Genesis of an organ: molecular analysis of the pha-1 gene

Development ◽  
1994 ◽  
Vol 120 (10) ◽  
pp. 3005-3017 ◽  
Author(s):  
M. Granato ◽  
H. Schnabel ◽  
R. Schnabel
Keyword(s):  
Terminal Differentiation ◽  
Cell Types ◽  
Transcriptional Level ◽  
Lethal Gene ◽  
C Elegans ◽  
Mosaic Analysis ◽  
Late Step ◽  
Organ Specific ◽  
Differentiation Marker ◽  
Bzip Family

The organisation of organ formation is still an unsolved problem. Mutations in the zygotic lethal gene pha-1 affect a late step during organ development in the nematode C. elegans. In mutant embryos all tissues in the pharynx fail to undergo terminal differentiation and morphogenesis. The expression of an early differentiation marker in pharyngeal muscle precursors is not impaired in mutant embryos, which suggests that pharynx cells still acquire their identity. Therefore the gene defines an organ-specific terminal differentiation function. We cloned and sequenced the pha-1 gene and found that the deduced protein sequence contains features characteristic of the bZIP family of transcription factors. During embryogenesis a transgenic pha-1 reporter construct is expressed transiently in all pharynx precursor cells at the time when these cells become restricted to form the pharynx organ. A mosaic analysis of the requirement of pha-1 activity during pharynx formation is consistent with the notion that pha-1 acts cell-autonomously in all cells of the pharynx primordium. The data suggest that pha-1 initiates and coordinates programs required for cytodifferentiation and morphogenesis in all cell types of the entire organ on the transcriptional level. We propose that organs are independent developmental units whose identity is reflected on the gene regulatory level.

A Deficiency Screen for Zygotic Loci Required for Establishment and Patterning of the Epidermis in Caenorhabditis elegans

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 185-206 ◽  
Author(s):  
Rebecca M Terns ◽  
Peggy Kroll-Conner ◽  
Jiangwen Zhu ◽  
Sooyoun Chung ◽  
Joel H Rothman
Keyword(s):  
Caenorhabditis Elegans ◽  
Cell Types ◽  
Epidermal Cells ◽  
Epidermal Differentiation ◽  
Apparent Effect ◽  
Internal Organs ◽  
C Elegans ◽  
Seam Cell ◽  
Genomic Regions ◽  
Caenorhabditis Elegans Genome

To identify genomic regions required for establishment and patterning of the epidermis, we screened 58 deficiencies that collectively delete at least ∼67% of the Caenorhabditis elegans genome. The epidermal pattern of deficiency homozygous embryos was analyzed by examining expression of a marker specific for one of the three major epidermal cell types, the seam cells. The organization of the epidermis and internal organs was also analyzed using a monoclonal antibody specific for epithelial adherens junctions. While seven deficiencies had no apparent effect on seam cell production, 21 were found to result in subnormal, and five in excess numbers of these cells. An additional 23 deficiencies blocked expression of the seam cell marker, in some cases without preventing cell proliferation. Two deficiencies result in multinucleate seam cells. Deficiencies were also identified that result in subnormal numbers of epidermal cells, hyperfusion of epidermal cells into a large syncytium, or aberrant epidermal differentiation. Finally, analysis of internal epithelia revealed deficiencies that cause defects in formation of internal organs, including circularization of the intestine and bifurcation of the pharynx lumen. This study reveals that many regions of the C. elegans genome are required zygotically for patterning of the epidermis and other epithelia.

scholarly journals Molecular characteristics and spatial distribution of adult human corneal cell subtypes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ann J. Ligocki ◽  
Wen Fury ◽  
Christian Gutierrez ◽  
Christina Adler ◽  
Tao Yang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cross Sections ◽  
Cell Types ◽  
Marker Genes ◽  
Molecular Characteristics ◽  
Transcriptional Level ◽  
Human Cornea ◽  
Adult Human ◽  
And Migration

