Abstract
Neural circuit activity representing sensorimotor experiences trigger molecular mechanisms that drive long-lasting changes in brain circuits underlying learning and memory. Recent advancements in molecular genetics have led to development of rich toolboxes, e.g. optogenetics and CRISPR, that enable precise temporal and cell type-specific control of neural circuit activity and downstream activity-dependent mechanisms. One such molecular mechanism, the organization of three-dimensional (3D) genome architecture, has emerged as a powerful regulator of rapid and coordinated gene expression in response to neural circuit activity. Here, we describe how to perform optogenetic stimulation of granule neurons at the input layer of the cerebellar cortex in mice and how to profile activity-dependent changes in neuronal genome architecture. In addition, we will discuss how to genetically knock out chromatin regulators specifically in granule neurons in adult mice to study the functions of genome organization in activity-dependent gene expression and cerebellar-dependent motor learning.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Lisman J et al (2018) Memory formation depends on both synapse-specific modifications of synaptic strength and cell-specific increases in excitability. Nat Neurosci 21:309–314
Yap EL, Greenberg ME (2018) Activity-regulated transcription: bridging the gap between neural activity and behavior. Neuron 100:330–348
Han JH et al (2007) Neuronal competition and selection during memory formation. Science 316:457–460
Cai DJ et al (2016) A shared neural ensemble links distinct contextual memories encoded close in time. Nature 534:115–118
Kelleher RJ 3rd, Govindarajan A, Tonegawa S (2004) Translational regulatory mechanisms in persistent forms of synaptic plasticity. Neuron 44:59–73
Zhai S et al (2013) Long-distance integration of nuclear ERK signaling triggered by activation of a few dendritic spines. Science 342:1107–1111
Mardinly AR et al (2016) Sensory experience regulates cortical inhibition by inducing IGF1 in VIP neurons. Nature 531:371–375
Sun X et al (2020) Functionally distinct neuronal ensembles within the memory engram. Cell 181(410–423):e417
Herre M, Korb E (2019) The chromatin landscape of neuronal plasticity. Curr Opin Neurobiol 59:79–86
Tyssowski KM, Gray JM (2019) The neuronal stimulation-transcription coupling map. Curr Opin Neurobiol 59:87–94
Heinz DA, Bloodgood BL (2020) Mechanisms that communicate features of neuronal activity to the genome. Curr Opin Neurobiol 63:131–136
Zheng H, Xie W (2019) The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol 20:535–550
Bashkirova E, Lomvardas S (2019) Olfactory receptor genes make the case for inter-chromosomal interactions. Curr Opin Genet Dev 55:106–113
Sawtell NB (2010) Multimodal integration in granule cells as a basis for associative plasticity and sensory prediction in a cerebellum-like circuit. Neuron 66:573–584
Giovannucci A et al (2017) Cerebellar granule cells acquire a widespread predictive feedback signal during motor learning. Nat Neurosci 20:727–734
Wagner MJ et al (2017) Cerebellar granule cells encode the expectation of reward. Nature 544:96–100
Wagner MJ et al (2019) Shared cortex-cerebellum dynamics in the execution and learning of a motor task. Cell 177(669–682):e624
Yamada T et al (2019) Sensory experience remodels genome architecture in neural circuit to drive motor learning. Nature 569:708–713
Markwalter KH et al (2019) Sensorimotor coding of Vermal granule neurons in the developing mammalian cerebellum. J Neurosci 39:6626–6643
Stoodley CJ, Schmahmann JD (2010) Evidence for topographic organization in the cerebellum of motor control versus cognitive and affective processing. Cortex 46:831–844
King M et al (2019) Functional boundaries in the human cerebellum revealed by a multi-domain task battery. Nat Neurosci 22:1371–1378
Chambers WW, Sprague JM (1951) Differential effects of cerebellar anterior lobe cortex and fastigial nuclei on postural tonus in the cat. Science 114:324–325
Mauritz KH, Dichgans J, Hufschmidt A (1979) Quantitative analysis of stance in late cortical cerebellar atrophy of the anterior lobe and other forms of cerebellar ataxia. Brain 102:461–482
Heiney SA et al (2018) Single-unit extracellular recording from the cerebellum during Eyeblink conditioning in head-fixed mice. In: Sillitoe R (ed) Extracellular recording approaches, Neuromethods, vol 134. Humana Press, New York, NY, pp 39–71
Heiney SA et al (2014) Cerebellar-dependent expression of motor learning during eyeblink conditioning in head-fixed mice. J Neurosci 34:14845–14853
Rao SS et al (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665–1680
Fang R et al (2016) Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res 26:1345–1348
Madisen L et al (2012) A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing. Nat Neurosci 15:793–802
Pan N et al (2009) Defects in the cerebella of conditional Neurod1 null mice correlate with effective Tg(Atoh1-cre) recombination and granule cell requirements for Neurod1 for differentiation. Cell Tissue Res 337:407–428
Platt RJ et al (2014) CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159:440–455
Funfschilling U, Reichardt LF (2002) Cre-mediated recombination in rhombic lip derivatives. Genesis 33:160–169
Powell K et al (2015) Synaptic representation of locomotion in single cerebellar granule cells. eLife 4:e07290
Herman AM et al (2014) Cell type-specific and time-dependent light exposure contribute to silencing in neurons expressing Channelrhodopsin-2. eLife 3:e01481
Lin JY (2011) A user’s guide to channelrhodopsin variants: features, limitations and future developments. Exp Physiol 96:19–25
Yizhar O et al (2011) Optogenetics in neural systems. Neuron 71:9–34
Incontro S et al (2014) Efficient, complete deletion of synaptic proteins using CRISPR. Neuron 83:1051–1057
Yeomans JS et al (2002) Tactile, acoustic and vestibular systems sum to elicit the startle reflex. Neurosci Biobehav Rev 26:1–11
Bonev B, Cavalli G (2016) Organization and function of the 3D genome. Nat Rev Genet 17:661–678
Kempfer R, Pombo A (2020) Methods for mapping 3D chromosome architecture. Nat Rev Genet 21:207–226
Durand NC et al (2016) Juicer provides a one-click system for analyzing loop-resolution hi-C experiments. Cell Syst 3:95–98
Servant N et al (2015) HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16:259
Singh VP, Gerton JL (2015) Cohesin and human disease: lessons from mouse models. Curr Opin Cell Biol 37:9–17
Gabel HW et al (2015) Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. Nature 522:89–93
Ronan JL, Wu W, Crabtree GR (2013) From neural development to cognition: unexpected roles for chromatin. Nat Rev Genet 14:347–359
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Valnegri, P., Yamada, T., Yang, Y. (2022). Activity-Dependent Chromatin Mechanisms in Cerebellar Motor Learning. In: Sillitoe, R.V. (eds) Measuring Cerebellar Function. Neuromethods, vol 177. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2026-7_7
Download citation
DOI: https://doi.org/10.1007/978-1-0716-2026-7_7
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-2025-0
Online ISBN: 978-1-0716-2026-7
eBook Packages: Springer Protocols