DAF-16/FoxO and DAF-12/VDR control cellular plasticity both cell-autonomously and via interorgan signaling

Many cell types display the remarkable ability to alter their cellular phenotype in response to specific external or internal signals. Such phenotypic plasticity is apparent in the nematode C. elegans when adverse environmental conditions trigger entry into the dauer diapause stage. This entry is accompanied by structural, molecular and functional remodeling of a number of distinct tissue types of the animal, including its nervous system. The transcription factor effectors of three different hormonal signaling systems, the insulin-responsive DAF-16/FoxO transcription factor, the TGFβ-responsive DAF-3/SMAD transcription factor and the steroid nuclear hormone receptor, DAF-12/VDR, a homolog of the vitamin D receptor, were previously shown to be required for entering the dauer arrest stage, but their cellular and temporal focus of action for the underlying cellular remodeling processes remained incompletely understood. Through the generation of conditional alleles that allowed us to spatially and temporally control gene activity, we show here that all three transcription factors are not only required to initiate tissue remodeling upon entry into the dauer stage, as shown before, but are also continuously required to maintain the remodeled state. We show that DAF-3/SMAD is required in sensory neurons to promote and then maintain animal-wide tissue remodeling events. In contrast, DAF-16/FoxO or DAF-12/VDR act cell autonomously to control anatomical, molecular and behavioral remodeling events in specific cell types. Intriguingly, we also uncover non-cell autonomous function of DAF-16/FoxO and DAF-12/VDR in nervous system remodeling, indicating the presence of several insulin-dependent inter-organ signaling axes. Our findings provide novel perspectives on how hormonal systems control tissue remodeling.

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DAF-16/FoxO and DAF-12/VDR control cellular plasticity both cell-autonomously and via interorgan signaling

PLoS Biology ◽

10.1371/journal.pbio.3001204 ◽

2021 ◽

Vol 19 (4) ◽

pp. e3001204

Author(s):

Ulkar Aghayeva ◽

Abhishek Bhattacharya ◽

Surojit Sural ◽

Eliza Jaeger ◽

Matthew Churgin ◽

...

Keyword(s):

Nervous System ◽

Tissue Remodeling ◽

Cell Types ◽

Nuclear Hormone Receptor ◽

Specific Cell ◽

Signaling Systems ◽

Autonomous Function ◽

Insulin Dependent ◽

Adverse Environmental Conditions ◽

Temporal Focus

Many cell types display the remarkable ability to alter their cellular phenotype in response to specific external or internal signals. Such phenotypic plasticity is apparent in the nematodeCaenorhabditis eleganswhen adverse environmental conditions trigger entry into the dauer diapause stage. This entry is accompanied by structural, molecular, and functional remodeling of a number of distinct tissue types of the animal, including its nervous system. The transcription factor (TF) effectors of 3 different hormonal signaling systems, the insulin-responsive DAF-16/FoxO TF, the TGFβ-responsive DAF-3/SMAD TF, and the steroid nuclear hormone receptor, DAF-12/VDR, a homolog of the vitamin D receptor (VDR), were previously shown to be required for entering the dauer arrest stage, but their cellular and temporal focus of action for the underlying cellular remodeling processes remained incompletely understood. Through the generation of conditional alleles that allowed us to spatially and temporally control gene activity, we show here that all 3 TFs are not only required to initiate tissue remodeling upon entry into the dauer stage, as shown before, but are also continuously required to maintain the remodeled state. We show that DAF-3/SMAD is required in sensory neurons to promote and then maintain animal-wide tissue remodeling events. In contrast, DAF-16/FoxO or DAF-12/VDR act cell-autonomously to control anatomical, molecular, and behavioral remodeling events in specific cell types. Intriguingly, we also uncover non-cell autonomous function of DAF-16/FoxO and DAF-12/VDR in nervous system remodeling, indicating the presence of several insulin-dependent interorgan signaling axes. Our findings provide novel perspectives into how hormonal systems control tissue remodeling.

