2019
DOI: 10.1093/nar/gkz739
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Genome reading by the NF-κB transcription factors

Abstract: The NF-κB family of dimeric transcription factors regulates transcription by selectively binding to DNA response elements present within promoters or enhancers of target genes. The DNA response elements, collectively known as κB sites or κB DNA, share the consensus 5′-GGGRNNNYCC-3′ (where R, Y and N are purine, pyrimidine and any nucleotide base, respectively). In addition, several DNA sequences that deviate significantly from the consensus have been shown to accommodate binding by NF-κB dimers. X-ray crystal … Show more

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Cited by 90 publications
(88 citation statements)
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“…Interestingly, the expression of several of these lncRNAs, such as lincRNA-Cox2 is regulated by the proin ammatory transcription factor NF-κB (31,38,65). NF-κB-mediated transcription of lincRNAs likely coincides with the new protein synthesis driven by early response genes (66) and may allow for lincRNA and protein interactions necessary for secondary and late gene transcription. Similar to lincRNA-Cox2, one of the major ndings of this study is that LPS-induced upregulation of Nostrill appears to be dependent upon NF-κB signaling since two inhibitors of the NF-κB signaling pathway (SC-514, an IKK-2 inhibitor, and JSH-23, an NF-κB p65 inhibitor) signi cantly attenuated Nostrill expression in LPSstimulated BV2 cells (Fig.…”
Section: Discussionmentioning
confidence: 99%
“…Interestingly, the expression of several of these lncRNAs, such as lincRNA-Cox2 is regulated by the proin ammatory transcription factor NF-κB (31,38,65). NF-κB-mediated transcription of lincRNAs likely coincides with the new protein synthesis driven by early response genes (66) and may allow for lincRNA and protein interactions necessary for secondary and late gene transcription. Similar to lincRNA-Cox2, one of the major ndings of this study is that LPS-induced upregulation of Nostrill appears to be dependent upon NF-κB signaling since two inhibitors of the NF-κB signaling pathway (SC-514, an IKK-2 inhibitor, and JSH-23, an NF-κB p65 inhibitor) signi cantly attenuated Nostrill expression in LPSstimulated BV2 cells (Fig.…”
Section: Discussionmentioning
confidence: 99%
“…In addition, stains have been found to ameliorate semen quality characteristics in reproductive toxicity conditions in in vivo systems via other mechanistic routes; for example, a study on obese male rats suggested that fluvastatin protects reproductive function, and hence semen quality, mostly by enhancing signalling of mTOR, which is a human kinase (serine/threonine kinase) involved in several cellular processes such as cell proliferation, cell growth, cell survival and cell motility (Cui, Long, Zhu, & Tian, 2017; Saxton & Sabatini, 2017). Also, oral administration of rosuvastatin at 5 or 10 mg/kg, for 8 weeks, was found to reduce inflammation and cell necrosis may be by decreasing the expression of nuclear factor kappa light‐chain‐enhancer of activated B cells (Mulero, Wang, Huxford, & Ghosh, 2019), a protein that controls DNA transcription and cell survival, caspase‐3, a protein has a vital role in cell apoptosis (Rogers et al, 2017; Wang et al, 2017; Zhu et al, 2018), and inducible nitric oxide synthase, which is an isoform of nitric oxide synthases catalysing the synthesis of nitric oxide from L‐arginine (Banihani, Abu‐Alhayjaa, Amarin, & Alzoubi, 2018; Nathan, 2011), in diabetic rats (Heeba & Hamza, 2015). Furthermore, administration of rosuvastatin restored the degenerative effects in seminiferous tubules as well as weights of epididymis and testes in diabetic rats (Heeba & Hamza, 2015).…”
Section: Mechanistic Studiesmentioning
confidence: 99%
“…S4c). These nuances may correspond in part to technical noise from model over-parametrization 16 , but they are also expected from known degeneracy in TF binding specificity, which is further influenced by interactions within dimers, as exemplified by the NF-kb family 20 . AI-TAC filters indeed distinguished the canonical NF-kb hetero-dimer (filter231) and homodimer (filter247) motifs.…”
Section: Learned Motifs Are Associated With Known Pioneer Factors Andmentioning
confidence: 99%
“…S5). Some of the unannotated filters may represent "half-sites", perhaps mere building blocks used by the CNN 43 or perhaps biologically relevant half-sites as reported for NF-kb or NRSF 20,44 .…”
Section: ) T Cells As a Default Pathway?mentioning
confidence: 99%
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