Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses

The spike architecture of wheat plays a crucial role in determining grain number, making it a key trait for optimization in wheat breeding programs. In this study, we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages, revealing coordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition. We constructed a core transcriptional regulatory network (TRN) that drives wheat spike formation and experimentally validated a multi-layer regulatory module involving TaSPL15, TaAGLG1, and TaFUL2. By integrating the TRN with genome-wide association studies, we identified 227 transcription factors, including 42 with known functions and 185 with unknown functions. Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time, such as TaMYC2-A1, TaMYB30-A1, and TaWRKY37-A1. Of particular interest, TaMYB30-A1, downstream of and repressed by WFZP, was found to regulate fertile spikelet number. Notably, the excellent haplotype of TaMYB30-A1, which contains a C allele at the WFZP binding site, was enriched during wheat breeding improvement in China, leading to improved agronomic traits. Finally, we constructed a free and open access Wheat Spike Multi-Omic Database (http://39.98.48.156:8800/#/). Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development, with practical value for wheat breeding.

The Thalamocortical Mechanism Underlying the Generation and Regulation of the Auditory Steady-State Responses in Awake Mice

The auditory steady-state response (ASSR) is a cortical oscillation induced by trains of 40 Hz acoustic stimuli. While the ASSR has been widely used in clinic measurement, the underlying neural mechanism remains poorly understood. In this study, we investigated the contribution of different stages of auditory thalamocortical pathway-medial geniculate body (MGB), thalamic reticular nucleus (TRN), and auditory cortex (AC)-to the generation and regulation of 40 Hz ASSR in C57BL/6 mice of both sexes. We found that the neural response synchronizing to 40 Hz sound stimuli was most prominent in the GABAergic neurons in the granular layer of AC and the ventral division of MGB (MGBv), which were regulated by optogenetic manipulation of TRN neurons. Behavioral experiments confirmed that disrupting TRN activity has a detrimental effect on the ability of mice to discriminate 40 Hz sounds. These findings revealed a thalamocortical mechanism helpful to interpret the results of clinical ASSR examinations.Significance Statement Our study contributes to clarifying the thalamocortical mechanisms underlying the generation and regulation of the auditory steady-state response (ASSR), which is commonly used in both clinical and neuroscience research to assess the integrity of auditory function. Combining a series of electrophysiological and optogenetic experiments, we demonstrate that the generation of cortical ASSR is dependent on the lemniscal thalamocortical projections originating from the ventral division of medial geniculate body to the GABAergic interneurons in the granule layer of the auditory cortex. Furthermore, the thalamocortical process for ASSR is strictly regulated by the activity of thalamic reticular nucleus (TRN) neurons. Behavioral experiments confirmed that dysfunction of TRN would cause a disruption of mice's behavioral performance in the auditory discrimination task.

Generation of ventralized human thalamic organoids with thalamic reticular nucleus

Human brain organoids provide unique platforms for modeling several aspects of human brain development and pathology. However, current brain organoid systems mostly lack the resolution to recapitulate the development of finer brain structures with subregional identity, including functionally distinct nuclei in the thalamus. Here, we report a method for converting human embryonic stem cells (hESCs) into ventral thalamic organoids (vThOs) with transcriptionally diverse nuclei identities. Notably, single-cell RNA sequencing revealed previously unachieved thalamic patterning with a thalamic reticular nucleus (TRN) signature, a GABAergic nucleus located in the ventral thalamus. Using vThOs, we explored the functions of TRN-specific, disease-associated genes patched domain containing 1 (PTCHD1) and receptor tyrosine-protein kinase (ERBB4) during human thalamic development. Perturbations in PTCHD1 or ERBB4 impaired neuronal functions in vThOs, albeit not affecting the overall thalamic lineage development. Together, vThOs present an experimental model for understanding nuclei-specific development and pathology in the thalamus of the human brain.

