Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LADL: Light-activated dynamic looping for endogenous gene expression control

ABSTRACT: LADL: Light-activated dynamic looping for endogenous gene expression control

PROVIDER: PRJNA476597 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8504940_1.fastq.gz	Fastqsanger.gz
	SRR8504940_2.fastq.gz	Fastqsanger.gz
	SRR8504950_1.fastq.gz	Fastqsanger.gz
	SRR8504950_2.fastq.gz	Fastqsanger.gz
	SRR8504941_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 40

Similar Datasets

LADL: Light-activated dynamic looping for endogenous gene expression control

Project description:Mammalian genomes are folded into tens of thousands of long-range looping interactions1,2. The cause and effect relationship between looping and genome function is poorly understood, and the extent to which chromatin loops are dynamic on short time scales remains a fundamental unanswered question. Currently available strategies for loop engineering involve synthetic transcription factors tethered to dCas93,4or zinc fingers5,6, which are constitutively expressed5,6or induced on long time scales by the presence of a small molecule3.Here we report a new class of 3D optoepigenetic toolsfor the directed rearrangement of 3D chromatin looping on short time scales using blue light. We create synthetic architectural proteins by fusing the CIBN protein subunit from Arabidopsis thaliana with enzymatically dead Cas9 (dCas9). We target our light-activated dynamic looping system (LADL) to two genomic anchors with CRISPR guide RNAs and engineer their spatial co-localization via light-induced heterodimerization of the cryptochrome 2 (CRY2) protein with dCas9-CIBN. We apply LADL to redirect a stretch enhancer(SE)away from its endogenous Klf4target gene and to the Zfp462promoter. Looping changes occur as early as four hours after light induction. Using single molecule RNA FISH, we observe a LADL-induced increase in the total nascent Zfp462transcripts and the number of Zfp462 alleles expressing simultaneously per cell.Moreover, LADL also increased synchronous Sox2 expression after reinforcement of a known Sox2-SElooping interaction. LADL facilitates loop synchronization across a large population of cells without exogenous chemical cofactors and can enable future efforts to engineer reversible and oscillatory looping on short time scales.

2019-06-24 | GSE115963 | GEO

LADL: light-activated dynamic looping for endogenous gene expression control.

Project description:Mammalian genomes are folded into tens of thousands of long-range looping interactions. The cause-and-effect relationship between looping and genome function is poorly understood, and the extent to which loops are dynamic on short time scales remains an unanswered question. Here, we engineer a new class of synthetic architectural proteins for directed rearrangement of the three-dimensional genome using blue light. We target our light-activated-dynamic-looping (LADL) system to two genomic anchors with CRISPR guide RNAs and induce their spatial colocalization via light-induced heterodimerization of cryptochrome 2 and a dCas9-CIBN fusion protein. We apply LADL to redirect a stretch enhancer (SE) away from its endogenous Klf4 target gene and to the Zfp462 promoter. Using single-molecule RNA-FISH, we demonstrate that de novo formation of the Zfp462-SE loop correlates with a modest increase in Zfp462 expression. LADL facilitates colocalization of genomic loci without exogenous chemical cofactors and will enable future efforts to engineer reversible and oscillatory loops on short time scales.

| S-EPMC6599567 | biostudies-literature

Francisella orientalis LADL 07-285A strain:LADL--07-285A

Project description:Francisella orientalis LADL 07-285A strain:LADL--07-285A Genome sequencing

| PRJNA210898 | ENA

Light induced targeting enables proteomics on endogenous condensates

Project description:Light induced targeting enables proteomics on endogenous condensates

| PRJNA1128148 | ENA

Light induced targeting enables proteomics on endogenous condensates

Project description:Endogenous condensates with transient constituents are notoriously difficult to study with common biological assays like mass-spectrometry and other proteomics profiling. Here we report a method for light-induced targeting of endogenous condensates (LiTEC) in living cells. LiTEC combines the identification of molecular zip codes that target the endogenous condensates with optogenetics to enable controlled and reversible partitioning of an arbitrary cargo, such as enzymes commonly used in proteomics, into the condensate in a blue light dependent manner. We demonstrate a proof of concept by combining LiTEC with proximity-based biotinylation (BioID) and uncover putative components of transcriptional condensates in mouse embryonic stem cells. Our approach opens the road to genome-wide functional studies of endogenous condensates.

2024-10-18 | GSE270770 | GEO

Light-induced targeting enables proteomics on endogenous condensates

2024-10-25 | PXD049054 | Pride

GBS strain LADL-90-503

Project description:Genome sequencing of Streptococcus agalactiae strain LADL-90-503 isolated from fish

| PRJEB1142 | ENA

Edwardsiella ictaluri strain:LADL-11-184-A

Project description:Edwardsiella ictaluri LADL 11-184-A Genome sequencing and assembly

| PRJNA904692 | ENA

Edwardsiella ictaluri strain:LADL-11-149-B

Project description:Edwardsiella ictaluri LADL-11-149-B Genome sequencing and assembly

| PRJNA903867 | ENA

Temporal analysis of physiological and transcriptome responses during high light exposure that lead to dynamic acclimation in Arabidopsis

Project description:The photosynthetic capacity of mature leaves increases upon exposing plants to continuous or intermittent high light (HL). This is termed dynamic acclimation, which is an important determinant of plant productivity. We hypothesized that genes coding for transcription regulators (TRs), which respond rapidly (≤1h) and transiently to HL, initiate dynamic acclimation. To find such genes, a highly replicated time series transcriptomic dataset was generated from leaf 7 of low light (LL)-grown Arabidopsis thaliana plants subjected to HL for up to 6h. This revealed 3844 HL-responsive differentially expressed genes (DEGs). 49 transiently HL-induced TR DEGs were selected for Bayesian modeling, which revealed that B-BOX TRANSCRIPTION (CO) FACTOR32 (BBX32) was the most connected gene in an inferred network. Dynamic acclimation was elicited in Arabidopsis Col-0 by exposure to daily 4h HL over 5 days. Using this procedure on over-expressing (OE) and null mutant plants, it was shown that BBX32 is a negative regulator of dynamic acclimation. The same modeling connected BBX32 to the TR gene LONG HYPOCOTYL5 (HY5), but unlike BBX32, HY5 was shown to positively regulate dynamic acclimation. The severely diminished response to daily HL of BBX32–OE/hy5 plants suggest that in wild type plants, BBX32 and HY5 exert a balanced, flexible and complete regulation of dynamic acclimation.

2018-08-03 | GSE78251 | 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