scholarly journals Transcriptional profiling of sequentially generated septal neuron fates

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Miguel Turrero García ◽  
Sarah K Stegmann ◽  
Tiara E Lacey ◽  
Christopher M Reid ◽  
Sinisa Hrvatin ◽  
...  
Keyword(s):  
Transcriptional Profiling ◽  
Neural Progenitors ◽  
Proliferative Capacity ◽  
Proliferative Zone ◽  
Single Cell Rna Sequencing ◽  
Septal Nuclei ◽  
Neuronal Types ◽  
Septal Neurons ◽  
Innate Behaviors ◽  
Insight Into

The septum is a ventral forebrain structure known to regulate innate behaviors. During embryonic development, septal neurons are produced in multiple proliferative areas from neural progenitors following transcriptional programs that are still largely unknown. Here, we use a combination of single cell RNA sequencing, histology and genetic models to address how septal neuron diversity is established during neurogenesis. We find that the transcriptional profiles of septal progenitors change along neurogenesis, coinciding with the generation of distinct neuron types. We characterize the septal eminence, an anatomically distinct and transient proliferative zone composed of progenitors with distinctive molecular profiles, proliferative capacity and fate potential compared to the rostral septal progenitor zone. We show that Nkx2.1-expressing septal eminence progenitors give rise to neurons belonging to at least three morphological classes, born in temporal cohorts that are distributed across different septal nuclei in a sequential fountain-like pattern. Our study provides insight into the molecular programs that control the sequential production of different neuronal types in the septum, a structure with important roles in regulating mood and motivation.

scholarly journals Transcriptional profiling of sequentially generated septal neuron fates

2021 ◽  
Author(s):  
Corey C Harwell ◽  
Miguel Turrero García ◽  
Sarah K Stegmann ◽  
Tiara Lacey ◽  
Christopher M Reid ◽  
...  
Keyword(s):  
Transcriptional Profiling ◽  
Neural Progenitors ◽  
Proliferative Capacity ◽  
Proliferative Zone ◽  
Single Cell Rna Sequencing ◽  
Septal Nuclei ◽  
Neuronal Types ◽  
Septal Neurons ◽  
Innate Behaviors ◽  
Insight Into

The septum is a ventral forebrain structure known to regulate innate behaviors. During embryonic development, septal neurons are produced in multiple proliferative areas from neural progenitors following transcriptional programs that are still largely unknown. Here, we use a combination of single cell RNA sequencing, histology and genetic models to address how septal neuron diversity is established during neurogenesis. We find that the transcriptional profiles of septal progenitors change along neurogenesis, coinciding with the generation of distinct neuron types. We characterize the septal eminence, a spatially distinct and transient proliferative zone composed of progenitors with distinctive molecular profiles, proliferative capacity and fate potential compared to the rostral septal progenitor zone. We show that Nkx2.1-expressing septal eminence progenitors give rise to neurons belonging to at least three morphological classes, born in temporal cohorts that are distributed across different septal nuclei in a sequential fountain-like pattern. Our study provides insight into the molecular programs that control the sequential production of different neuronal types in the septum, a structure with important roles in regulating mood and motivation.

scholarly journals Identification of a regeneration-organizing cell in the Xenopus tail

Science ◽  
2019 ◽  
Vol 364 (6441) ◽  
pp. 653-658 ◽  
Author(s):  
C. Aztekin ◽  
T. W. Hiscock ◽  
J. C. Marioni ◽  
J. B. Gurdon ◽  
B. D. Simons ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Transcriptional Profiling ◽  
Cellular Mechanism ◽  
Cell Type ◽  
Genetic Ablation ◽  
Tail Development ◽  
Naturally Occurring ◽  
Early Embryos ◽  
Single Cell Rna Sequencing ◽  
Wound Epidermis

Unlike mammals, Xenopus laevis tadpoles have a high regenerative potential. To characterize this regenerative response, we performed single-cell RNA sequencing after tail amputation. By comparing naturally occurring regeneration-competent and -incompetent tadpoles, we identified a previously unrecognized cell type, which we term the regeneration-organizing cell (ROC). ROCs are present in the epidermis during normal tail development and specifically relocalize to the amputation plane of regeneration-competent tadpoles, forming the wound epidermis. Genetic ablation or manual removal of ROCs blocks regeneration, whereas transplantation of ROC-containing grafts induces ectopic outgrowths in early embryos. Transcriptional profiling revealed that ROCs secrete ligands associated with key regenerative pathways, signaling to progenitors to reconstitute lost tissue. These findings reveal the cellular mechanism through which ROCs form the wound epidermis and ensure successful regeneration.

