Enhancer viruses for combinatorial cell-subclass-specific labeling

Graybuck, Lucas T.; Daigle, Tanya L.; Sedeño-Cortés, Adriana E.; Walker, Miranda; Kalmbach, Brian; Lenz, Garreck H.; Morin, Elyse; Nguyen, Thuc Nghi; Garren, Emma; Bendrick, Jacqueline L.; Kim, Tae Kyung; Zhou, Thomas; Mortrud, Marty; Yao, Shenqin; Siverts, La’ Akea; Larsen, Rachael; Gore, Bryan B.; Szelenyi, Eric R.; Trader, Cameron; Balaram, Pooja; Velthoven, Cindy T. J. van; Chiang, Megan; Mich, John K.; Dee, Nick; Goldy, Jeff; Çetin, Ali; Smith, Kimberly A.; Way, Sharon W.; Esposito, Luke; Yao, Zizhen; Gradinaru, Viviana; Sunkin, Susan M.; Lein, Ed; Levi, Boaz P.; Ting, Jonathan T.; Zeng, Hongkui; Tasic, Bosiljka

doi:10.1016/j.neuron.2021.03.011

Cited by 130 publications

(145 citation statements)

References 86 publications

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“…24 ). Other future modifications could include the insertion of cell type specific regulatory elements 58 , activity indicators 59 , optogenetic 60 or chemogenetic 61 probes for functional interrogation of clonally related cells 62,63 . Overall, we believe that an integrated approach such as Space-TREX is required to disentangle the complex relationships between cell identity, cell history and tissue anatomy required to understand both the healthy and diseased brain.…”

Section: Discussionmentioning

confidence: 99%

Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

Ratz

Berlin

Larsson

et al. 2021

Preprint

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The mammalian brain contains a large number of specialized cells that develop from a thin sheet of neuroepithelial progenitor cells. Recently, high throughput single-cell technologies have been used to define the molecular diversity of hundreds of cell types in the nervous system. However, the lineage relationships between mature brain cells and progenitor cells are not well understood, because transcriptomic studies do not allow insights into clonal relationships and classical fate-mapping techniques are not scalable. Here we show in vivo barcoding of early progenitor cells that enables simultaneous profiling of cell phenotypes and clonal relations in the mouse brain using single-cell and spatial transcriptomics. We reconstructed thousands of clones to uncover the existence of fate-restricted progenitor cells in the mouse hippocampal neuroepithelium and show that microglia are derived from few primitive myeloid precursors that massively expand to generate widely dispersed progeny. By coupling spatial transcriptomics with clonal barcoding, we disentangle migration patterns of clonally related cells in densely labelled tissue sections. Compared to classical fate mapping, our approach enables high-throughput dense reconstruction of cell phenotypes and clonal relations at the single-cell and tissue level in individual animals and provides an integrated approach for understanding tissue architecture.

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Section: Discussionmentioning

confidence: 99%

Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

Ratz

Berlin

Larsson

et al. 2021

Preprint

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“…Such an absence of differences, however, is not surprising, because our manipulation approaches nonspecifically suppressed all L6 CT neuron subtypes. Once genetic targeting of L6 CT subtypes is possible [99, 100], it will be important to test the stream-specificity of CT feedback in the mouse.…”

Section: Discussionmentioning

confidence: 99%

Robust effects of corticothalamic feedback and behavioral state on movie responses in mouse dLGN

Špaček¹,

Born²,

Crombie³

et al. 2019

Preprint

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8Neurons in the dorsolateral geniculate nucleus (dLGN) of the thalamus are contacted by a large number of feedback synapses from cortex, whose role in visual processing is poorly understood. Past studies investigating this role have mostly used simple visual stimuli and anesthetized animals, but corticothalamic (CT) feedback might be particularly relevant during processing of complex visual stimuli, and its effects might depend on behavioral state. Here, we find that CT feedback robustly modulates responses to naturalistic movie clips by increasing response gain and promoting tonic firing mode. Compared to these robust effects for naturalistic movies, CT feedback effects were less consistent for simple grating stimuli. Finally, while CT feedback and locomotion affected dLGN responses in similar ways, we found their effects to be largely independent. We propose that CT feedback and behavioral state use separate routes to powerfully modulate visual information on its way to cortex.

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“…Our approach of selecting putative enhancers based on specific H3K27ac ChIP-seq peaks, located close to differentially expressed genes, resulted in a high success rate (60 to 75%) akin to other studies leveraging a similar approach (Gorkin et al, 2020;Graybuck et al, 2021). In contrast, our large-scale library based solely on ATAC-seq peaks that decrease after SOX10 KD contained only 15.1% of active enhancers (Supplementary Fig 8).…”

Section: Discussionmentioning

confidence: 82%

“…Another strategy to identify candidate enhancers is to use active enhancer marks such as H3K27ac and chromatin accessibility (Gray et al, 2017;Minnoye et al, 2021;Rada-Iglesias et al, 2011). The most successful studies, combining this approach with transcriptome data, generated libraries with up to 60% of active enhancers in the target cell type (Gorkin et al, 2020;Graybuck et al, 2021). Massively parallel reporter assays (MPRA) have been developed to screen the activity of thousands of sequences simultaneously (Inoue and Ahituv, 2015;Melnikov et al, 2012;White et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Analysis of long and short enhancers in melanoma cell states

Mauduit

Minnoye

Taskiran

et al. 2021

Preprint

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Understanding how enhancers drive cell type specificity and efficiently identifying them is essential for the development of innovative therapeutic strategies. In melanoma, the melanocytic (MEL) and the mesenchymal-like (MES) states present themselves with different responses to therapy, making the identification of specific enhancers highly relevant. Using massively parallel reporter assay (MPRA) in a panel of patient-derived melanoma lines (MM lines), we set to identify and decipher melanoma enhancers by first focusing on regions with state specific H3K27 acetylation close to differentially expressed genes. A more in-depth evaluation of those regions was then pursued by investigating the activity of ATAC-seq peaks found therein along with a full tiling of the acetylated regions with 190 bp sequences. Activity was observed in more than 60% of the selected regions and we were able to precisely locate the active regions within ATAC-seq peaks. Comparison of sequence content with activity, using the deep learning model DeepMEL2, revealed that AP-1 alone is responsible for the MES enhancer activity, while SOX and MITF both influence MEL enhancer activity with SOX being required to achieve high levels of activity. Overall, our MPRA assays shed light on the relationship between long and short sequences in terms of their sequence content, enhancer activity, and specificity as reporters across melanoma cell states.

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Enhancer viruses for combinatorial cell-subclass-specific labeling

Cited by 130 publications

References 86 publications

Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

Robust effects of corticothalamic feedback and behavioral state on movie responses in mouse dLGN

Analysis of long and short enhancers in melanoma cell states

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