Visual Deprivation Selectively Reduces Thalamic Reticular Nucleus-Mediated Inhibition of the Auditory Thalamus in Adults

Sensory loss leads to widespread cross-modal plasticity across brain areas to allow the remaining senses to guide behavior. While multimodal sensory interactions are often attributed to higher-order sensory areas, cross-modal plasticity has been observed at the level of synaptic changes even across primary sensory cortices. In particular, vision loss leads to widespread circuit adaptation in the primary auditory cortex (A1) even in adults. Here we report using mice of both sexes in which cross-modal plasticity occurs even earlier in the sensory-processing pathway at the level of the thalamus in a modality-selective manner. A week of visual deprivation reduced inhibitory synaptic transmission from the thalamic reticular nucleus (TRN) to the primary auditory thalamus (MGBv) without changes to the primary visual thalamus (dLGN). The plasticity of TRN inhibition to MGBv was observed as a reduction in postsynaptic gain and short-term depression. There was no observable plasticity of the cortical feedback excitatory synaptic transmission from the primary visual cortex to dLGN or TRN and A1 to MGBv, which suggests that the visual deprivation-induced plasticity occurs predominantly at the level of thalamic inhibition. We provide evidence that visual deprivation-induced change in the short-term depression of TRN inhibition to MGBv involves endocannabinoid CB1 receptors. TRN inhibition is considered critical for sensory gating, selective attention, and multimodal performances; hence, its plasticity has implications for sensory processing. Our results suggest that selective disinhibition and altered short-term dynamics of TRN inhibition in the spared thalamic nucleus support cross-modal plasticity in the adult brain.SIGNIFICANCE STATEMENT Losing vision triggers adaptation of the brain to enhance the processing of the remaining senses, which can be observed as better auditory performance in blind subjects. We previously found that depriving vision of adult rodents produces widespread circuit reorganization in the primary auditory cortex and enhances auditory processing at a neural level. Here we report that visual deprivation-induced plasticity in adults occurs much earlier in the auditory pathway, at the level of thalamic inhibition. Sensory processing is largely gated at the level of the thalamus via strong cortical feedback inhibition mediated through the thalamic reticular nucleus (TRN). We found that TRN inhibition of the auditory thalamus is selectively reduced by visual deprivation, thus playing a role in adult cross-modal plasticity.

Excitatory neuronal CHD8 in the regulation of neocortical development and sensory-motor behaviors

CHD8 (chromodomain helicase DNA-binding protein 8) is a chromatin remodeler associated with autism spectrum disorders. Homozygous Chd8 deletion in mice leads to embryonic lethality, making it difficult to assess whether CHD8 regulates brain development and whether CHD8 haploinsufficiency-related macrocephaly reflects normal CHD8 functions. Here, we report that homozygous conditional knockout of Chd8 restricted to neocortical glutamatergic neurons causes apoptosis-dependent near-complete elimination of neocortical structures. These mice, however, display normal survival and hyperactivity, anxiolytic-like behavior, and increased social interaction. They also show largely normal auditory function and moderately impaired visual and motor functions but enhanced whisker-related somatosensory function. These changes accompany thalamic hyperactivity, revealed by 15.2-Tesla fMRI, and increased intrinsic excitability and decreased inhibitory synaptic transmission in thalamic ventral posterior medial (VPM) neurons involved in somatosensation. These results suggest that excitatory neuronal CHD8 critically regulates neocortical development through anti-apoptotic mechanisms, neocortical elimination distinctly affects cognitive behaviors and sensory-motor functions in mice, and Chd8 haploinsufficiency-related macrocephaly might represent compensatory responses.

Context-dependent and dynamic functional influence of corticothalamic pathways to first- and higher-order visual thalamus

Layer 6 (L6) is the sole purveyor of corticothalamic (CT) feedback to first-order thalamus and also sends projections to higher-order thalamus, yet how it engages the full corticothalamic circuit to contribute to sensory processing in an awake animal remains unknown. We sought to elucidate the functional impact of L6CT projections from the primary visual cortex to the dorsolateral geniculate nucleus (first-order) and pulvinar (higher-order) using optogenetics and extracellular electrophysiology in awake mice. While sustained L6CT photostimulation suppresses activity in both visual thalamic nuclei in vivo, moderate-frequency (10 Hz) stimulation powerfully facilitates thalamic spiking. We show that each stimulation paradigm differentially influences the balance between monosynaptic excitatory and disynaptic inhibitory corticothalamic pathways to the dorsolateral geniculate nucleus and pulvinar, as well as the prevalence of burst versus tonic firing. Altogether, our results support a model in which L6CTs modulate first- and higher-order thalamus through parallel excitatory and inhibitory pathways that are highly dynamic and context-dependent.

