Longitudinal assessment of neuronal 3D genomes in mouse prefrontal cortex

Mitchell, Amanda; Javidfar, Behnam; Bicks, Lucy K.; Neve, Rachael L.; Garbett, Krassimira A.; Lander, Sharon S; Mirnics, Károly; Morishita, Hirofumi; Wood, Marcelo A.; Jiang, Yan; Gaisler‐Salomon, Inna; Akbarian, Schahram

doi:10.1038/ncomms12743

Cited by 17 publications

(28 citation statements)

References 64 publications

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“…Secondly, while not explored here, one could envision simple manipulations of the AAV calling cards system to allow for temporal control of the system (43). Such adaptations could allow for innovative studies in which TF binding is recorded only during defined windows of time (22). In a similar vein, we have demonstrated here the ability of AAV calling cards to integrate TF-binding information over time, which will allow for retrospective analysis of historical TF activity in cells.…”

Section: Discussionmentioning

confidence: 92%

“…Prominent among these are two techniques: DNA adenine methylation identification (DamID) (17), which records TF binding through local adenine methylation by an Escherichia coli Dam methylase fused to a TF of interest, and calling cards (18,21), in which a TF is fused to a transposase enzyme and binding events are recorded through transposon insertion proximal to the TF-binding site. Importantly, TF-tagging techniques do not require TF-specific antibodies and have the ability to record and integrate occupancy information across time (22), while requiring…”

mentioning

confidence: 99%

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A viral toolkit for recording transcription factor–DNA interactions in live mouse tissues

Cammack

Moudgil

Chen

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Transcription factors (TFs) enact precise regulation of gene expression through site-specific, genome-wide binding. Common methods for TF-occupancy profiling, such as chromatin immunoprecipitation, are limited by requirement of TF-specific antibodies and provide only end-point snapshots of TF binding. Alternatively, TF-tagging techniques, in which a TF is fused to a DNA-modifying enzyme that marks TF-binding events across the genome as they occur, do not require TF-specific antibodies and offer the potential for unique applications, such as recording of TF occupancy over time and cell type specificity through conditional expression of the TF–enzyme fusion. Here, we create a viral toolkit for one such method, calling cards, and demonstrate that these reagents can be delivered to the live mouse brain and used to report TF occupancy. Further, we establish a Cre-dependent calling cards system and, in proof-of-principle experiments, show utility in defining cell type-specific TF profiles and recording and integrating TF-binding events across time. This versatile approach will enable unique studies of TF-mediated gene regulation in live animal models.

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Section: Discussionmentioning

confidence: 92%

mentioning

confidence: 99%

A viral toolkit for recording transcription factor–DNA interactions in live mouse tissues

Cammack

Moudgil

Chen

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…Determining how these long-range interactions and the 3D architecture of the genome regulate neuronal gene expression, as recently investigated in several studies 33,231,232 , will be an important area of research.…”

Section: Conclusion and Outstanding Questionsmentioning

confidence: 99%

How the epigenome integrates information and reshapes the synapse

2019

Self Cite

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In the past few decades, the field of neuroepigenetics has investigated how the brain encodes information to form long-lasting memories that lead to stable changes in behaviour. Activitydependent molecular mechanisms, including, but not limited to, histone modification, DNA methylation and nucleosome remodelling, dynamically regulate the gene expression required for memory formation. Recently, the field has begun to examine how a learning experience is integrated at the level of both chromatin structure and synaptic physiology. Here, we provide an overview of key established epigenetic mechanisms that are important for memory formation. We explore how epigenetic mechanisms give rise to stable alterations in neuronal function by modifying synaptic structure and function, and highlight studies that demonstrate how manipulating epigenetic mechanisms may push the boundaries of memory.

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“…Secondly, while not explored here, one could envision simple manipulations of the AAV calling cards system to allow for temporal control of the system 43 . Such adaptations could allow for innovative studies in which TF binding is recorded only during defined windows of time 22 . In a similar vein, we have demonstrated here the ability of AAV calling cards to integrate TF binding information over time, which will allow for retrospective analysis of historical TF activity in cells.…”

Section: Discussionmentioning

confidence: 99%

Transposon-mediated, cell type-specific transcription factor recording in the mouse brain

Aj¹,

Moudgil²,

Lagunas³

et al. 2019

Preprint

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Transcription factors (TFs) enact precise regulation of gene expression through site-specific, genome-wide binding. Common methods for TF occupancy profiling, such as chromatin immunoprecipitation, are limited by requirement of TF-specific antibodies and provide only endpoint snapshots of TF binding. Alternatively, TFtagging techniques, in which a TF is fused to a DNA-modifying enzyme that marks TF binding events across the genome as they occur, do not require TF-specific antibodies and offer the potential for unique applications, such as recording of TF occupancy over time and cell type-specificity through conditional expression of the TFenzyme fusion. Here we create a viral toolkit for one such method, calling cards, and demonstrate that these reagents can be delivered to the live mouse brain and used to report TF occupancy. Further, we establish a Cre-dependent calling cards system, termed Flip-Excision (FLEX) calling cards and, in proof-of-principle experiments, show utility in defining cell type-specific TF profiles and recording and integrating TF binding events across time. This versatile approach will enable unique studies of TF-mediated gene regulation in live animal models.Proper cellular development and function is a complex process established by elaborate gene expression networks. These networks are fundamentally regulated by transcription factors (TF), which bind to regulatory elements (RE) across the genome and facilitate gene expression through a variety of mechanisms, including recruitment of transcriptional co-factors and modulation of chromatin state 1 . Extensive efforts to profile TF genome occupancy and identify active REs across the genome have highlighted the profound diversity of TF binding, providing important insights into TF-mediated gene regulation 2-5 . Further, a large portion of genetic variation associated with improper cellular function or disease has been shown to exist in TFbound REs 3,6-10 , demonstrating the criticality of proper TF binding in maintaining cellular homeostasis.Several methods exist for profiling TF occupancy across the genome. Antibody-based techniques, such as chromatin immunoprecipitation followed by sequencing (ChIP-seq), and more recently Cleavage Under Targets and Release Using Nuclease (CUT&RUN) 11 or Tagmentation (CUT&Tag) 12 , are widely used and have provided numerous insights into the cellular functions of TFs 2-4,7 . Notably however, these methods require the availability and individual optimization of TF-specific antibodies, limiting the throughput and breadth of genomewide TF profiling. Further, ChIP-seq provides only a snapshot of TF activity at the moment of cell lysis and thus may be inefficient at detecting transient or infrequent TF binding events. Finally, while robust for non-cell typeselective, tissue-level analyses, it is often challenging to interpret ChIP-seq data obtained from complex tissues such as the brain, which is comprised of many different interconnected cell types. Because of this limitation, efforts have recently been made to...

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Longitudinal assessment of neuronal 3D genomes in mouse prefrontal cortex

Cited by 17 publications

References 64 publications

A viral toolkit for recording transcription factor–DNA interactions in live mouse tissues

A viral toolkit for recording transcription factor–DNA interactions in live mouse tissues

How the epigenome integrates information and reshapes the synapse

Transposon-mediated, cell type-specific transcription factor recording in the mouse brain

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