scholarly journals Transcriptional Profiling of Rapidly Growing Cucumber Fruit by 454-Pyrosequencing Analysis

2010 ◽  
Vol 135 (4) ◽  
pp. 291-302 ◽  
Author(s):  
Kaori Ando ◽  
Rebecca Grumet
Keyword(s):  
Gene Expression ◽  
454 Pyrosequencing ◽  
Transcriptional Profiling ◽  
Transcript Abundance ◽  
Yield And Quality ◽  
Cucumber Fruit ◽  
Polymerase Chain ◽  
Expressed Sequence ◽  
Development Proceeds ◽  
Insight Into

Fruit development proceeds from cell division to expansion, maturation, and ripening. Expansion is critical for size, yield, and quality; however, this period of development has received little attention. We used 454-pyrosequencing to develop a cucumber (Cucumis sativus) fruit transcriptome, identify highly expressed transcripts, and characterize key functions during exponential fruit growth. The resulting 187,406 expressed sequence tags (ESTs) were assembled into 13,878 contigs. Quantitative real-time polymerase chain reaction (qRT-PCR) verification of differentially expressed genes from fruit of different ages, and high correlation in transcript frequency between replicates, indicated that number of reads/contig reflects transcript abundance. Putative homologs were identified in Arabidopsis thaliana for 89% of the contigs represented by at least 10 ESTs; another 4% had homologs in other species. The remainder had homologs only in cucurbit species. The most highly expressed contigs were strongly enriched for growth (aquaporins, vacuolar ATPase, phloem proteins, tubulins, actins, cell wall-associated, and hormone-related), lipid, latex, and defense-related homologs. These results provide a resource for gene expression analysis in cucumber, profile gene expression in rapidly growing fruit, and shed insight into an important, but poorly characterized, developmental stage influencing fruit yield and quality.

scholarly journals Single-Cell RNA-Sequencing Identifies Infrapatellar Fat Pad Macrophage Polarization in Acute Synovitis/Fat Pad Fibrosis and Cell Therapy

2021 ◽  
Vol 8 (11) ◽  
pp. 166
Author(s):  
Dimitrios Kouroupis ◽  
Thomas M. Best ◽  
Lee D. Kaplan ◽  
Diego Correa ◽  
Anthony J. Griswold
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Transcriptional Profiling ◽  
Macrophage Polarization ◽  
Myeloid Cells ◽  
Cellular Heterogeneity ◽  
Joint Disease ◽  
Infrapatellar Fat Pad ◽  
Fat Pad ◽  
Single Cell Rna Sequencing

The pathogenesis and progression of knee inflammatory pathologies is modulated partly by residing macrophages in the infrapatellar fat pad (IFP), thus, macrophage polarization towards pro-inflammatory (M1) or anti-inflammatory (M2) phenotypes is important in joint disease pathologies. Alteration of M1/M2 balance contributes to the initiation and progression of joint inflammation and can be potentially altered with mesenchymal stem cell (MSC) therapy. In an acute synovial/IFP inflammation rat model a single intra-articular injection of IFP-MSC was performed, having as controls (1) diseased rats not receiving IFP-MSC and (2) non-diseased rats. After 4 days, cell specific transcriptional profiling via single-cell RNA-sequencing was performed on isolated IFP tissue from each group. Eight transcriptomically distinct cell populations were identified within the IFP across all three treatment groups with a noted difference in the proportion of myeloid cells across the groups. Largely myeloid cells consisted of macrophages (>90%); one M1 sub-cluster highly expressing pro-inflammatory markers and two M2 sub-clusters with one of them expressing higher levels of canonical M2 markers. Notably, the diseased samples (11.9%) had the lowest proportion of cells expressing M2 markers relative to healthy (14.8%) and MSC treated (19.4%) samples. These results suggest a phenotypic polarization of IFP macrophages towards the pro-inflammatory M1 phenotype in an acute model of inflammation, which are alleviated by IFP-MSC therapy inducing a switch towards an alternate M2 status. Understanding the IFP cellular heterogeneity and associated transcriptional programs may offer insights into novel therapeutic strategies for disabling joint disease pathologies.

scholarly journals Transcriptional regulation of MGE progenitor proliferation by PRDM16 controls cortical GABAergic interneuron production

