Bmp-4 acts as a morphogen in dorsoventral mesoderm patterning in Xenopus

Development ◽  
1997 ◽  
Vol 124 (12) ◽  
pp. 2325-2334 ◽  
Author(s):  
R. Dosch ◽  
V. Gawantka ◽  
H. Delius ◽  
C. Blumenstock ◽  
C. Niehrs
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Marginal Zone ◽  
Cell Types ◽  
Dorsoventral Patterning ◽  
Mesodermal Cell ◽  
Amphibian Embryos ◽  
Mesoderm Patterning ◽  
Early Gastrula ◽  
Different Doses

The marginal zone is a ring of tissue that gives rise to a characteristic dorsoventral pattern of mesoderm in amphibian embryos. Bmp-4 is thought to play an important role in specifying ventral mesodermal fate. Here we show (1) that different doses of Bmp-4 are sufficient to pattern four distinct mesodermal cell types and to pattern gene expression in the early gastrula marginal zone into three domains, (2) that there is a graded requirement for a Bmp signal in mesodermal patterning, and (3) that Bmp-4 has long-range activity which can become graded in the marginal zone by the antagonizing action of noggin. The results argue that Bmp-4 acts as a morphogen in dorsoventral patterning of mesoderm.

A novel Xenopus mix-like gene milk involved in the control of the endomesodermal fates

Development ◽  
1998 ◽  
Vol 125 (14) ◽  
pp. 2577-2585 ◽  
Author(s):  
V. Ecochard ◽  
C. Cayrol ◽  
S. Rey ◽  
F. Foulquier ◽  
D. Caillol ◽  
...  
Keyword(s):  
Marginal Zone ◽  
Ectopic Expression ◽  
Homeobox Gene ◽  
Early Response ◽  
Response Gene ◽  
Mesodermal Cell ◽  
Early Response Gene ◽  
Mesoderm Formation ◽  
Definition Of ◽  
Early Gastrula

Here we describe a novel Xenopus homeobox gene, milk, related by sequence homology and expression pattern to the vegetally expressed Mix.1. As is the case with Mix.1, milk is an immediate early response gene to the mesoderm inducer activin. milk is expressed at the early gastrula stage in the vegetal cells, fated to form endoderm, and in the marginal zone fated to form mesoderm. During gastrulation, expression of milk becomes progressively reduced in the involuting mesodermal cells but is retained in the endoderm, suggesting that it may play a key role in the definition of the endo-mesodermal boundary in the embryo. Overexpression of milk in the marginal zone blocks mesodermal cell involution, represses the expression of several mesodermal genes such as Xbra, goosecoid, Xvent-1 or Xpo and increases the expression of the endodermal gene, endodermin. In the dorsal marginal zone, overexpression of milk leads to a severe late phenotype including the absence of axial structures. Ectopic expression of milk in the animal hemisphere or in ectodermal explants induces a strong expression of endodermin. Taken together, we propose that milk plays a role in the correct patterning of the embryo by repressing mesoderm formation and promoting endoderm identity.

scholarly journals Determinants of transcription factor regulatory range

2019 ◽  
Author(s):  
Chen-Hao Chen ◽  
Rongbin Zheng ◽  
Jingyu Fan ◽  
Myles Brown ◽  
Jun S. Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cell Types ◽  
Chromatin State ◽  
Specific Cell ◽  
Regulatory Influence ◽  
State Dependent ◽  
Functional Classes

AbstractTo characterize the genomic distances over which transcription factors (TFs) influence gene expression, we examined thousands of TF and histone modification ChIP-seq datasets and thousands of gene expression profiles. A model integrating these data revealed two classes of TF: one with short-range regulatory influence, the other with long-range regulatory influence. The two TF classes also had distinct chromatin-binding preferences and auto-regulatory properties. The regulatory range of a single TF bound within different topologically associating domains (TADs) depended on intrinsic TAD properties such as local gene density and G/C content, but also on the TAD chromatin state in specific cell types. Our results provide evidence that most TFs belong to one of these two functional classes, and that the regulatory range of long-range TFs is chromatin-state dependent. Thus, consideration of TF type, distance-to-target, and chromatin context is likely important in identifying TF regulatory targets and interpreting GWAS and eQTL SNPs.