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The role of globins in cardiovascular physiology

Physiological Reviews ◽

10.1152/physrev.00037.2020 ◽

2021 ◽

Author(s):

T.C. Steven Keller ◽

Christophe Lechauve ◽

Alexander S Keller ◽

Steven Brooks ◽

Mitchell J Weiss ◽

...

Keyword(s):

Skeletal Muscle ◽

Central Nervous System ◽

Nervous System ◽

Smooth Muscle ◽

Vascular Smooth Muscle ◽

Smooth Muscle Cells ◽

Muscle Cells ◽

Cell Types ◽

Specific Cell ◽

In Cells

Globin proteins exist in every cell type of the vasculature, from erythrocytes to endothelial cells, vascular smooth muscle cells, and peripheral nerve cells. Many globin subtypes are also expressed in muscle tissues (including cardiac and skeletal muscle), in other organ-specific cell types, and in cells of the central nervous system. The ability of each of these globins to interact with molecular oxygen (O2) and nitric oxide (NO) is preserved across these contexts. Endothelial α-globin is an example of extra-erythrocytic globin expression. Other globins, including myoglobin, cytoglobin, and neuroglobin are observed in other vascular tissues. Myoglobin is observed primarily in skeletal muscle and smooth muscle cells surrounding the aorta or other large arteries. Cytoglobin is found in vascular smooth muscle but can also be expressed in non-vascular cell types, especially in oxidative stress conditions after ischemic insult. Neuroglobin was first observed in neuronal cells, and its expression appears to be restricted mainly to the central and peripheral nervous systems. Brain and central nervous system neurons expressing neuroglobin are positioned close to many arteries within the brain parenchyma and can control smooth muscle contraction and, thus, tissue perfusion and vascular reactivity. Overall, reactions between NO and globin heme-iron contribute to vascular homeostasis by regulating vasodilatory NO signals and scaveging reactive species in cells of the mammalian vascular system. Here, we discuss how globin proteins affect vascular physiology with a focus on NO biology, and offer perspectives for future study of these functions.

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Localization of phosphotyrosine adaptor protein ShcD/SHC4 in the adult rat central nervous system

BMC Neuroscience ◽

10.1186/s12868-019-0541-5 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Hannah N. Robeson ◽

Hayley R. Lau ◽

Laura A. New ◽

Jasmin Lalonde ◽

John N. Armstrong ◽

...

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Olfactory Bulb ◽

Adaptor Protein ◽

Cell Types ◽

Olfactory Nerve ◽

Adult Brain ◽

Specific Cell ◽

Adult Rat ◽

Fiber Tracts

Abstract Background Mammalian Shc (Src homology and collagen) proteins comprise a family of four phosphotyrosine adaptor molecules which exhibit varied spatiotemporal expression and signaling functions. ShcD is the most recently discovered homologue and it is highly expressed in the developing central nervous system (CNS) and adult brain. Presently however, its localization within specific cell types of mature neural structures has yet to be characterized. Results In the current study, we examine the expression profile of ShcD in the adult rat CNS using immunohistochemistry, and compare with those of the neuronally enriched ShcB and ShcC proteins. ShcD shows relatively widespread distribution in the adult brain and spinal cord, with prominent levels of staining throughout the olfactory bulb, as well as in sub-structures of the cerebellum and hippocampus, including the subgranular zone. Co-localization studies confirm the expression of ShcD in mature neurons and progenitor cells. ShcD immunoreactivity is primarily localized to axons and somata, consistent with the function of ShcD as a cytoplasmic adaptor. Regional differences in expression are observed among neural Shc proteins, with ShcC predominating in the hippocampus, cerebellum, and some fiber tracts. Interestingly, ShcD is uniquely expressed in the olfactory nerve layer and in glomeruli of the main olfactory bulb. Conclusions Together our findings suggest that ShcD may provide a distinct signaling contribution within the olfactory system, and that overlapping expression of ShcD with other Shc proteins may allow compensatory functions in the brain.

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An activation domain of the helix-loop-helix transcription factor E2A shows cell type preference in vivo in microinjected zebra fish embryos.