The thalamic reticular nucleus: A common nucleus of neuropsychiatric diseases and deep brain stimulation

This review focuses on the studies that have been reviewed to determine the influence of the thalamic reticular nucleus on neuropsychiatric diseases and deep brain stimulation. The literature reviewed to date describes how alterations in the thalamic reticular nucleus affect several functions that regulated brain rhythms and provokes symptoms of many disorders. The observations as the basis for the renewed interest in the thalamic reticular nucleus in experimental models and testing its effectiveness in patients with resistant neuropsychiatric disorders. The preclinical studies showed that deep brain stimulation in the thalamic reticular nucleus could have beneficial effects on EEG activity, including synchronization and desynchronization activity of the brain, as well as promoting an alleviate to neuropsychiatric diseases. These observations open up the possibility of studying the role played by neurotransmitters in the pathologic process and the deep brain stimulation in the thalamic reticular nucleus in experimental animal models and offer evidence of its possible action in the human brain.

How Sleep Shapes Thalamocortical Circuit Function in the Visual System

Recent data have shown that sleep plays a beneficial role for cognitive functions such as declarative memory consolidation and perceptual learning. In this article, we review recent findings on the role of sleep in promoting adaptive visual response changes in the lateral geniculate nucleus and primary visual cortex following novel visual experiences. We discuss these findings in the context of what is currently known about how sleep affects the activity and function of thalamocortical circuits and current hypotheses regarding how sleep facilitates synaptic plasticity.

Thalamic Reticular Dysfunction as a Circuit Endophenotype in Neurodevelopmental Disorders

Diagnoses of behavioral disorders such as autism spectrum disorder and schizophrenia are based on symptomatic descriptions that have been difficult to connect to mechanism. Although psychiatric genetics provide insight into the genetic underpinning of such disorders, with a majority of cases explained by polygenic factors, it remains difficult to design rational treatments. In this review, we highlight the value of understanding neural circuit function both as an intermediate level of explanatory description that links gene to behavior and as a pathway for developing rational diagnostics and therapeutics for behavioral disorders. As neural circuits perform hierarchically organized computational functions and give rise to network-level processes (e.g., macroscopic rhythms and goal-directed or homeostatic behaviors), correlated network-level deficits may indicate perturbation of a specific circuit. Therefore, identifying such correlated deficits or a circuit endophenotype would provide a mechanistic point of entry, enhancing both diagnosis and treatment of a given behavioral disorder. We focus on a circuit endophenotype of the thalamic reticular nucleus (TRN) and how its impairment in neurodevelopmental disorders gives rise to a correlated set of readouts across sleep and attention. Because TRN neurons express several disorder-relevant genes identified through genome-wide association studies, exploring the consequences of different TRN disruptions may be of broad translational significance.

Distinct Thalamic Reticular Cell Types Differentially Modulate Normal and Pathological Cortical Rhythms

Integrative brain functions depend on widely distributed, rhythmically coordinated computations. Through its long-ranging connections with cortex and most senses, the thalamus orchestrates the flow of cognitive and sensory information. Essential in this process, the nucleus reticularis thalami (nRT) gates different information streams through its extensive inhibition onto other thalamic nuclei, however, we lack an understanding of how different inhibitory neuron subpopulations in nRT function as gatekeepers. We dissociated the connectivity, physiology, and circuit functions of neurons within rodent nRT, based on parvalbumin (PV) and somatostatin (SOM) expression, and validated the existence of such populations in human nRT. We found that PV, but not SOM, cells are rhythmogenic, and that PV and SOM neurons are connected to and modulate distinct thalamocortical circuits. Notably, PV, but not SOM, neurons modulate somatosensory behavior and disrupt seizures. These results provide a conceptual framework for how nRT may gate incoming information to modulate brain-wide rhythms.

