Chromatin organization in the female mouse brain fluctuates across the oestrous cycle

Jarić, Ivana; Rocks, Devin; Greally, John M.; Suzuki, Masako; Kundaković, Marija

doi:10.1038/s41467-019-10704-0

Cited by 82 publications

(157 citation statements)

References 68 publications

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“…We evaluated whether phase of estrus cycle impacted behavior in any test (for example, whether estrus reduced depression-like behavior, or failed to reduce depression-like behavior among ELS mice 14 ), but did not find a significant relationship.…”

Section: Results: Els Increases Susceptibility To Adult Stress In Femmentioning

confidence: 99%

Early life stress alters transcriptomic patterning across reward circuitry in male and female mice

Peña

Smith

Ramakrishnan

et al. 2019

Preprint

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Abuse, neglect, and other forms of early life stress (ELS) significantly increase risk for psychiatric disorders including depression. In this study, we show that ELS in a postnatal sensitive period increases sensitivity to adult stress in female mice, consistent with our earlier findings in male mice. We used RNA-sequencing in the ventral tegmental area, nucleus accumbens, and prefrontal cortex of male and female mice to show that adult stress is distinctly represented in the brain's transcriptome depending on ELS history. We identify: 1) biological pathways disrupted after ELS and associated with increased behavioral stress sensitivity, 2) putative transcriptional regulators of the effect of ELS on adult stress response, and 3) subsets of primed genes specifically associated with latent behavioral changes. We also provide transcriptomic evidence that ELS increases sensitivity to future stress through enhancement of known programs of cortical plasticity.

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Section: Results: Els Increases Susceptibility To Adult Stress In Femmentioning

confidence: 99%

Early life stress alters transcriptomic patterning across reward circuitry in male and female mice

Peña

Smith

Ramakrishnan

et al. 2019

Preprint

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“…For this study, we assessed the frontal cortex of adult male mice, using two biological replicates for each condition. We included male mice only to avoid the confounding biological effect of sex and estrous cycle on chromatin organization 6 . From each condition, nuclei were prepared using the sucrose gradient method, and the neuronal (NeuN+) nuclei fraction was purified by fluorescence-activated nuclei sorting (FANS), using an antibody against the neuronal nuclear marker NeuN 15 .…”

Section: Mouse Study Designmentioning

confidence: 99%

“…In neurons, chromatin mediates responses to both endogenous (e.g. hormones, neurotransmitters) 6 and exogenous (e.g. drugs, stress) 7 factors contributing to neuronal-specific information processing and neuroplasticity.…”

Section: Introductionmentioning

confidence: 99%

“…The original method seemed limited to the analyses of fresh cells and tissues, due to the disruptive effect of freezing on chromatin structure and integrity 16,18,19 . However, optimized assays such as omni-ATAC-seq 20 have been developed and several studies using ATAC-seq have now been performed to interrogate chromatin organization from frozen mouse and human brain tissue 6,[21][22][23][24][25][26] .…”

Section: Introductionmentioning

confidence: 99%

“…While working with frozen brain tissue is almost inevitable in neuroscience studies, the cryopreservation of the tissue can be done using different methods, and the data comparing different experimental conditions is missing. In this study, we examined the efficacy and reliability of a cell-type specific ATAC-seq assay 6 across three different experimental conditions. We selected scenarios that are compatible with the study designs that we and others typically use in our research, including flash-freezing of brain tissue using either liquid nitrogen 6 or dry ice cooled hexane 27,28 , and compared them with a slow freezing protocol using a cryoprotective medium 18 .…”

Section: Introductionmentioning

confidence: 99%

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Cell Type-Specific Chromatin Accessibility Analysis in the Mouse and Human Brain

Rocks

Jarić

Tesfa

et al. 2020

Preprint

Self Cite

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ABSTRACTThe Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming increasingly popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and the pathophysiology of neuropsychiatric disorders. The advantages of using this assay include a small amount of material needed, relatively simple and fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. However, with increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs in both animals and humans. Here we tested three different protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescent-activated nuclei sorting (FANS) and the ATAC-seq analysis. Our study shows that the cryopreservation method impacts the number of open chromatin regions that can be identified from frozen brain tissue using the cell-type specific ATAC-seq assay. However, we show that all three protocols generate consistent and robust data and enable the identification of functional regulatory elements, promoters and enhancers, in neuronal cells. Our study also implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. In comparison to the mouse brain analysis, we reveal the additional challenges of doing chromatin analysis on post mortem human brain tissue. However, we also show that these studies are revealing important cell type-specific information about gene regulation in the human brain. Overall, the ATAC-seq coupled with FANS is a powerful method to capture cell-type specific chromatin accessibility information in the mouse and human brain. Our study provides alternative brain preservation methods that generate high quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in healthy and malfunctioning brain.

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Mechanical, Elastic, and Adhesive Properties of Two‐Dimensional Materials: From Straining Techniques to State‐of‐the‐Art Local Probe Measurements

Giorgio

Blundo

Pettinari

et al. 2022

Adv Materials Inter

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While static methods are often essential to make a material suited to a specific application, by permanently altering its properties, dynamic ones potentially enable their real-time modulation, paving the way for the development of reconfigurable devices.Within this context, strain engineering has historically been regarded as a "static" tuning method, which exploited the crystal deformations induced by the juxtaposition of materials with different lattice constants to manipulate the properties of semiconductor heterostructures [1] and improve the performance of electronic devices (e.g., CMOS-based logic technologies [2] ). In recent years, however, strain-engineering paradigms have begun to shift, leading to the development of new devices, capable of generating a dynamic modulation of the mechanical deformations induced in the active materials (and, thus, of their optoelectronic properties).Micro-and nano-electromechanical systems (MEMS and NEMS), for example, have long been used for sensing applications, thanks to their ability to transduce external stresses (e.g., applied pressure/weights, molecule adsorption,...) into electrical signals. In the opposite regime they are, at least in principle, 2D materials, such as graphene, hexagonal boron nitride (hBN), and transition-metal dichalcogenides (TMDs), are intrinsically flexible, can withstand very large strains (>10% lattice deformations), and their optoelectronic properties display a clear and distinctive response to an applied stress. As such, they are uniquely positioned both for the investigation of the effects of mechanical deformations on solid-state systems and for the exploitation of these effects in innovative devices. For example, 2D materials can be easily employed to transduce nanometric mechanical deformations into, e.g., clearly detectable electrical signals, thus enabling the fabrication of high-performance sensors; just as easily, however, external stresses can be used as a "knob" to dynamically control the properties of 2D materials, thereby leading to the realization of strain-tuneable, fully reconfigurable devices. Here, the main methods are reviewed to induce and characterize, at the nm level, mechanical deformations in 2D materials. After presenting the latest results concerning the mechanical, elastic, and adhesive properties of these unique systems, one of their most promising applications is briefly discussed: the realization of nano-electromechanical systems based on vibrating 2D membranes, potentially capable of operating at high frequencies (>100 MHz) and over a large dynamic range.The ORCID identification number(s) for the author(s) of this article can be found under https://doi.org/10.1002/admi.202102220.

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Chromatin organization in the female mouse brain fluctuates across the oestrous cycle

Cited by 82 publications

References 68 publications

Early life stress alters transcriptomic patterning across reward circuitry in male and female mice

Early life stress alters transcriptomic patterning across reward circuitry in male and female mice

Cell Type-Specific Chromatin Accessibility Analysis in the Mouse and Human Brain

Mechanical, Elastic, and Adhesive Properties of Two‐Dimensional Materials: From Straining Techniques to State‐of‐the‐Art Local Probe Measurements

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