Hippocampal neurons’ cytosolic and membrane-bound ribosomal transcript profiles are differentially regulated by learning and subsequent sleep

Abstract

The hippocampus is essential for consolidating transient experiences into long-lasting memories. Memory consolidation is facilitated by postlearning sleep, although the underlying cellular mechanisms are largely unknown. We took an unbiased approach to this question by using a mouse model of hippocampally mediated, sleep-dependent memory consolidation (contextual fear memory). Because synaptic plasticity is associated with changes to both neuronal cell membranes (e.g., receptors) and cytosol (e.g., cytoskeletal elements), we characterized how these cell compartments are affected by learning and subsequent sleep or sleep deprivation (SD). Translating ribosome affinity purification was used to profile ribosome-associated RNAs in different subcellular compartments (cytosol and membrane) and in different cell populations (whole hippocampus, Camk2a+ neurons, or highly active neurons with phosphorylated ribosomal subunit S6 [pS6+]). We examined how transcript profiles change as a function of sleep versus SD and prior learning (contextual fear conditioning; CFC). While sleep loss altered many cytosolic ribosomal transcripts, CFC altered almost none, and CFC-driven changes were occluded by subsequent SD. In striking contrast, SD altered few transcripts on membrane-bound (MB) ribosomes, while learning altered many more (including long non-coding RNAs [lncRNAs]). The cellular pathways most affected by CFC were involved in structural remodeling. Comparisons of post-CFC MB transcript profiles between sleeping and SD mice implicated changes in cellular metabolism in Camk2a+ neurons and protein synthesis in highly active pS6+ (putative “engram”) neurons as biological processes disrupted by SD. These findings provide insights into how learning affects hippocampal neurons and suggest that the effects of SD on memory consolidation are cell type and subcellular compartment specific.

Perspective – ultrastructural analyses reflect the effects of sleep and sleep loss on neuronal cell biology

“…Across species, biochemical [ 8 , 49–52 ], transcriptomic [ 6 , 53 ], and ribosome profiling [ 8 , 11 ] data suggest that protein translation/quality control and transport are affected by acute sleep loss. For example, in nematodes, Drosophila , and mice [ 49 , 51 ], a brief period of SD leads to an enhanced unfolded protein response (UPR; the cellular stress response to accumulation of misfolded protein in the ER lumen) ( Figure 1 ).…”

“…Moreover, to date, there is no data on how sleep loss affects the subcellular distribution of the Golgi, ER, lysosomes, or endosomes in neurons. Appropriate subcellular localization and organization of these organelles is essential for spatial regulation of both protein and mRNA, which in neurons plays vital roles in neurotransmission, synaptic plasticity, and information storage [ 8 , 61 , 62 ]. Beyond these essential functions, the presence of Golgi and ER in neurites plays additional roles, including local calcium buffering, regulation of synaptic extracellular glycoproteins, and lipid biogenesis [ 63 , 64 ].…”

“…Sleep loss affects brain function in numerous ways, including disrupting both working and long-term memory, attention, and decision making. While the last two decades have provided new insights into how sleep loss affects neural activity [ 1–5 ], gene expression [ 6 , 7 ], and protein translation [ 8-11 ], a complete understanding of the cell biological effects of sleep deprivation (SD) in the brain is still lacking. A recent study by Flores et al in Sleep [ 12 ] addresses this question using serial block-face electron microscopy (SBEM) in a Drosophila brain structure involved in long-term memory storage.…”

Chemogenetic enhancement of cAMP signaling renders hippocampal synaptic plasticity resilient to the impact of acute sleep deprivation

“…2 ) demonstrate that chemogenetically enhancing cAMP levels at multiple time points during SD can render hippocampal LTP resilient to the impact of 5 hours of acute SD. Other studies have shown that shorter windows of sleep deprivation can also produce alterations in gene expression in the hippocampus (Delorme et al, 2021) and the cortex (Cirelli & Tononi, 2000) and impair memory and synaptic plasticity (Prince et al, 2014). These findings raise a question about whether the enhancement of cAMP levels in the early or late windows of SD have consistent or different effects on the maintenance of LTP.…”

Extracellular Matrix Recycling as a Novel Plasticity Mechanism With a Potential Role in Disease

“…For example, two members of the MMP family, MMP3 and MMP7, have both been shown to drive activity-dependent changes in synaptic structure ( Bilousova et al, 2006 ; Wójtowicz and Mozrzymas, 2014 ; Aerts et al, 2015 ; Brzdąk et al, 2017 ). Recently, the protease cathepsin-S was suggested to remodel PNNs in a circadian manner, which would presumably allow synapses to be modified during sleep ( Pantazopoulos et al, 2020 ; Delorme et al, 2021 ; Harkness et al, 2021 ). Additional proteases, including neurotrypsin and members of the “a disintegrin and metalloproteinase with TSP motifs” (ADAMTS) family, may also be involved in mediating synaptic plasticity.…”