Systematic examination of the impact of depolarization duration on thalamic reticular nucleus firing in vivo

The thalamic reticular nucleus (TRN) is optimally positioned to regulate information processing and state dynamics in dorsal thalamus. Distinct inputs depolarize TRN on multiple time scales, including thalamocortical afferents, corticothalamic 'feedback', and neuromodulation. Here, we systematically tested the concurrent and after-effects of depolarization duration on TRN firing in vivo using selective optogenetic drive. In VGAT-ChR2 mice, we isolated TRN single units (SU: N = 100 neurons) that responded at brief latency (≤5 ms) to stimulation. These units, and multi-unit activity (MUA) on corresponding electrodes, were analyzed in detail. Consistent with prior findings in relay neurons, after light cessation, burst-like events occurred in 74% of MUA sites, and 16% of SU. Increasing optical duration from 2 to 330 ms enhanced this burst probability, and decreased the latency to the first burst after stimulation. During stimulation, neurons demonstrated a 'plateau' firing response lasting 20-30 ms in response to light, but significant heterogeneity existed in the minimal stimuli required to drive this response. Two distinct types were evident, more sensitive 'non-linear' neurons that were driven to the plateau response by 2 or 5 ms pulses, versus 'linear' neurons that fired proportionally to optical duration, and reached the plateau with ∼20-ms optical drive. Non-linear neurons showed higher evoked firing rates and burst probability, but spontaneous rate did not differ between types. These findings provide direct predictions for TRN responses to a range of natural depolarizing inputs, and a guide for the optical control of this key structure in studies of network function and behavior.

Reduced sleep spindle activity point to a TRN-MD thalamus-PFC circuit dysfunction in schizophrenia

Sleep disturbances have been reliably reported in patients with schizophrenia, thus suggesting that abnormal sleep may represent a core feature of this disorder. Traditional electroencephalographic studies investigating sleep architecture have found reduced deep non-rapid eye movement (NREM) sleep, or slow wave sleep (SWS), and increased REM density. However, these findings have been inconsistently observed, and have not survived meta-analysis. By contrast, several recent EEG studies exploring brain activity during sleep have established marked deficits in sleep spindles in schizophrenia, including first-episode and early-onset patients, compared to both healthy and psychiatric comparison subjects. Spindles are waxing and waning, 12-16Hz NREM sleep oscillations that are generated within the thalamus by the thalamic reticular nucleus (TRN), and are then synchronized and sustained in the cortex. While the functional role of sleep spindles still needs to be fully established, increasing evidence has shown that sleep spindles are implicated in learning and memory, including sleep dependent memory consolidation, and spindle parameters have been associated to general cognitive ability and IQ. In this article we will review the EEG studies demonstrating sleep spindle deficits in patients with schizophrenia, and show that spindle deficits can predict their reduced cognitive performance. We will then present data indicating that spindle impairments point to a TRN-MD thalamus-prefrontal cortex circuit deficit, and discuss about the possible molecular mechanisms underlying thalamo-cortical sleep spindle abnormalities in schizophrenia.

Morphology of visual sector thalamic reticular neurons in the macaque monkey suggests retinotopically specialized, parallel stream-mixed input to the lateral geniculate nucleus

The thalamic reticular nucleus (TRN) is a unique brain structure at the interface between the thalamus and the cortex. Because the TRN receives bottom-up sensory input and top-down cortical input, it could serve as an integration hub for sensory and cognitive signals. Functional evidence supports broad roles for the TRN in arousal, attention, and sensory selection. How specific circuits connecting the TRN with sensory thalamic structures implement these functions is not known. The structural organization and function of the TRN is particularly interesting in the context of highly organized sensory systems, such as the primate visual system, where neurons in the retina and dorsal lateral geniculate nucleus of the thalamus (dLGN) are morphologically and physiologically distinct and also specialized for processing particular features of the visual environment. To gain insight into the functional relationship between the visual sector of the TRN and the dLGN, we reconstructed a large number of TRN neurons that were retrogradely labeled following injections of rabies virus expressing enhanced green fluorescent protein (EGFP) into the dLGN. An independent cluster analysis, based on 10 morphological metrics measured for each reconstructed neuron, revealed three clusters of TRN neurons that differed in cell body shape and size, dendritic arborization patterns, and medial-lateral position within the TRN. TRN dendritic and axonal morphologies are inconsistent with visual stream-specific projections to the dLGN. Instead, TRN neuronal organization could facilitate transmission of global arousal and/or cognitive signals to the dLGN with retinotopic precision that preserves specialized processing of foveal versus peripheral visual information. J. Comp. Neurol. 525:1273-1290, 2017. © 2016 Wiley Periodicals, Inc.