Molecular and Cellular Biology ◽

10.1128/mcb.16.4.1714 ◽

1996 ◽

Vol 16 (4) ◽

pp. 1714-1721 ◽

Cited By ~ 19

Author(s):

F Argenton ◽

Y Arava ◽

A Aronheim ◽

M D Walker

Keyword(s):

Gene Expression ◽

Nervous System ◽

Transcription Factor ◽

Transcription Activation ◽

Cell Types ◽

Zebra Fish ◽

Reporter Plasmid ◽

Activation Domains ◽

Helix Loop Helix

The E2A protein is a mammalian transcription factor of the helix-loop-helix family which is implicated in cell-specific gene expression in several cell lineages. Mouse E2A contains two independent transcription activation domains, ADI and ADII; whereas ADI functions effectively in a variety of cultured cell lines, ADII shows preferential activity in pancreatic beta cells. To analyze this preferential activity in an in vivo setting, we adapted a system involving transient gene expression in microinjected zebra fish embryos. Fertilized one- to four-cell embryos were coinjected with an expression plasmid and a reporter plasmid. The expression plasmids used encode the yeast Gal4 DNA-binding domain (DBD) alone, or Gal4 DBD fused to ADI, ADII, or VP16. The reporter plasmid includes the luciferase gene linked to a promoter containing repeats of UASg, the Gal4-binding site. Embryo extracts prepared 24 h after injection showed significant luciferase activity in response to each of the three activation domains. To determine the cell types in which the activation domains were functioning, a reporter plasmid encoding beta-galactosidase and then in situ staining of whole embryos were used. Expression of ADI led to activation in all major groups of cell types of the embryo (skin, sclerotome, myotome, notochord, and nervous system). On the other hand, ADII led to negligible expression in the sclerotome, notochord, and nervous system and much more frequent expression in the myotome. Parallel experiments conducted with transfected mammalian cells have confirmed that ADII shows significant activity in myoblast cells but little or no activity in neuronal precursor cells, consistent with our observations in zebra fish. This transient-expression approach permits rapid in vivo analysis of the properties of transcription activation domains: the data show that ADII functions preferentially in cells of muscle lineage, consistent with the notion that certain activation domains contribute to selective gene activation in vivo.

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Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells

10.1101/538553 ◽

2019 ◽

Cited By ~ 3

Author(s):

Arnav Moudgil ◽

Michael N. Wilkinson ◽

Xuhua Chen ◽

June He ◽

Alex J. Cammack ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Single Cell ◽

Binding Sites ◽

Expression Profiles ◽

Single Cells ◽

Gene Expression Profiles ◽

Cell Types ◽

Specific Cell

AbstractIn situ measurements of transcription factor (TF) binding are confounded by cellular heterogeneity and represent averaged profiles in complex tissues. Single cell RNA-seq (scRNA-seq) is capable of resolving different cell types based on gene expression profiles, but no technology exists to directly link specific cell types to the binding pattern of TFs in those cell types. Here, we present self-reporting transposons (SRTs) and their use in single cell calling cards (scCC), a novel assay for simultaneously capturing gene expression profiles and mapping TF binding sites in single cells. First, we show how the genomic locations of SRTs can be recovered from mRNA. Next, we demonstrate that SRTs deposited by the piggyBac transposase can be used to map the genome-wide localization of the TFs SP1, through a direct fusion of the two proteins, and BRD4, through its native affinity for piggyBac. We then present the scCC method, which maps SRTs from scRNA-seq libraries, thus enabling concomitant identification of cell types and TF binding sites in those same cells. As a proof-of-concept, we show recovery of cell type-specific BRD4 and SP1 binding sites from cultured cells. Finally, we map Brd4 binding sites in the mouse cortex at single cell resolution, thus establishing a new technique for studying TF biology in situ.

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A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

Science ◽

10.1126/science.aax1971 ◽

2019 ◽

Vol 365 (6459) ◽

pp. eaax1971 ◽

Cited By ~ 65

Author(s):

Jonathan S. Packer ◽

Qin Zhu ◽

Chau Huynh ◽

Priya Sivaramakrishnan ◽

Elicia Preston ◽

...

