Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells

Nucleic Acids Research
Enara ArretxeMaría José Martínez

Abstract

The NF-κB-inducible Staphylococcal nuclease and tudor domain-containing 1 gene (SND1) encodes a coactivator involved in inflammatory responses and tumorigenesis. While SND1 is known to interact with certain transcription factors and activate client gene expression, no comprehensive mapping of SND1 target genes has been reported. Here, we have approached this question by performing ChIP-chip assays on human hepatoma HepG2 cells and analyzing SND1 binding modulation by proinflammatory TNFα. We show that SND1 binds 645 gene promoters in control cells and 281 additional genes in TNFα-treated cells. Transcription factor binding site analysis of bound probes identified motifs for established partners and for novel transcription factors including HSF, ATF, STAT3, MEIS1/AHOXA9, E2F and p300/CREB. Major target genes were involved in gene expression and RNA metabolism regulation, as well as development and cellular metabolism. We confirmed SND1 binding to 21 previously unrecognized genes, including a set of glycerolipid genes. Knocking-down experiments revealed that SND1 deficiency compromises the glycerolipid gene reprogramming and lipid phenotypic responses to TNFα. Overall, our findings uncover an unexpected large set of potential SND...Continue Reading

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Citations

Dec 24, 2015·International Journal of Molecular Sciences·Jinxia AoXuejun Gao
May 31, 2016·Biochimica Et Biophysica Acta·Hiart Navarro-ImazOlatz Fresnedo
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Aug 25, 2021·Cellular & Molecular Biology Letters·Ghazaleh Khalili-Tanha, Meysam Moghbeli

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Methods Mentioned

BETA
immunoprecipitation
ChIP-chip
transfection
transfections
Assay
ChIP
Feature Extraction
PCR
electrophoresis
nuclear translocation

Software Mentioned

Jaspar
Feature Extraction
PinkThing
QuantityOne
CEAS
Genomic Workbench Lite Edition
Agilent Feature Extraction
DAVID
GeNorm
MEME

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