receive tVNS or sham stimulation during a fear extinction phase. Retention of extinction memory was tested 24 hours later. tVNS accelerated explicit fear extinction learning (US expectancy ratings), but did not lead to better retention of extinction memory 24 hours later. We did not find a differential physiological conditioning response during the acquisition of fear and thus were unable to assess potential effects of tVNS on the extinction of physiological indices of fear.

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Epigenetic mechanisms in sexual differentiation of the brain and behaviour

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0114 ◽

2016 ◽

Vol 371 (1688) ◽

pp. 20150114 ◽

Cited By ~ 34

Author(s):

Nancy G. Forger

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Sexual Differentiation ◽

Wide Distribution ◽

Epigenetic Modifications ◽

Epigenetic Mechanism ◽

Epigenetic Mechanisms ◽

Genome Wide ◽

The Brain

Circumstantial evidence alone argues that the establishment and maintenance of sex differences in the brain depend on epigenetic modifications of chromatin structure. More direct evidence has recently been obtained from two types of studies: those manipulating a particular epigenetic mechanism, and those examining the genome-wide distribution of specific epigenetic marks. The manipulation of histone acetylation or DNA methylation disrupts the development of several neural sex differences in rodents. Taken together, however, the evidence suggests there is unlikely to be a simple formula for masculine or feminine development of the brain and behaviour; instead, underlying epigenetic mechanisms may vary by brain region or even by dependent variable within a region. Whole-genome studies related to sex differences in the brain have only very recently been reported, but suggest that males and females may use different combinations of epigenetic modifications to control gene expression, even in cases where gene expression does not differ between the sexes. Finally, recent findings are discussed that are likely to direct future studies on the role of epigenetic mechanisms in sexual differentiation of the brain and behaviour.

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Scapinin-induced Inhibition of Axon Elongation Is Attenuated by Phosphorylation and Translocation to the Cytoplasm

Journal of Biological Chemistry ◽

10.1074/jbc.m110.205781 ◽

2011 ◽

Vol 286 (22) ◽

pp. 19724-19734 ◽

Cited By ~ 14

Author(s):

Hovik Farghaian ◽

Yu Chen ◽

Ada W. Y. Fu ◽

Amy K. Y. Fu ◽

Jacque P. K. Ip ◽

...

Keyword(s):

Cortical Neurons ◽

Brain Cortex ◽

Inhibitory Effect ◽

Adult Brain ◽

Actin Binding ◽

Mutant Form ◽

Axon Elongation ◽

Rat Cortical Neurons ◽

The Brain

Scapinin is an actin- and PP1-binding protein that is exclusively expressed in the brain; however, its function in neurons has not been investigated. Here we show that expression of scapinin in primary rat cortical neurons inhibits axon elongation without affecting axon branching, dendritic outgrowth, or polarity. This inhibitory effect was dependent on its ability to bind actin because a mutant form that does not bind actin had no effect on axon elongation. Immunofluorescence analysis showed that scapinin is predominantly located in the distal axon shaft, cell body, and nucleus of neurons and displays a reciprocal staining pattern to phalloidin, consistent with previous reports that it binds actin monomers to inhibit polymerization. We show that scapinin is phosphorylated at a highly conserved site in the central region of the protein (Ser-277) by Cdk5 in vitro. Expression of a scapinin phospho-mimetic mutant (S277D) restored normal axon elongation without affecting actin binding. Instead, phosphorylated scapinin was sequestered in the cytoplasm of neurons and away from the axon. Because its expression is highest in relatively plastic regions of the adult brain (cortex, hippocampus), scapinin is a new regulator of neurite outgrowth and neuroplasticity in the brain.

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The brain-specific microRNA miR-128b regulates the formation of fear-extinction memory

Nature Neuroscience ◽

10.1038/nn.2891 ◽

2011 ◽

Vol 14 (9) ◽

pp. 1115-1117 ◽

Cited By ~ 125

Author(s):

Quan Lin ◽

Wei Wei ◽

Carlos M Coelho ◽

Xiang Li ◽

Danay Baker-Andresen ◽

...

Keyword(s):

Fear Extinction ◽

Extinction Memory ◽

The Brain

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Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals

10.1101/506758 ◽

2018 ◽

Author(s):

Boxun Zhao ◽

Qixi Wu ◽

Adam Yongxin Ye ◽

Jing Guo ◽

Xianing Zheng ◽

...

