Tracking cell-type-specific temporal dynamics in human and mouse brains

Lu, Ziyu; Zhang, Melissa; Lee, Jasper; Sziraki, Andras; Anderson, Sonya; Zhang, Zehao; Xu, Zihan; Jiang, Weirong; Ge, Shaoyu; Nelson, Peter T.; Zhou, Wei; Cao, Junyue

doi:10.1016/j.cell.2023.08.042

Cited by 5 publications

(1 citation statement)

References 148 publications

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“…Prior studies uncovered the prevalence of CREs in plants, highlighting their dynamic nature throughout evolution and their involvement in regulating gene expression via distinct chromatin pathways 3–8 . Across diverse cell types, gene expression is intricately regulated by multipl 9 e distinct CREs, each exerting control within specific cell or tissue types or during particular developmental stages and environmental cues 10–12 . Several studies have identified CREs functioning in a cell-type-specific manner within various plant species 9,13–19 .…”

Section: Mainmentioning

confidence: 99%

Evolution of plant cell-type-specificcis-regulatory elements

Yan,

Mendieta,

Zhang

et al. 2024

Preprint

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Cis-regulatory elements (CREs) are critical in coordinating the regulation of gene expression. Understanding how CREs evolve represents a challenging endeavor. Here, we constructed a comprehensive single-cell atlas of CRE activity inOryza sativa, integrating data from 104,029 nuclei representing 128 discrete cell states across nine distinct organs. We used a comparative genomic approach to analyze cell-type-specific CRE activity betweenOryza sativaand four additional grass species (Zea mays, Sorghum bicolor, Panicum miliaceum, andUrochloa fusca). We revealed a complex interplay whereby accessible chromatin regions (ACRs) had different levels of conservation dependent on if these regions were broadly accessible, or cell-type specific. We found that on average epidermal ACRs were less conserved in regions of synteny compared to other cell types, potentially indicating that large amounts of regulatory evolution have taken place in the epidermal layers of these species. We found a significant overlap between cell-type-specific ACRs and conserved non-coding sequences. Finally, we identified a subset of ACRs that were overlapping the repressive histone modification H3k27me3, which were conserved across evolutionary time, implicating them as potentially critical silencer CREs. Collectively, these results highlight the dynamic evolution of cell-type-specific CRE activity using comparative genomics.

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Section: Mainmentioning

confidence: 99%

Evolution of plant cell-type-specificcis-regulatory elements

Yan,

Mendieta,

Zhang

et al. 2024

Preprint

View full text Add to dashboard Cite

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Advancements and applications of single-cell multi-omics techniques in cancer research: Unveiling heterogeneity and paving the way for precision therapeutics

Liang,

Kong,

Chen

et al. 2024

Biochemistry and Biophysics Reports

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Dentate gyrus is needed for memory retrieval

Carretero-Guillén,

Treviño,

Gómez-Climent

et al. 2024

Mol Psychiatry

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The hippocampus is crucial for acquiring and retrieving episodic and contextual memories. In previous studies, the inactivation of dentate gyrus (DG) neurons by chemogenetic- and optogenetic-mediated hyperpolarization led to opposing conclusions about DG’s role in memory retrieval. One study used Designer Receptors Exclusively Activated by Designer Drugs (DREADD)-mediated clozapine N-oxide (CNO)-induced hyperpolarization and reported that the previously formed memory was erased, thus concluding that denate gyrus is needed for memory maintenance. The other study used optogenetic with halorhodopsin induced hyperpolarization and reported and dentate gyrus is needed for memory retrieval. We hypothesized that this apparent discrepancy could be due to the length of hyperpolarization in previous studies; minutes by optogenetics and several hours by DREADD/CNO. Since hyperpolarization interferes with anterograde and retrograde neuronal signaling, it is possible that the memory engram in the dentate gyrus and the entorhinal to hippocampus trisynaptic circuit was erased by long-term, but not with short-term hyperpolarization. We developed and applied an advanced chemogenetic technology to selectively silence synaptic output by blocking neurotransmitter release without hyperpolarizing DG neurons to explore this apparent discrepancy. We performed in vivo electrophysiology during trace eyeblink in a rabbit model of associative learning. Our work shows that the DG output is required for memory retrieval. Based on previous and recent findings, we propose that the actively functional anterograde and retrograde neuronal signaling is necessary to preserve synaptic memory engrams along the entorhinal cortex to the hippocampal trisynaptic circuit.

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Tracking cell-type-specific temporal dynamics in human and mouse brains

Cited by 5 publications

References 148 publications

Evolution of plant cell-type-specificcis-regulatory elements

Evolution of plant cell-type-specificcis-regulatory elements

Advancements and applications of single-cell multi-omics techniques in cancer research: Unveiling heterogeneity and paving the way for precision therapeutics

Dentate gyrus is needed for memory retrieval

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