scholarly journals Graph-based data integration predicts long-range regulatory interactions across the human genome

2014 ◽  
Author(s):  
Sofie Demeyer ◽  
Tom Michoel
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Exon Array ◽  
Regulatory Elements ◽  
Computational Method ◽  
Open Chromatin ◽  
Transcription Start Sites ◽  
Distal Regulatory Elements

Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites (TSS) of the genes. We developed a computational method that combines open chromatin and gene expression information for a large number of cell types to identify these distal regulatory elements. Our method builds correlation graphs for publicly available DNase-seq and exon array datasets with matching samples and uses graph-based methods to filter findings supported by multiple datasets and remove indirect interactions. The resulting set of interactions was validated with both anecdotal information of known long-range interactions and unbiased experimental data deduced from Hi-C and CAGE experiments. Our results provide a novel set of high-confidence candidate open chromatin regions involved in gene regulation, often located several Mb away from the TSS of their target gene.

scholarly journals Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features

2017 ◽  
Author(s):  
Yan Kai ◽  
Jaclyn Andricovich ◽  
Zhouhao Zeng ◽  
Jun Zhu ◽  
Alexandros Tzatsos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Zinc Finger Protein ◽  
Cell Types ◽  
Learning Framework ◽  
Chromatin Interactions ◽  
Long Range Interactions ◽  
Extensive Cell ◽  
Cell Type Specific ◽  
And Function

AbstractThe CCCTC-binding zinc finger protein (CTCF)-mediated network of long-range chromatin interactions is important for genome organization and function. Although this network has been considered largely invariant, we found that it exhibits extensive cell-type-specific interactions that contribute to cell identity. Here we present Lollipop—a machine-learning framework—which predicts CTCF-mediated long-range interactions using genomic and epigenomic features. Using ChIA-PET data as benchmark, we demonstrated that Lollipop accurately predicts CTCF-mediated chromatin interactions both within and across cell-types, and outperforms other methods based only on CTCF motif orientation. Predictions were confirmed computationally and experimentally by Chromatin Conformation Capture (3C). Moreover, our approach reveals novel determinants of CTCF-mediated chromatin wiring, such as gene expression within the loops. Our study contributes to a better understanding about the underlying principles of CTCF-mediated chromatin interactions and their impact on gene expression.

scholarly journals Mesodermal Gene Expression in the Acoel Isodiametra pulchra Indicates a Low Number of Mesodermal Cell Types and the Endomesodermal Origin of the Gonads

PLoS ONE ◽  
2013 ◽  
Vol 8 (2) ◽  
pp. e55499 ◽  
Author(s):  
Marta Chiodin ◽  
Aina Børve ◽  
Eugene Berezikov ◽  
Peter Ladurner ◽  
Pedro Martinez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Types ◽  
Mesodermal Cell

Blastomere derivation and domains of gene expression in the Spemann Organizer of Xenopus laevis

Development ◽  
1995 ◽  
Vol 121 (11) ◽  
pp. 3505-3518 ◽  
Author(s):  
M.A. Vodicka ◽  
J.C. Gerhart
Keyword(s):  
Gene Expression ◽  
Marginal Zone ◽  
Early Stage ◽  
Fate Map ◽  
Early Cleavage ◽  
Spemann Organizer ◽  
Spemann's Organizer ◽  
Cell Embryo ◽  
Early Gastrula

