Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling

Alyagor, Idan; Berkun, Victoria; Keren‐Shaul, Hadas; Marmor-Kollet, Neta; David, Eyal; Mayseless, Oded; Issman-Zecharya, Noa; Amit, Ido; Schuldiner, Oren

doi:10.1016/j.devcel.2018.09.013

Cited by 60 publications

(85 citation statements)

References 65 publications

(102 reference statements)

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“…To test whether the absence of GFP+ axons within the a'b' lobes in babo and EcR-DN mutants was due to the loss of axonal projections or the loss of neuronal identity, we used two antibodies against molecular markers that strongly label a'b' neuron cell bodies in the adult: Trio and Mamo (Figures 1A', S1N) (Alyagor et al, 2018;Awasaki et al, 2000;Croset et al, 2018;Liu et al, 2019). In wildtype clones induced at L1 and analyzed in the adult, we detected strong Trio+ and Mamo+ cells within GFP+ clones ( Figures 1E, S1K).…”

Section: Resultsmentioning

confidence: 99%

Extrinsic Activin signaling cooperates with an intrinsic temporal program to increase mushroom body neuronal diversity

Rossi

Desplan

2019

Preprint

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How diverse neuronal types are sequentially generated from individual neural stem cells is a central question in neurobiology. This "temporal patterning" is controlled by both intrinsic and extrinsic cues. Whether and how extrinsic cues interact with intrinsic programs to increase neuronal diversity, or if they only fine-tune the timing of temporal transitions, is not known. We use the simple Drosophila mushroom body lineage, comprised of only three neuronal types that are sequentially produced, to address the role of extrinsic cues in temporal patterning. As they age, mushroom body stem cells (neuroblasts) advance through intrinsic and opposing temporal gradients of two RNA-binding proteins, Imp and Syp. These intrinsic gradients are used to first produce g, then a'b', and finally ab neurons. The specification of each neuronal type is temporally confined to specific developing stages, and progression from one temporal window to the next occurs concurrently with key, developmental events. This suggests that extrinsic cues play important roles in patterning temporal identity in this lineage. We show that an extrinsic cue, Activin, not only times the young (Imp) to old (Syp) neuroblast fate transition but that it is also essential for increasing neuronal diversity by defining the mid-temporal window (a'b'). Activin reduces the levels of the intrinsic factor Imp, creating a scenario where Imp and Syp are both at low levels for an extended period. In Activin receptor mutants, a'b' neurons are not generated because high Imp levels inhibit the activation of a'b' effectors, including ecdysone receptor signaling.Additionally, the g temporal window appears to be extended and the ab window is shortened, due to a delayed Imp to Syp transition. Our results illustrate that temporal extrinsic cues during neurogenesis can modify an intrinsic temporal program to increase neuronal diversity.

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Section: Resultsmentioning

confidence: 99%

Extrinsic Activin signaling cooperates with an intrinsic temporal program to increase mushroom body neuronal diversity

Rossi

Desplan

2019

Preprint

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“…Thus a network-driven integrative analysis is needed to distinguish hub genes in neuronal remodeling. Idan Alyagor et al [19] (Alyagor et al 2018) investigated their dataset using WGCNA and constructed a co-expression network of three key TFs, in which both DEGs and their intercommunications were studied.…”

Section: Resultsmentioning

confidence: 99%

Co-expression network analysis identifies specific hub genes in association with developmental neuronal remodeling in Drosophila melanogaster

Liu

Sun

2019

Preprint

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As an evolutionarily conserved mechanism, developmental neuronal remodeling is needed for the proper wiring of the nervous system and is critical for understanding the neurodevelopment mechanisms. Previous studies have shown that during metamorphosis lots of Drosophila melanogaster mushroom body neurons experience stereotypic remodeling. However, the related regulators and downstream executors of pathways are yet unclear, especially studies of transcriptional gene co-expression analysis of nervous systems remain insufficient. In this study, we develop a weighted gene co-expression network (WGCNA) to classify gene modules associated with neuronal remodeling. Moreover, functional and pathway enrichment analysis with protein-protein network construction is applied to detect high informative hub genes in the targeted gene module. Thus, we select a total of five hub genes that play critical roles in neuronal remodeling and identify them with functional enrichment analysis and protein-protein interaction network. Overall, this study provides insight into the underlying molecular mechanism of developmental neuronal remodeling in Drosophila melanogaster.

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“…Perturb-seq (81) combines genewise perturbation by CRISPR with single-cell RNA-seq to identify gene sets dysregulated by loss of function of each candidate gene. These have, for example, been used to discover co-transcribed gene networks involved in neuronal remodeling (82), and for in vivo assessment of a set of genes discovered to harbor de novo loss of function mutations in ASDs (83). CRISPR editing has been used in vitro to assess single transcript variant effects by comparing reference and allelic RNA and genomic DNA abundances in edited cultures (84).…”

Section: Mpras Enable Identification Of Functional Regulators and Varmentioning

confidence: 99%

The Oft-Overlooked Massively Parallel Reporter Assay: Where, When, and Which Psychiatric Genetic Variants are Functional?

Mulvey¹,

Lagunas²,

Dougherty³

2020

Preprint

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Neuropsychiatric phenotypes have been long known to be influenced by heritable risk factors. The past decade of genetic studies have confirmed this directly, revealing specific common and rare genetic variants enriched in disease cohorts. However, the early hope for these studies-that only a small set of genes would be responsible for a given disorder-proved false. The picture that has emerged is far more complex: a given disorder may be influenced by myriad coding and noncoding variants of small effect size, and/or by rare but severe variants of large effect size, many de novo.Noncoding genomic sequences harbor a large portion of these variants, the molecular functions of which cannot usually be inferred from sequence alone. This creates a substantial barrier to understanding the higher-order molecular and biological systems underlying disease risk. Fortunately, a proliferation of genetic technologies-namely, scalable oligonucleotide synthesis, high-throughput RNA sequencing, CRISPR, and CRISPR derivatives-have opened novel avenues to experimentally identify biologically significant variants en masse. These advances have yielded an especially versatile technique adaptable to large-scale functional assays of variation in both untranscribed and untranslated regulatory features: Massively Parallel Reporter Assays (MPRAs). MPRAs are powerful molecular genetic tools that can be used to screen tens of thousands of predefined sequences for functional effects in a single experiment. This approach has several ideal features for psychiatric genetics, but remains underutilized in the field to date. To emphasize the opportunities MPRA holds for dissecting psychiatric polygenicity, we review here its applications in the literature, discuss its ability to test several biological variables implicated in psychiatric disorders, illustrate this flexibility with a proof-of-principle, in vivo cell-type specific implementation of the assay, and envision future outcomes of applying MPRA to both computational and experimental neurogenetics.

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Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling

Cited by 60 publications

References 65 publications

Extrinsic Activin signaling cooperates with an intrinsic temporal program to increase mushroom body neuronal diversity

Extrinsic Activin signaling cooperates with an intrinsic temporal program to increase mushroom body neuronal diversity

Co-expression network analysis identifies specific hub genes in association with developmental neuronal remodeling in Drosophila melanogaster

The Oft-Overlooked Massively Parallel Reporter Assay: Where, When, and Which Psychiatric Genetic Variants are Functional?

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