AbstractBulk RNA sequencing of a tissue captures the gene expression profile from all cell types combined. Single-cell RNA sequencing identifies discrete cell-signatures based on transcriptomic identities. Six adult human corneas were processed for single-cell RNAseq and 16 cell clusters were bioinformatically identified. Based on their transcriptomic signatures and RNAscope results using representative cluster marker genes on human cornea cross-sections, these clusters were confirmed to be stromal keratocytes, endothelium, several subtypes of corneal epithelium, conjunctival epithelium, and supportive cells in the limbal stem cell niche. The complexity of the epithelial cell layer was captured by eight distinct corneal clusters and three conjunctival clusters. These were further characterized by enriched biological pathways and molecular characteristics which revealed novel groupings related to development, function, and location within the epithelial layer. Moreover, epithelial subtypes were found to reflect their initial generation in the limbal region, differentiation, and migration through to mature epithelial cells. The single-cell map of the human cornea deepens the knowledge of the cellular subsets of the cornea on a whole genome transcriptional level. This information can be applied to better understand normal corneal biology, serve as a reference to understand corneal disease pathology, and provide potential insights into therapeutic approaches.

scholarly journals Tissue-specific regulation of dipeptidyl peptidase IV expression during development

1991 ◽  
Vol 277 (2) ◽  
pp. 331-334 ◽  
Author(s):  
M Hildebrandt ◽  
W Reutter ◽  
J D Gitlin
Keyword(s):  
Lung Development ◽  
Kidney Development ◽  
Blot Hybridization ◽  
Dipeptidyl Peptidase ◽  
Transcriptional Level ◽  
Northern Blot Hybridization ◽  
Dpp Iv ◽  
Organ Specific ◽  
Specific Regulation ◽  
Lung And Kidney

The patterns of dipeptidyl peptidase (DPP) IV activity and protein amount in different rat organs during development were compared. In order to elucidate the molecular basis for these patterns, total RNA was isolated from lung and kidney at different stages of development and analysed by Northern-blot hybridization using an oligonucleotide derived from the DPP IV cDNA sequence. This oligonucleotide hybridized to two distinct mRNAs of approx. 3.2 and 4.8 kb respectively. During kidney development, the pattern for DPP IV mRNA paralleled that of DPP IV activity and protein amount, suggesting that, in kidney, the expression of DPP IV is primarily controlled at the transcriptional level. In contrast, the magnitude of DPP IV activity during lung development compared with that of DPP IV mRNA in lung suggests that post-transcriptional mechanisms are involved in regulating the expression of DPP IV in lung. Organ-specific regulation of DPP IV expression may provide a useful model for further comparative studies of transcriptional and post-transcriptional mechanisms of DPP IV expression within the same organism.

5-Bromo-2-deoxyuridine regulates invasiveness and expression of integrins and matrix-degrading proteinases in a differentiated hamster melanoma cell

1993 ◽  
Vol 105 (1) ◽  
pp. 191-201 ◽  
Author(s):  
L. Thomas ◽  
P.W. Chan ◽  
S. Chang ◽  
C. Damsky
Keyword(s):  
Extracellular Matrix ◽  
Tumor Progression ◽  
Melanoma Cell ◽  
Critical Role ◽  
Terminal Differentiation ◽  
Cell System ◽  
Melanocyte Stimulating Hormone ◽  
Complex Processes ◽  
Differentiation Marker ◽  
Stimulating Hormone

Cell interactions with the extracellular matrix play a critical role in regulating complex processes such as terminal differentiation and tumor progression. In these studies we describe a melanoma cell system that should be useful in addressing the regulation of cell-matrix interactions and the roles they play in regulating differentiation and cell invasiveness. CS (suspension)-1 melanoma cells are relatively well differentiated: they are melanotic, responsive to melanocyte-stimulating hormone, and express TA99, a melanosome membrane differentiation marker. Their repertoire of integrin receptors for extracellular matrix ligands is limited; in particular, they lack receptors for vitronectin, accounting for the observation that they are nonadherent when cultured in the presence of serum. CS-1 cells are noninvasive as well, and express low levels of both metalloproteinases and activated plasminogen activators. Treatment of these cells with melanocyte-stimulating hormone causes them to increase melanin production and assume an arborized phenotype, suggesting that it promotes their further differentiation. In contrast, treatment of CS-1 with the thymidine analog 5-bromodeoxyuridine, converts them to a highly invasive cell population (termed BCS-1) that loses its differentiated properties and responsiveness to melanocyte-stimulating hormone, acquires a broad integrin repertoire (including vitronectin receptors), and expresses elevated levels of metalloproteinases and activated urokinase. From these observations and findings of others on BrdU treatment of other developmental lineages, we hypothesize that BrdU both suppresses differentiation and promotes invasiveness of CS-1 cells. The demonstrated manipulability of CS-1 cells should make them extremely useful for studying the regulation of both terminal differentiation and tumor progression in the melanocyte lineage.