Spemann's Organizer, located in the dorsal marginal zone of the amphibian gastrula, induces and differentiates dorsal axial structures characteristic of this and other vertebrates. To trace the cellular origins of the Xenopus Organizer, we labelled dorsal blastomeres of three of the four tiers (A, B and C) of the 32-cell embryo with green, red and blue fluorescent lineage tracers. A strong vegetalward displacement of labelled clones occurs between the late blastula and early gastrula stages but clones mix only slightly at their borders. The typical early gastrula Organizer is composed of approximately 10% A1 progeny in its animalmost region, 70% B1 progeny in the central region, and 20% C1 progeny in vegetal and deep regions. Variability in the composition of the early gastrula Organizer results from variability in the position of early cleavage planes and in pregastrulation movements. As the Organizer involutes during gastrulation, forming dorsal axial mesoderm, clonal boundaries are greatly dispersed by cell intermixing. Within a clone, deep cells are displaced and intermixed more than superficial cells. Variability in the distribution of progeny in the dorsal axial mesoderm of the late gastrula results mostly from variable intermixing of cells during gastrulation. Experiments to perturb later developmental events by molecular or embryonic manipulations at an early stage must take this variability into account along with the majority distributions of the fate map. Within the early gastrula Organizer, the genes Xbra, goosecoid, noggin and xNR3 are expressed differently in the animal-vegetal and superficial-deep dimensions. In situ hybridization and lineage labelling define distinct regions of the dorsal marginal zone. By the end of gastrulation, dorsal axial mesoderm cells derived from the Organizer have altered their expression of the genes Xbra, goosecoid, noggin and xNR3. At a given stage, a cell's position in the embryo rather than its lineage may be more important in determining which genes it will express.

scholarly journals Embryonic circular RNAs at tandem duplicated genes in zebrafish present new paradigm in gene expression

2017 ◽  
Author(s):  
Vanessa Chong-Morrison ◽  
Tatjana Sauka-Spengler
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Long Range ◽  
Closed Loop ◽  
Cell Types ◽  
Circular Rnas ◽  
Loop Structure ◽  
Duplicated Genes ◽  
New Paradigm ◽  
Mrna Transcripts

AbstractCircular RNAs are a puzzling class of RNAs with covalently closed loop structure, lacking 5’ and 3’ ends. Present in all cells, no unifying theme has emerged regarding their function. Here, we use transcriptional data obtained by biotagging in zebrafish to uncover a high-resolution cohort of embryonic circRNAs expressed in nuclear and polysomal subcellular compartments in three developmental cell types. The ample presence of embryonic circRNAs on polysomes contradicts previous reports suggesting predominant nuclear localisation. We uncover a novel class of circRNAs, significantly enriched at tandem duplicated genes. Using newly-developed NGS-based approach, we simultaneously resolve the full sequence of putative "tandem-circRNAs" and their underlying mRNAs. These form by long-range cis-splicing events often between distant tandem duplicated genes, resulting in chimaeric mRNA transcripts and circRNAs containing their supernumerary excised exons, integrated from multiple tandem loci. Taken together, our results suggest that circularisation events rather than circRNAs themselves are functionally important.

Initiation of mesodermal cell migration and spreading relative to gastrulation in the urodele amphibian Pleurodeles waltl

Development ◽  
1989 ◽  
Vol 105 (2) ◽  
pp. 351-363 ◽  
Author(s):  
D.-L. Shi ◽  
T. Darribere ◽  
K.E. Johnson ◽  
J.-C. Boucaut
Keyword(s):  
Cell Migration ◽  
Marginal Zone ◽  
Gastrula Stage ◽  
Cell Stage ◽  
Animal Pole ◽  
Mesodermal Cell ◽  
Marginal Cells ◽  
Pleurodeles Waltl ◽  
Early Gastrula