Selectively driving cholinergic fibers optically in the thalamic reticular nucleus promotes sleep

Cholinergic projections from the basal forebrain and brainstem are thought to play important roles in rapid eye movement (REM) sleep and arousal. Using transgenic mice in which channelrhdopsin-2 is selectively expressed in cholinergic neurons, we show that optical stimulation of cholinergic inputs to the thalamic reticular nucleus (TRN) activates local GABAergic neurons to promote sleep and protect non-rapid eye movement (NREM) sleep. It does not affect REM sleep. Instead, direct activation of cholinergic input to the TRN shortens the time to sleep onset and generates spindle oscillations that correlate with NREM sleep. It does so by evoking excitatory postsynaptic currents via α7-containing nicotinic acetylcholine receptors and inducing bursts of action potentials in local GABAergic neurons. These findings stand in sharp contrast to previous reports of cholinergic activity driving arousal. Our results provide new insight into the mechanisms controlling sleep.

DOI:http://dx.doi.org/10.7554/eLife.10382.001

Sleep is one of the most familiar activities in our lives and yet there are still many unanswered questions related to how it is regulated. The cholinergic system (or the part of the nervous system that sends signals using a chemical called acetylcholine) is thought to be important for the phase of sleep that is most similar to being awake, so-called REM sleep. This collection of nerve cells has also been implicated in the process of waking up from sleep. However, it remains unclear how the cholinergic system acts on sleep.

Ni, Hou et al. have now used a technique called optogenetics to use light to stimulate the cholinergic system in specific areas in the brains of mice. These experiments found that the activation of the cholinergic system caused awake mice to fall asleep, and promoted more non-REM sleep in sleeping mice. As such, this discovery challenges the previously held view that cholinergic activity was linked to waking up.

Acetylcholine affects cells in a similar way to nicotine from cigarettes. In the future, Ni, Hou et al. would like to explore how many nicotine-like substances are released by the cholinergic system in specific brain areas, and to further investigate when and how sleep is promoted.

DOI:http://dx.doi.org/10.7554/eLife.10382.002

Expression of the calcium binding proteins Necab-1,-2 and -3 in the adult mouse hippocampus and dentate gyrus

The family of EF-hand calcium binding proteins is composed of more than 250 members. In search for other neuronal markers, we studied the expression pattern of Necab-1, -2 and -3 in the Ammons horn of adult mice at the gene- and protein levels using in-situ hybridization and immunohistochemistry. The genes for the three Necab's were expressed in specific, non-overlapping areas of the hippocampus. A minority of the Necab-positive interneurons were GABA-ergic, and they virtually never coexpressed one of the classical calcium binding proteins (calretinin, calbindin D-28k and parvalbumin). Necab's are promising new neuronal markers in the brain.

Neurons in the thalamic reticular nucleus are selective for diverse and complex visual features

All visual signals the cortex receives are influenced by the perigeniculate sector (PGN) of the thalamic reticular nucleus, which receives input from relay cells in the lateral geniculate and provides feedback inhibition in return. Relay cells have been studied in quantitative depth; they behave in a roughly linear fashion and have receptive fields with a stereotyped center-surround structure. We know far less about reticular neurons. Qualitative studies indicate they simply pool ascending input to generate non-selective gain control. Yet the perigeniculate is complicated; local cells are densely interconnected and fire lengthy bursts. Thus, we employed quantitative methods to explore the perigeniculate using relay cells as controls. By adapting methods of spike-triggered averaging and covariance analysis for bursts, we identified both first and second order features that build reticular receptive fields. The shapes of these spatiotemporal subunits varied widely; no stereotyped pattern emerged. Companion experiments showed that the shape of the first but not second order features could be explained by the overlap of On and Off inputs to a given cell. Moreover, we assessed the predictive power of the receptive field and how much information each component subunit conveyed. Linear-non-linear (LN) models including multiple subunits performed better than those made with just one; further each subunit encoded different visual information. Model performance for reticular cells was always lesser than for relay cells, however, indicating that reticular cells process inputs non-linearly. All told, our results suggest that the perigeniculate encodes diverse visual features to selectively modulate activity transmitted downstream.