The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR.

BMC Genomics
Marta IwanaszkoMarek Kimmel

Abstract

The NF-κB family plays a prominent role in the innate immune response, cell cycle activation or cell apoptosis. Upon stimulation by pathogen-associated patterns, such as viral RNA a kinase cascade is activated, which strips the NF-κB of its inhibitor IκBα molecule and allows it to translocate into the nucleus. Once in the nucleus, it activates transcription of approximately 90 genes whose kinetics of expression differ relative to when NF-κB translocates into the nucleus, referred to as Early, Middle and Late genes. It is not obvious what mechanism is responsible for segregation of the genes' timing of transcriptional response. It is likely that the differences in timing are due, in part, to the number and type of transcription factor binding sites (TFBS), required for NF-κB itself as well as for the putative cofactors, in the Early versus Late genes. We therefore applied an evolutionary analysis of conserved TFBS. We also examined whether transcription dynamic was related to the presence of AU-rich elements (ARE) located in 3'UTR of the mRNA because recent studies have shown that the presence of AREs is associated with rapid gene induction. We found that Early genes were significantly enriched in NF-κB binding sites occurring i...Continue Reading

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Citations

Jun 13, 2014·Reproduction : the Official Journal of the Society for the Study of Fertility·Georgios MichailidisPascal Froment
Nov 23, 2017·Scientific Reports·Karolina TudelskaTomasz Lipniacki
Apr 19, 2015·BMC Genomics·Marta Iwanaszko, Marek Kimmel
Jun 6, 2017·Nature Communications·Sivakumar PeriasamyJonathan A Harton

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Methods Mentioned

BETA
acetylation
phylogenetic footprinting
NucleoSeq

Software Mentioned

MOPAT
ConSite
Cister
oPOSSUM
FootPrinter
TRANSFAC
Cluster
TRAP
CisPlusFinder
Crème

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