Keyword(s):

Cortical Neurons ◽

Genomic Diversity ◽

Healthy Controls ◽

Genome Wide ◽

Retrotransposon Family ◽

Somatic Tissues ◽

The Brain ◽

Specific Line ◽

Human Specific ◽

Brain Tissues

AbstractMounting evidence supports that LINE-1 (L1) retrotransposition can occur postzygotically in healthy and diseased human tissues, contributing to genomic mosaicism in the brain and other somatic tissues of an individual. However, the genomic distribution of somatic L1Hs (Human-specific LINE-1) insertions and their potential impact on carrier cells remain unclear. Here, using a PCR-based targeted bulk sequencing approach, we profiled 9,181 somatic insertions from 20 postmortem tissues from five Rett patients and their matched healthy controls. We identified and validated somatic L1Hs insertions in both cortical neurons and non-brain tissues. In Rett patients, somatic insertions were significantly depleted in exons—mainly contributed by long genes—than healthy controls, implying that cells carrying MECP2 mutations might be defenseless against a second exonic L1Hs insertion. We observed a significant increase of somatic L1Hs insertions in the brain compared with non-brain tissues from the same individual. Compared to germline insertions, somatic insertions were less sense-depleted to transcripts, indicating that they underwent weaker selective pressure on the orientation of insertion. Our observations demonstrate that somatic L1Hs insertions contribute to genomic diversity and MECP2 dysfunction alters their genomic patterns in Rett patients.Author SummaryHuman-specific LINE-1 (L1Hs) is the most active autonomous retrotransposon family in the human genome. Mounting evidence supports that L1Hs retrotransposition occurs postzygotically in the human brain cells, contributing to neuronal genomic diversity, but the extent of L1Hs-driven mosaicism in the brain is debated. In this study, we profiled genome-wide L1Hs insertions among 20 postmortem tissues from Rett patients and matched controls. We identified and validated somatic L1Hs insertions in both cortical neurons and non-brain tissues, with a higher jumping activity in the brain. We further found that MECP2 dysfunction might alter the genomic pattern of somatic L1Hs in Rett patients.

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Acute exercise enhances the consolidation of fear extinction memory and reduces conditioned fear relapse in a sex-dependent manner

Learning & Memory ◽

10.1101/lm.045195.117 ◽

2017 ◽

Vol 24 (8) ◽

pp. 358-368 ◽

Cited By ~ 18

Author(s):

Courtney A. Bouchet ◽

Brian A. Lloyd ◽

Esteban C. Loetz ◽

Caroline E. Farmer ◽

Mykola Ostrovskyy ◽

...

Keyword(s):

Acute Exercise ◽

Conditioned Fear ◽

Fear Extinction ◽

Dependent Manner ◽

Extinction Memory

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Coordination between Prefrontal Cortex Clock Gene Expression and Corticosterone Contributes to Enhanced Conditioned Fear Extinction Recall

eNeuro ◽

10.1523/eneuro.0455-18.2018 ◽

2018 ◽

Vol 5 (6) ◽

pp. ENEURO.0455-18.2018 ◽

Cited By ~ 3

Author(s):

Elizabeth R. Woodruff ◽

Lauren E. Chun ◽

Laura R. Hinds ◽

Nicholas M. Varra ◽

Daniel Tirado ◽

...

Keyword(s):

Gene Expression ◽

Prefrontal Cortex ◽

Clock Gene ◽

Conditioned Fear ◽

Fear Extinction ◽

Clock Gene Expression

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From compartments to gene loops: Functions of the 3D genome in the human brain

10.1101/2021.10.12.464094 ◽

2021 ◽

Author(s):

Samir Rahman ◽

Pengfei Dong ◽

Pasha Apontes ◽

Michael B. Fernando ◽

Kayla G. Townsley ◽

...

Keyword(s):

Gene Expression ◽

Human Brain ◽

Neural Development ◽

Cortical Neurons ◽

Regulation Of Gene Expression ◽

Cortical Plate ◽

3D Genome ◽

Prefrontal Cortical ◽

Loop Domains ◽

The Relationship

The 3D genome plays a key role in the regulation of gene expression. However, little is known about the spatiotemporal organization of chromatin during human brain development. We investigated the 3D genome in human fetal cortical plate and in adult prefrontal cortical neurons and glia. We found that neurons have weaker compartments than glia that emerge during fetal development. Furthermore, neurons form loop domains whereas glia form compartment domains. We show through CRISPRi on CNTNAP2 that transcription is coupled to loop domain insulation. Gene regulation during neural development involves increased use of enhancer-promoter and repressor-promoter loops. Finally, transcription is associated with gene loops. Altogether, we provide novel insights into the relationship between gene expression and different scales of chromatin organization in the human brain.

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