scholarly journals Multiple neural bHLHs ensure the precision of a neuronal specification event in C. elegans

Biology Open ◽  
2021 ◽  
Author(s):  
Konstantina Filippopoulou ◽  
Carole Couillault ◽  
Vincent Bertrand
Keyword(s):  
Transcription Factors ◽  
Quantitative Imaging ◽  
Terminal Differentiation ◽  
Cholinergic Neurons ◽  
Antagonistic Effect ◽  
Specific Class ◽  
C Elegans ◽  
Neuronal Specification ◽  
Bhlh Transcription Factors ◽  
Deleterious Genes

Neural bHLH transcription factors play a key role in the early steps of neuronal specification in many animals. We have previously observed that the Achaete-Scute HLH-3, the Olig HLH-16 and their binding partner the E protein HLH-2 activate the terminal differentiation program of a specific class of cholinergic neurons, AIY, in C. elegans. Here we identify a role for a fourth bHLH, the Neurogenin NGN-1, in this process, raising the question of why so many neural bHLHs are required for a single neuronal specification event. Using quantitative imaging we show that the combined action of different bHLHs is needed to activate the correct level of expression of the terminal selector transcription factors TTX-3 and CEH-10 that subsequently initiate and maintain the expression of a large battery of terminal differentiation genes. Surprisingly, the different bHLHs have an antagonistic effect on another target, the proapoptotic BH3-only factor EGL-1, normally not expressed in AIY and otherwise detrimental for its specification. We propose that the use of multiple neural bHLHs allows robust neuronal specification while, at the same time, preventing spurious activation of deleterious genes.

scholarly journals SPARC Data Structure: Rationale and Design of a FAIR Standard for Biomedical Research Data

2021 ◽  
Author(s):  
Anita Bandrowski ◽  
Jeffrey S. Grethe ◽  
Anna Pilko ◽  
Tom Gillespie ◽  
Gabi Pine ◽  
...  
Keyword(s):  
Data Structure ◽  
Biomedical Research ◽  
Large Scale ◽  
Open Data ◽  
Cell Types ◽  
Research Data ◽  
Imaging Data ◽  
Organ Specific ◽  
The Rich ◽  
Automated Tools

AbstractThe NIH Common Fund’s Stimulating Peripheral Activity to Relieve Conditions (SPARC) initiative is a large-scale program that seeks to accelerate the development of therapeutic devices that modulate electrical activity in nerves to improve organ function. Integral to the SPARC program are the rich anatomical and functional datasets produced by investigators across the SPARC consortium that provide key details about organ-specific circuitry, including structural and functional connectivity, mapping of cell types and molecular profiling. These datasets are provided to the research community through an open data platform, the SPARC Portal. To ensure SPARC datasets are Findable, Accessible, Interoperable and Reusable (FAIR), they are all submitted to the SPARC portal following a standard scheme established by the SPARC Curation Team, called the SPARC Data Structure (SDS). Inspired by the Brain Imaging Data Structure (BIDS), the SDS has been designed to capture the large variety of data generated by SPARC investigators who are coming from all fields of biomedical research. Here we present the rationale and design of the SDS, including a description of the SPARC curation process and the automated tools for complying with the SDS, including the SDS validator and Software to Organize Data Automatically (SODA) for SPARC. The objective is to provide detailed guidelines for anyone desiring to comply with the SDS. Since the SDS are suitable for any type of biomedical research data, it can be adopted by any group desiring to follow the FAIR data principles for managing their data, even outside of the SPARC consortium. Finally, this manuscript provides a foundational framework that can be used by any organization desiring to either adapt the SDS to suit the specific needs of their data or simply desiring to design their own FAIR data sharing scheme from scratch.

