1
|
Carretero-Guillén A, Treviño M, Gómez-Climent MÁ, Dogbevia GK, Bertocchi I, Sprengel R, Larkum ME, Vlachos A, Gruart A, Delgado-García JM, Hasan MT. Dentate gyrus is needed for memory retrieval. Mol Psychiatry 2024:10.1038/s41380-024-02546-0. [PMID: 38609585 DOI: 10.1038/s41380-024-02546-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/03/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
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.
Collapse
Affiliation(s)
- Alejandro Carretero-Guillén
- Division of Neuroscience, University Pablo de Olavide, Seville, Spain
- Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Mario Treviño
- Max Planck Institute for Medical Research, Heidelberg, Germany
- Instituto de Neurociencias, Universidad de Guadalajara, Guadalajara, 44130, México
| | | | - Godwin K Dogbevia
- Max Planck Institute for Medical Research, Heidelberg, Germany
- Health Canada, Ottawa, ON, Canada
| | - Ilaria Bertocchi
- Max Planck Institute for Medical Research, Heidelberg, Germany
- Neuroscience Institute Cavalieri-Ottolenghi (NICO), University of Turin, Turin, Italy
| | - Rolf Sprengel
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | | | - Agnès Gruart
- Division of Neuroscience, University Pablo de Olavide, Seville, Spain
| | | | - Mazahir T Hasan
- Achucarro Basque Center for Neuroscience, Leioa, Spain.
- Max Planck Institute for Medical Research, Heidelberg, Germany.
- NeuroCure, Charité - Universitätsmedizin, Berlin, Germany.
- Ikerbasque - Basque Foundation for Science, Bilbao, Spain.
| |
Collapse
|
2
|
Yan H, Mendieta JP, Zhang X, Marand AP, Liang Y, Luo Z, Minow MAA, Roulé T, Wagner D, Tu X, Wang Y, Zhong S, Wessler SR, Schmitz RJ. Evolution of plant cell-type-specific cis -regulatory elements. bioRxiv 2024:2024.01.08.574753. [PMID: 38260561 PMCID: PMC10802394 DOI: 10.1101/2024.01.08.574753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cis -regulatory elements (CREs) are critical in regulating gene expression, and yet our understanding of CRE evolution remains a challenge. Here, we constructed a comprehensive single-cell atlas of chromatin accessibility in Oryza sativa , integrating data from 104,029 nuclei representing 128 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved chromatin accessibility between O. sativa and 57,552 nuclei from four additional grass species ( Zea mays, Sorghum bicolor, Panicum miliaceum , and Urochloa fusca ). Accessible chromatin regions (ACRs) had different levels of conservation depending on the degree of cell-type specificity. We found a complex relationship between ACRs with conserved noncoding sequences, cell-type specificity, conservation, and tissue-specific switching. Additionally, we found that epidermal ACRs were less conserved compared to other cell types, potentially indicating that more rapid regulatory evolution has occurred in the L1 epidermal layer of these species. Finally, we identified and characterized a conserved subset of ACRs that overlapped the repressive histone modification H3K27me3, implicating them as potentially critical silencer CREs maintained by evolution. Collectively, this comparative genomics approach highlights the dynamics of cell-type-specific CRE evolution in plants.
Collapse
|
4
|
Sziraki A, Lu Z, Lee J, Banyai G, Anderson S, Abdulraouf A, Metzner E, Liao A, Banfelder J, Epstein A, Schaefer C, Xu Z, Zhang Z, Gan L, Nelson PT, Zhou W, Cao J. A global view of aging and Alzheimer's pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains. Nat Genet 2023; 55:2104-2116. [PMID: 38036784 PMCID: PMC10703679 DOI: 10.1038/s41588-023-01572-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Conventional methods fall short in unraveling the dynamics of rare cell types related to aging and diseases. Here we introduce EasySci, an advanced single-cell combinatorial indexing strategy for exploring age-dependent cellular dynamics in the mammalian brain. Profiling approximately 1.5 million single-cell transcriptomes and 400,000 chromatin accessibility profiles across diverse mouse brains, we identified over 300 cell subtypes, uncovering their molecular characteristics and spatial locations. This comprehensive view elucidates rare cell types expanded or depleted upon aging. We also investigated cell-type-specific responses to genetic alterations linked to Alzheimer's disease, identifying associated rare cell types. Additionally, by profiling 118,240 human brain single-cell transcriptomes, we discerned cell- and region-specific transcriptomic changes tied to Alzheimer's pathogenesis. In conclusion, this research offers a valuable resource for probing cell-type-specific dynamics in both normal and pathological aging.
Collapse
Affiliation(s)
- Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Gabor Banyai
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Sonya Anderson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Abdulraouf Abdulraouf
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Eli Metzner
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Andrew Liao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Jason Banfelder
- High Performance Computing Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexander Epstein
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Chloe Schaefer
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Li Gan
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Peter T Nelson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| |
Collapse
|