Development ◽  
2020 ◽  
Vol 147 (22) ◽  
pp. dev187526
Author(s):  
Miguel Turrero García ◽  
José-Manuel Baizabal ◽  
Diana N. Tran ◽  
Rui Peixoto ◽  
Wengang Wang ◽  
...  
Keyword(s):  
Cortical Neurons ◽  
Radial Glia ◽  
Regulatory Elements ◽  
Neural Progenitors ◽  
Gabaergic Interneuron ◽  
Gabaergic Interneurons ◽  
Proliferative Capacity ◽  
Medial Ganglionic Eminence ◽  
Developmental Gene Expression ◽  
Dorsal Telencephalon

ABSTRACTThe mammalian cortex is populated by neurons derived from neural progenitors located throughout the embryonic telencephalon. Excitatory neurons are derived from the dorsal telencephalon, whereas inhibitory interneurons are generated in its ventral portion. The transcriptional regulator PRDM16 is expressed by radial glia, neural progenitors present in both regions; however, its mechanisms of action are still not fully understood. It is unclear whether PRDM16 plays a similar role in neurogenesis in both dorsal and ventral progenitor lineages and, if so, whether it regulates common or unique networks of genes. Here, we show that Prdm16 expression in mouse medial ganglionic eminence (MGE) progenitors is required for maintaining their proliferative capacity and for the production of proper numbers of forebrain GABAergic interneurons. PRDM16 binds to cis-regulatory elements and represses the expression of region-specific neuronal differentiation genes, thereby controlling the timing of neuronal maturation. PRDM16 regulates convergent developmental gene expression programs in the cortex and MGE, which utilize both common and region-specific sets of genes to control the proliferative capacity of neural progenitors, ensuring the generation of correct numbers of cortical neurons.

scholarly journals Single-cell transcriptomics allows novel insights into aging and circadian processes

2020 ◽  
Vol 19 (5-6) ◽  
pp. 343-349
Author(s):  
Sara S Fonseca Costa ◽  
Marc Robinson-Rechavi ◽  
Jürgen A Ripperger
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Cellular Level ◽  
Biological Processes ◽  
New Methods ◽  
New Findings ◽  
Single Cell Rna Sequencing ◽  
Aging And Circadian Rhythms ◽  
Insight Into ◽  
Different Time Scales

Abstract Aging and circadian rhythms are two biological processes that affect an organism, although at different time scales. Nevertheless, due to the overlap of their actions, it was speculated that both interfere or interact with each other. However, to address this question, a much deeper insight into these processes is necessary, especially at the cellular level. New methods such as single-cell RNA-sequencing (scRNA-Seq) have the potential to close this gap in our knowledge. In this review, we analyze applications of scRNA-Seq from the aging and circadian rhythm fields and highlight new findings emerging from the analysis of single cells, especially in humans or rodents. Furthermore, we judge the potential of scRNA-Seq to identify common traits of both processes. Overall, this method offers several advantages over more traditional methods analyzing gene expression and will become an important tool to unravel the link between these biological processes.

scholarly journals Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Floor Hugenholtz ◽  
Jarmo Ritari ◽  
Lotta Nylund ◽  
Mark Davids ◽  
Reetta Satokari ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Transcriptional Profiling ◽  
Lactobacillus Rhamnosus ◽  
Rna Seq ◽  
Faecal Samples ◽  
Carbohydrate Fermentation ◽  
Stool Samples ◽  
The Impact ◽  
Increased Activity ◽  
Insight Into

Newborns are rapidly colonized by microbes and their intestinal tracts contain highly dynamic and rapidly developing microbial communities in the first months of life. In this study, we describe the feasibility of isolating mRNA from rapidly processed faecal samples and applying deep RNA-Seq analysis to provide insight into the active contributors of the microbial community in early life. Specific attention is given to the impact of removing rRNA from the mRNA on the phylogenetic and transcriptional profiling and its analysis depth. A breastfed baby was followed in the first six months of life during adaptation to solid food, dairy products, and formula. It was found that, in the weaning period, the total transcriptional activity of Actinobacteria, mainly represented by Bifidobacterium, decreased while that of Firmicutes increased over time. Moreover, Firmicutes and Actinobacteria, including the canonical Bifidobacteria as well as Collinsella, were found to be important contributors to carbohydrate fermentation and vitamin biosynthesis in the infant intestine. Finally, the expression of Lactobacillus rhamnosus-like genes was detected, likely following transfer from the mother who consumed L. rhamnosus GG. The study indicates that metatranscriptome analysis of the infant gut microbiota is feasible on infant stool samples and can be used to provide insight into the core activities of the developing community.