Keyword(s):

Nervous System ◽

Caenorhabditis Elegans ◽

Single Cell ◽

Molecular Basis ◽

Cell Types ◽

Embryonic Cells ◽

Cell Type ◽

C Elegans ◽

Exact Position ◽

Sister Cells

Caenorhabditis elegans is an animal with few cells but a wide diversity of cell types. In this study, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and preterminal cell types, mapping most single-cell transcriptomes to their exact position in C. elegans’ invariant lineage. Using these annotations, we find that (i) the correlation between a cell’s lineage and its transcriptome increases from middle to late gastrulation, then falls substantially as cells in the nervous system and pharynx adopt their terminal fates; (ii) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and (iii) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state.

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FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system

Nucleic Acids Research ◽

10.1093/nar/gkz968 ◽

2019 ◽

Cited By ~ 2

Author(s):

Ryoji Amamoto ◽

Emanuela Zuccaro ◽

Nathan C Curry ◽

Sonia Khurana ◽

Hsu-Hsin Chen ◽

...

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Rna Sequencing ◽

Human Tissue ◽

Transcriptional Profiling ◽

Cell Types ◽

Specific Cell ◽

Human Central Nervous System ◽

Tissue Samples ◽

Rna Profiling

Abstract Thousands of frozen, archived tissue samples from the human central nervous system (CNS) are currently available in brain banks. As recent developments in RNA sequencing technologies are beginning to elucidate the cellular diversity present within the human CNS, it is becoming clear that an understanding of this diversity would greatly benefit from deeper transcriptional analyses. Single cell and single nucleus RNA profiling provide one avenue to decipher this heterogeneity. An alternative, complementary approach is to profile isolated, pre-defined cell types and use methods that can be applied to many archived human tissue samples that have been stored long-term. Here, we developed FIN-Seq (Frozen Immunolabeled Nuclei Sequencing), a method that accomplishes these goals. FIN-Seq uses immunohistochemical isolation of nuclei of specific cell types from frozen human tissue, followed by bulk RNA-Sequencing. We applied this method to frozen postmortem samples of human cerebral cortex and retina and were able to identify transcripts, including low abundance transcripts, in specific cell types.

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Exploratory analysis of transposable elements expression in the C. elegans early embryo

BMC Bioinformatics ◽

10.1186/s12859-019-3088-7 ◽

2019 ◽

Vol 20 (S9) ◽

Cited By ~ 3

Author(s):

Federico Ansaloni ◽

Margherita Scarpato ◽

Elia Di Schiavi ◽

Stefano Gustincich ◽

Remo Sanges

Keyword(s):

Nervous System ◽

Transposable Elements ◽

Embryo Development ◽

Cell Types ◽

Early Embryo ◽

Bioinformatics Pipeline ◽

Early Embryo Development ◽

C Elegans ◽

Differentiated Cells ◽

Different Cell Types

Abstract Background Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is becoming evident that TE have a role in several physiological and pathological processes. In particular, it has been shown that TE transcription is necessary for the correct development of mice embryos and that their expression is able to finely modulate transcription of coding and non-coding genes. Moreover, their activity in the central nervous system (CNS) and other tissues has been correlated with the creation of somatic mosaicisms and with pathologies such as neurodevelopmental and neurodegenerative diseases as well as cancers. Results We analyzed TE expression among different cell types of the Caenorhabditis elegans (C. elegans) early embryo asking if, where and when TE are expressed and whether their expression is correlated with genes playing a role in early embryo development. To answer these questions, we took advantage of a public C. elegans embryonic single-cell RNA-seq (sc-RNAseq) dataset and developed a bioinformatics pipeline able to quantify reads mapping specifically against TE, avoiding counting reads mapping on TE fragments embedded in coding/non-coding transcripts. Our results suggest that i) canonical TE expression analysis tools, which do not discard reads mapping on TE fragments embedded in annotated transcripts, may over-estimate TE expression levels, ii) Long Terminal Repeats (LTR) elements are mostly expressed in undifferentiated cells and might play a role in pluripotency maintenance and activation of the innate immune response, iii) non-LTR are expressed in differentiated cells, in particular in neurons and nervous system-associated tissues, and iv) DNA TE are homogenously expressed throughout the C. elegans early embryo development. Conclusions TE expression appears finely modulated in the C. elegans early embryo and different TE classes are expressed in different cell types and stages, suggesting that TE might play diverse functions during early embryo development.