We have investigated the autonomous migration of marginal cells and their interactions with extracellular matrix (ECM) located on the inner surface of the blastocoel roof in the urodele amphibian, Pleurodeles waltl, using a novel in vitro migration assay. Animal hemispheres containing equatorial cells removed at different cleavage stages and dorsal marginal zone (DMZ) explants of early gastrula stage were cultured either on fibronectin (FN)-coated or ECM-conditioned substrata. In explanted animal hemispheres, dorsal marginal cells showed autonomous migration on FN-coated substratum at the same time as the onset of gastrulation in control embryos. They acquired this capacity at least at the 32-cell stage, whereas lateral and ventral marginal cells acquired it after the 64-cell stage. DMZ outgrowths of early gastrula stage exhibited autonomous spreading on both substrata. In addition, we showed that they spread preferentially toward the animal pole when deposited on substratum conditioned by the dorsal roof of the blastocoel. By culturing dissociated marginal cells on ECM- conditioned substratum, we also found that increased spreading capacity of marginal cells was related to the initiation of their migration. A comparative study of the migration of marginal cells in ultraviolet (u.v.)-irradiated and normal embryos was also made. The results indicate that dorsal marginal cell migration was absent or dramatically reduced by u.v.-irradiation. These results suggest that the differential acquisition in the spreading capacity both in timing and in intensity around the marginal zone was correlated with the sequential involution of mesodermal cells in the course of gastrulation.

scholarly journals Effective gene expression prediction from sequence by integrating long-range interactions

2021 ◽  
Vol 18 (10) ◽  
pp. 1196-1203 ◽  
Author(s):  
Žiga Avsec ◽  
Vikram Agarwal ◽  
Daniel Visentin ◽  
Joseph R. Ledsam ◽  
Agnieszka Grabska-Barwinska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Dna Sequences ◽  
Human Genetics ◽  
Cell Types ◽  
Saturation Mutagenesis ◽  
Noncoding Dna ◽  
Long Range Interactions ◽  
Disease Associations ◽  
Reporter Assays

AbstractHow noncoding DNA determines gene expression in different cell types is a major unsolved problem, and critical downstream applications in human genetics depend on improved solutions. Here, we report substantially improved gene expression prediction accuracy from DNA sequences through the use of a deep learning architecture, called Enformer, that is able to integrate information from long-range interactions (up to 100 kb away) in the genome. This improvement yielded more accurate variant effect predictions on gene expression for both natural genetic variants and saturation mutagenesis measured by massively parallel reporter assays. Furthermore, Enformer learned to predict enhancer–promoter interactions directly from the DNA sequence competitively with methods that take direct experimental data as input. We expect that these advances will enable more effective fine-mapping of human disease associations and provide a framework to interpret cis-regulatory evolution.

scholarly journals Control of impulsivity by Gi-protein signalling in layer-5 pyramidal neurons of the anterior cingulate cortex

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Bastiaan van der Veen ◽  
Sampath K. T. Kapanaiah ◽  
Kasyoka Kilonzo ◽  
Peter Steele-Perkins ◽  
Martin M. Jendryka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Anterior Cingulate Cortex ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Pyramidal Neurons ◽  
Treatment Options ◽  
Pyramidal Cells ◽  
Cingulate Cortex ◽  
Cell Types ◽  
Anterior Cingulate

AbstractPathological impulsivity is a debilitating symptom of multiple psychiatric diseases with few effective treatment options. To identify druggable receptors with anti-impulsive action we developed a systematic target discovery approach combining behavioural chemogenetics and gene expression analysis. Spatially restricted inhibition of three subdivisions of the prefrontal cortex of mice revealed that the anterior cingulate cortex (ACC) regulates premature responding, a form of motor impulsivity. Probing three G-protein cascades with designer receptors, we found that the activation of Gi-signalling in layer-5 pyramidal cells (L5-PCs) of the ACC strongly, reproducibly, and selectively decreased challenge-induced impulsivity. Differential gene expression analysis across murine ACC cell-types and 402 GPCRs revealed that - among Gi-coupled receptor-encoding genes - Grm2 is the most selectively expressed in L5-PCs while alternative targets were scarce. Validating our approach, we confirmed that mGluR2 activation reduced premature responding. These results suggest Gi-coupled receptors in ACC L5-PCs as therapeutic targets for impulse control disorders.

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