scholarly journals Molecular identification of sixty-three amacrine cell types completes a mouse retinal cell atlas

2020 ◽  
Author(s):  
Wenjun Yan ◽  
Mallory A. Laboulaye ◽  
Nicholas M. Tran ◽  
Irene E. Whitney ◽  
Inbal Benhar ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
High Throughput ◽  
Amacrine Cells ◽  
Cell Types ◽  
Retinal Cell ◽  
Mouse Retina ◽  
Single Cell Rna Sequencing ◽  
Neuronal Types ◽  
The Brain

ABSTRACTAmacrine cells (ACs) are a diverse class of interneurons that modulate input from photoreceptors to retinal ganglion cells (RGCs), rendering each RGC type selectively sensitive to particular visual features, which are then relayed to the brain. While many AC types have been identified morphologically and physiologically, they have not been comprehensively classified or molecularly characterized. We used high-throughput single-cell RNA sequencing (scRNA-seq) to profile >32,000 ACs from mouse retina, and applied computational methods to identify 63 AC types. We identified molecular markers for each type, and used them to characterize the morphology of multiple types. We show that they include nearly all previously known AC types as well as many that had not been described. Consistent with previous studies, most of the AC types express markers for the canonical inhibitory neurotransmitters GABA or glycine, but several express neither or both. In addition, many express one or more neuropeptides, and two express glutamatergic markers. We also explored transcriptomic relationships among AC types and identified transcription factors expressed by individual or multiple closely related types. Noteworthy among these were Meis2 and Tcf4, expressed by most GABAergic and most glycinergic types, respectively. Together, these results provide a foundation for developmental and functional studies of ACs, as well as means for genetically accessing them. Along with previous molecular, physiological and morphological analyses, they establish the existence of at least 130 neuronal types and nearly 140 cell types in mouse retina.SIGNIFICANCE STATEMENTThe mouse retina is a leading model for analyzing the development, structure, function and pathology of neural circuits. A complete molecular atlas of retinal cell types provides an important foundation for these studies. We used high-throughput single-cell RNA sequencing (scRNA-seq) to characterize the most heterogeneous class of retinal interneurons, amacrine cells, identifying 63 distinct types. The atlas includes types identified previously as well as many novel types. We provide evidence for use of multiple neurotransmitters and neuropeptides and identify transcription factors expressed by groups of closely related types. Combining these results with those obtained previously, we proposed that the mouse retina contains 130 neuronal types, and is therefore comparable in complexity to other regions of the brain.

scholarly journals Distinct roles for dynein light intermediate chains in neurogenesis, migration, and terminal somal translocation

2019 ◽  
Vol 218 (3) ◽  
pp. 808-819 ◽  
Author(s):  
João Carlos Gonçalves ◽  
Tiago J. Dantas ◽  
Richard B. Vallee
Keyword(s):  
Neuronal Migration ◽  
Cytoplasmic Dynein ◽  
Neural Progenitors ◽  
In Utero Electroporation ◽  
Neocortical Development ◽  
Newborn Neurons ◽  
Dynein Light Intermediate Chains ◽  
Intermediate Chains ◽  
Developing Rat ◽  
Insight Into

Cytoplasmic dynein participates in multiple aspects of neocortical development. These include neural progenitor proliferation, morphogenesis, and neuronal migration. The cytoplasmic dynein light intermediate chains (LICs) 1 and 2 are cargo-binding subunits, though their relative roles are not well understood. Here, we used in utero electroporation of shRNAs or LIC functional domains to determine the relative contributions of the two LICs in the developing rat brain. We find that LIC1, through BicD2, is required for apical nuclear migration in neural progenitors. In newborn neurons, we observe specific roles for LIC1 in the multipolar to bipolar transition and glial-guided neuronal migration. In contrast, LIC2 contributes to a novel dynein role in the little-studied mode of migration, terminal somal translocation. Together, our results provide novel insight into the LICs’ unique functions during brain development and dynein regulation overall.

scholarly journals Insight into Genes Regulating Postharvest Aflatoxin Contamination of Tetraploid Peanut from Transcriptional Profiling

Genetics ◽  
2018 ◽  
Vol 209 (1) ◽  
pp. 143-156 ◽  
Author(s):  
Walid Korani ◽  
Ye Chu ◽  
C. Corley Holbrook ◽  
Peggy Ozias-Akins
Keyword(s):  
Transcriptional Profiling ◽  
Aflatoxin Contamination ◽  
Insight Into
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