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A transcription factor collective defines the HSN serotonergic neuron regulatory landscape

eLife ◽

10.7554/elife.32785 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 17

Author(s):

Carla Lloret-Fernández ◽

Miren Maicas ◽

Carlos Mora-Martínez ◽

Alejandro Artacho ◽

Ángela Jimeno-Martín ◽

...

Keyword(s):

De Novo ◽

Cell Types ◽

Specific Cell ◽

Serotonergic Neuron ◽

C Elegans ◽

Mouse Orthologs ◽

Deep Homology ◽

Regulatory Landscape ◽

Neuronal Type ◽

Selection Of

Cell differentiation is controlled by individual transcription factors (TFs) that together activate a selection of enhancers in specific cell types. How these combinations of TFs identify and activate their target sequences remains poorly understood. Here, we identify the cis-regulatory transcriptional code that controls the differentiation of serotonergic HSN neurons in Caenorhabditis elegans. Activation of the HSN transcriptome is directly orchestrated by a collective of six TFs. Binding site clusters for this TF collective form a regulatory signature that is sufficient for de novo identification of HSN neuron functional enhancers. Among C. elegans neurons, the HSN transcriptome most closely resembles that of mouse serotonergic neurons. Mouse orthologs of the HSN TF collective also regulate serotonergic differentiation and can functionally substitute for their worm counterparts which suggests deep homology. Our results identify rules governing the regulatory landscape of a critically important neuronal type in two species separated by over 700 million years.

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Developmental regulation and tissue distribution of the liver transcription factor LFB1 (HNF1) in Xenopus laevis.

Molecular and Cellular Biology ◽

10.1128/mcb.13.1.421 ◽

1993 ◽

Vol 13 (1) ◽

pp. 421-431 ◽

Cited By ~ 28

Author(s):

S Bartkowski ◽

D Zapp ◽

H Weber ◽

G Eberle ◽

C Zoidl ◽

...

Keyword(s):

Transcription Factor ◽

Xenopus Laevis ◽

Developmental Regulation ◽

Cdna Probe ◽

Cell Types ◽

Specific Gene ◽

Specific Cell ◽

Early Appearance ◽

Liver Cdna Library

The transcription factor LFB1 (HNF1) was initially identified as a regulator of liver-specific gene expression in mammals. It interacts with the promoter element HP1, which is functionally conserved between mammals and amphibians, suggesting that a homologous factor, XLFB1, also exists in Xenopus laevis. To study the role of LFB1 in early development, we isolated two groups of cDNAs coding for this factor from a Xenopus liver cDNA library by using a rat LFB1 cDNA probe. A comparison of the primary structures of the Xenopus and mammalian proteins shows that the myosin-like dimerization helix, the POU-A-related domain, the homeo-domain-related region, and the serine/threonine-rich activation domain are conserved between X. laevis and mammals, suggesting that all these features typical for LFB1 are essential for function. Using monoclonal antibodies, we demonstrate that XLFB1 is present not only in the liver but also in the stomach, intestine, colon, and kidney. In an analysis of the expression of XLFB1 in the developing Xenopus embryo, XLFB1 transcripts appear at the gastrula stage. The XLFB1 protein can be identified in regions of the embryo in which the liver diverticulum, stomach, gut, and pronephros are localized. The early appearance of XLFB1 expression during embryogenesis suggests that the tissue-specific transcription factor XLFB1 is involved in the determination and/or differentiation of specific cell types during organogenesis.

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