Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A global timing mechanism regulates cell-type specific wiring programs

ABSTRACT: A global timing mechanism regulates cell-type specific wiring programs

PROVIDER: PRJNA788151 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17206318_1.fastq.gz	Fastqsanger.gz
	SRR17206318_2.fastq.gz	Fastqsanger.gz
	SRR17206319_1.fastq.gz	Fastqsanger.gz
	SRR17206319_2.fastq.gz	Fastqsanger.gz
	SRR17206320_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 42

Similar Datasets

A global timing mechanism regulates cell-type specific wiring programs

Project description:The assembly of neural circuits is dependent upon precise spatiotemporal expression of cell recognition molecules1–6. Factors controlling cell-type specificity have been identified7–9, but how timing is determined remains unknown. Here we describe the induction of a cascade of transcription factors by a steroid hormone (Ecdysone) in all fly visual system neurons spanning target recognition and synaptogenesis. We demonstrate through single cell sequencing that the Ecdysone pathway regulates the expression of a common set of targets required for synaptic maturation and cell-type specific targets enriched for cell surface proteins regulating wiring specificity. Transcription factors in the cascade regulate the expression of the same wiring genes in complex ways, including activation in one cell-type and repression in another. We show that disruption of the Ecdysone-pathway generates specific defects in dendritic and axonal processes and synaptic connectivity, with the order of transcription factor expression correlating with sequential steps in wiring. We also identify shared targets of a cell-type specific transcription factor and the Ecdysone pathway which regulate specificity. We propose neurons integrate a global temporal transcriptional module with cell-type specific transcription factors to generate different cell-type specific patterns of cell recognition molecules regulating wiring.

2021-12-14 | GSE190714 | GEO

A global wiring diagram of stress response signaling

Project description:A global wiring diagram of stress response signaling

| PRJNA475469 | ENA

Modular transcriptional programs separately define axon and dendrite connectivity

Project description:Patterns of synaptic connectivity are remarkably precise and complex. Single-cell RNA sequencing has revealed a vast transcriptional diversity of neurons. Nevertheless, a clear logic underlying the transcriptional control of neuronal connectivity has yet to emerge. Here, we focused on Drosophila T4/T5 neurons, a class of closely related neuronal subtypes with different wiring patterns. Eight subtypes of T4/T5 neurons are defined by combinations of two patterns of dendritic inputs and four patterns of axonal outputs. Single-cell profiling during development revealed distinct transcriptional programs defining each dendrite and axon wiring pattern. These programs were defined by the expression of a few transcription factors and different combinations of cell surface proteins. Gain and loss of function studies provide evidence for independent control of different wiring features. We propose that modular transcriptional programs for distinct wiring features are assembled in different combinations to generate diverse patterns of neuronal connectivity.

2019-11-05 | GSE126139 | GEO

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

Project description:Significant insight about biological networks arises from the study of network motifs –overly abundant network subgraphs, but such wiring patterns do not specify when and how potential routes within a cellular network are used. To address this limitation, we introduce activity motifs, which capture patterns in the dynamic use of a network. Using this framework to analyze transcription in Saccharomyces cerevisiae metabolism, we find that cells use different timing activity motifs to optimize transcription timing in response to changing conditions: forward activation to produce metabolic compounds efficiently, backward shutoff to rapidly stop production of a detrimental product and synchronized activation for co-production of metabolites required for the same reaction Measuring protein abundance over a time course reveals that mRNA timing motifs also occur at the protein level. Timing motifs significantly overlap with binding activity motifs, where genes in a linear chain have ordered binding affinity to a transcription factor, suggesting a mechanism for ordered transcription. Finely timed transcriptional regulation is therefore abundant in yeast metabolism, optimizing the organism's adaptation to new environmental conditions.

2008-10-17 | GSE13219 | GEO

Identification of genes involved in GABAergic Wiring

Project description:How neurons are wired to form precise circuits is crucial to understand the development of cortical functions. Glutamatergic pyramidal cell and GABAergic interneuron wire up the cortex through differentiated cellular events. However, little is known about the molecular mechanisms that underlie the unique features of interneuron wiring. We performed a high-throughput genomic screen for genes upregulated specifically during GABAergic wiring.

2018-07-31 | GSE115948 | GEO

The Arabidopsis Mediator CDK8 module genes CCT and GCT are global regulators of developmental phase transitions.

2014-09-22 | GSE56155 | GEO

The timing mechanism for the first lineage specification in the mouse embryo

Project description:The timing mechanism for the first lineage specification in the mouse embryo

| PRJNA513332 | ENA

Global re-wiring of p53 transcription regulation by the hepatitis B virus X (HBx) protein

Project description:Global re-wiring of p53 transcription regulation by the hepatitis B virus X (HBx) protein

| PRJNA272404 | ENA

The Arabidopsis Mediator CDK8 module genes CCT and GCT are global regulators of developmental phase transitions.

Project description:Temporal coordination of developmental programs is necessary for normal ontogeny, but the mechanism by which this is accomplished is poorly understood. We have previously shown that two components of the Mediator CDK8 module, CENTER CITY (CCT/MED12) and GRAND CENTRAL (GCT/MED13), are required for timing of pattern formation during embryogenesis in Arabidopsis. Here, we performed global gene expression analyses of wild-type, cct-1, and gct-2 seedlings (above-ground portions only) to help analyze their post-embryonic phenotypes. Our results suggest that MED12 and MED13 act as global regulators of developmental timing by fine-tuning expression of temporal regulatory genes. Seeds of wild-type Col-0, cct-1, and gct-2 were sown in Fafard #2 soil. Seedlings (above-ground portions only) were harvested when the first two leaf primordia were 1 mm in length, which was at day 7 for wild-type seedlings and day 9 for the two mutants. 75-100 seedlings were used for each of three biological replicates.

2014-09-22 | E-GEOD-56155 | biostudies-arrayexpress

Aging disrupts gene expression timing during muscle regeneration

Project description:Skeletal muscle function and regenerative capacity decline during aging, yet factors driving these changes are incompletely understood. Muscle regeneration requires temporally coordinated transcriptional programs to drive myogenic stem cells to activate, proliferate, fuse to form myofibers, and to mature myonuclei, restoring muscle function after injury. We assessed global changes in myogenic transcription programs distinguishing muscle regeneration in aged mice from young mice by comparing pseudotime trajectories from single-nucleus RNA sequencing of myogenic nuclei. Aging-specific differences in coordinating myogenic transcription programs necessary for restoring muscle function occur following muscle injury, likely contributing to compromised regeneration in aged mice. Differences in pseudotime alignment of myogenic nuclei when comparing aged to young mice via Dynamic Time-Warping revealed pseudotemporal differences becoming progressively more severe as regeneration proceeds. Disruptions in timing of myogenic gene expression programs may contribute to incomplete skeletal muscle regeneration and declines in muscle function as organisms age.

2023-06-12 | GSE180225 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data