scholarly journals The C. elegans Hypertonic Stress Response: Big Insights from Shrinking Worms

2020 ◽  
Vol 55 (S1) ◽  
pp. 89-105
Keyword(s):  
Stress Response ◽  
Cell Volume ◽  
Molecular Mechanisms ◽  
Model Organism ◽  
Future Research ◽  
Transcriptional Level ◽  
Molecular Signaling ◽  
Hypertonic Stress ◽  
Macromolecular Assemblies ◽  
C Elegans

Cell volume is one of the most aggressively defended physiological set points in biology. Changes in intracellular ion and water concentrations, which are induced by changes in metabolism or environmental exposures, disrupt protein folding, enzymatic activity, and macromolecular assemblies. To counter these challenges, cells and organisms have evolved multifaceted, evolutionarily conserved molecular mechanisms to restore cell volume and repair stress induced damage. However, many unanswered questions remain regarding the nature of cell volume 'sensing' as well as the molecular signaling pathways involved in activating physiological response mechanisms. Unbiased genetic screening in the model organism C. elegans is providing new and unexpected insights into these questions, particularly questions relating to the hypertonic stress response (HTSR) pathway. One surprising characteristic of the HTSR pathway in C. elegans is that it is under strong negative regulation by proteins involved in protein homeostasis and the extracellular matrix (ECM). The role of the ECM in particular highlights the importance of studying the HTSR in the context of a live organism where native ECM-tissue associations are preserved. A second novel and recently discovered characteristic is that the HTSR is regulated at the post-transcriptional level. The goal of this review is to describe these discoveries, to provide context for their implications, and to raise outstanding questions to guide future research.

Opposite Effects of Ras or PKC Activation on the Expression of the SPRR2A Keratinocyte Terminal Differentiation Marker

1999 ◽  
Vol 250 (2) ◽  
pp. 475-484 ◽  
Author(s):  
Muriëlle W.J. Sark ◽  
Anne-Marijke Borgstein ◽  
Jan Paul Medema ◽  
Pieter van de Putte ◽  
Claude Backendorf
Keyword(s):  
Terminal Differentiation ◽  
Differentiation Marker ◽  
Pkc Activation ◽  
Terminal Differentiation Marker

The expression, lamin-dependent localization and RNAi depletion phenotype for emerin inC. elegans

2002 ◽  
Vol 115 (5) ◽  
pp. 923-929 ◽  
Author(s):  
Yosef Gruenbaum ◽  
Kenneth K. Lee ◽  
Jun Liu ◽  
Merav Cohen ◽  
Katherine L. Wilson
Keyword(s):  
Nuclear Envelope ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Growth Conditions ◽  
Rnai Phenotype ◽  
Lamin B ◽  
C Elegans ◽  
Nuclear Lamins ◽  
First Time

Emerin belongs to the LEM-domain family of nuclear membrane proteins, which are conserved in metazoans from C. elegans to humans. Loss of emerin in humans causes the X-linked form of Emery-Dreifuss muscular dystrophy(EDMD), but the disease mechanism is not understood. We have begun to address the function of emerin in C. elegans, a genetically tractable nematode. The emerin gene (emr-1) is conserved in C. elegans. We detect Ce-emerin protein in the nuclear envelopes of all cell types except sperm, and find that Ce-emerin co-immunoprecipitates with Ce-lamin from embryo lysates. We show for the first time in any organism that nuclear lamins are essential for the nuclear envelope localization of emerin during early development. We further show that four other types of nuclear envelope proteins, including fellow LEM-domain protein Ce-MAN1, as well as Ce-lamin, UNC-84 and nucleoporins do not depend on Ce-emerin for their localization. This result suggests that emerin is not essential to organize or localize the only lamin (B-type) expressed in C. elegans. We also analyzed the RNAi phenotype resulting from the loss of emerin function in C. elegans under laboratory growth conditions, and found no detectable phenotype throughout development. We propose that C. elegans is an appropriate system in which to study the molecular mechanisms of emerin function in vivo.

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