Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A 36-base hairpin within lncRNA DRAIC interacts with the IKKα coiled-coil domain, weakening the IKK complex and inhibiting NF-kappaB activation

ABSTRACT: A 36-base hairpin within lncRNA DRAIC interacts with the IKKα coiled-coil domain, weakening the IKK complex and inhibiting NF-kappaB activation

PROVIDER: PRJNA1171344 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

A 36-base hairpin within lncRNA DRAIC interacts with the IKKα coiled-coil domain, weakening the IKK complex and inhibiting NF-kappaB activation

Project description:Long noncoding RNAs have diverse functions, but not enough is known about the molecular mechanisms underlying their cellular functions. The 1.7 kb long down-regulated non-coding RNA in cancers (DRAIC) slows tumor growth and inhibits the activation of the transcription factor NF-kappaB through interactions with IKK subunits. Starting with SHAPE-MaP-based structure-function studies of DRAIC we have now identified the minimal regions of DRAIC and IKK involved in the interactions and the anti-cancer function of DRAIC. A hairpin structure comprised of bases 705-722/741-758 (referred to as A+B) within DRAIC is responsible for inhibiting NF-kappaB activity. A+B binds specifically with the IKKα coiled-coil domain with a KD of ~1-5 nM. The coiled-coil domain of IKKα (the kinase subunit) and NEMO (the substrate recognition subunit,) mediate the dimerization of the subunits in the functional kinase complex. Consistent with its interaction with the coiled-coil domain of IKKα, A+B weakens the interaction between NEMO and the IKKα coiled-coil domain in an in vitro complex formation assay. The 36 nt A+B RNA was sufficient and necessary for DRAIC to inhibit tumor cell migration, invasion, and clonal growth in multiple cancer cell-lines. Therefore, this minimal hairpin fragment of the growth-suppressive DRAIC lncRNA inhibits NF-kappaB activation by interacting with high affinity with the coiled-coil domain of IKKα, weakening the interaction between the kinase subunit and the substrate recognition subunit of IKK, thereby inhibiting IB phosphorylation and NF-kappaB activation, and suppressing tumor phenotypes.

2025-07-01 | GSE279192 | GEO

Expression data from HT-1080 cells incubated or not in the presence of laminin111 coiled-coiled recombinant fragment (rLCC111)

Project description:Laminins are large heterotrimeric cross-shaped extracellular matrix (ECM) glycoproteins with terminal globular domains and a coiled-coil region. We have produced for the first time a recombinant laminin coiled-coil domain and studied the transcriptional profile of cells incubated in coiled-coil-coated wells. Cells were incubated in 24w plates, onto coiled-coil-coated wells or control BSA-coated wells (one each), 24h

2011-10-11 | E-GEOD-32896 | biostudies-arrayexpress

Expression data from HT-1080 cells incubated or not in the presence of laminin111 coiled-coiled recombinant fragment (rLCC111)

2011-10-12 | GSE32896 | GEO

Effects of depletion of Rho-associated, coiled-coil-containing protein kinase 2 in the kidney medullary tussue of murine model.

Project description:Rho and its effector Rho-associated, coiled-coil–containing protein kinase 2 (ROCK2) play crucial roles in a variety of cellular functions, such as cell adhesion and cytoskeletal rearrangement . We here investigated the role of ROCK2 in the kidney medullary tissue using tubular specific ROCK2 knockout mice.

2024-07-01 | GSE246069 | GEO

Identification of the coiled-coil domain as an essential element of MBD3 for preserving lineage commitment potential of ESCs

Project description:As one of approaches for elucidating the molecular bases which define the difference for counteracting defect of Mbd3-knockout ESCs between MBD3a mutant lacking MBD domain and that lacking coiled-coil domain, we explored the possibility that these two mutants are different in their ability to recruit PRC2 complex in close vicinity by ChIP-sequence analyses.

2019-06-25 | GSE102643 | GEO

A BRCA1 coiled-coil domain variant disrupting PALB2 interaction predisposes to mammary tumors with a targetable defect in homologous recombination repair [CNV-seq]

Project description:The BRCA1 tumor suppressor gene encodes a multi-domain protein for which several functions have been described. These include a key role in homologous recombination repair (HRR) of DNA double-strand breaks (DSBs), which is shared with two other high-risk hereditary breast cancer suppressors, BRCA2 and PALB2. Although both BRCA1 and BRCA2 interact with PALB2, BRCA1 missense variants affecting its PALB2-interacting coiled-coil domain are considered sequence variants of uncertain clinical significance (VUS). Using genetically engineered mice, we now show that a BRCA1 coiled-coil domain VUS, Brca1 p.L1363P, disrupting the interaction with PALB2 leads to embryonic lethality and loss of breast cancer suppression. Brca1 p.L1363P mammary tumors develop with a similar latency as Brca1-null tumors, but show different histopathological features and more stable DNA copy number profiles. Nevertheless, Brca1 p.L1363P mammary tumors are HRR-incompetent and responsive to cisplatin and PARP inhibition.

2022-02-01 | GSE182449 | GEO

A BRCA1 coiled-coil domain variant disrupting PALB2 interaction predisposes to mammary tumors with a targetable defect in homologous recombination repair [RNA-seq]

2022-02-01 | GSE182448 | GEO

Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes

Project description:Cohesin’s association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being ‘clamped’ by Scc2 and ATP-dependent engagement of cohesin’s Smc1 and Smc3 head domains. Scc2’s replacement by Pds5 abrogates cohesin’s ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50 nm long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the apo form of cohesin that reveals the structure of folded and zipped up coils in unprecedented detail and shows that Scc2 can associate with Smc1’s ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific cross-linking, we show that cohesin’s coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation (SMC1D588Y) within Smc1’s hinge that alters how Scc2 and Pds5 interact with Smc1’s hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin’s hinge, which in turn requires coiled coil folding.

2021-07-21 | GSE167318 | GEO

Inhibition of Rho-associated, coiled-coil-containing protein kinase 2 in murine podocytes

Project description:Inhibition of Rho-associated, coiled-coil-containing protein kinase 2 in murine podocytes

| PRJNA1090039 | ENA

Inhibition of Rho-associated, coiled-coil-containing protein kinase 2 in murine podocytes

Project description:Focal segmental glomerulosclerosis (FSGS) is characterized by damage to podocytes, a crucial pathological feature. While several mechanisms of podocyte injury have been suggested, many questions remain unanswered. Rho-associated, coiled-coil-containing protein kinase 2 (ROCK2), a serine/threonine kinase with diverse cellular functions, appears to play a significant role. We observed activation of ROCK2 in podocytes of mice with FSGS induced by adriamycin (ADR), as well as in cultured podocytes exposed to ADR. To delve deeper, we used conditional knockout mice where the ROCK2 gene was specifically disrupted in podocytes (PR2KO). These mice showed resistance to ADR-induced albuminuria, glomerular sclerosis, and podocyte damage. Additionally, pharmacological inhibition of ROCK2 significantly improved podocyte loss and kidney sclerosis in a mouse model of FSGS by counteracting profibrotic factors. RNA sequencing of podocytes treated with a ROCK2 inhibitor confirmed ROCK2's role as a regulator of the cyclic nucleotide signaling pathway. Our findings underscore the potential of ROCK2 inhibition as a therapeutic avenue for FSGS.

2024-03-20 | GSE262013 | 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