HOMEPRODUCTSCOMPANYCONTACTFAQResearchDictionaryPharmaSign Up FREE or Login

The ChIP-seq-defined networks of Bcl-3 gene binding support its required role in skeletal muscle atrophy.

Abstract
NF-kappaB transcriptional activation is required for skeletal muscle disuse atrophy. We are continuing to study how the activation of NF-kB regulates the genes that encode the protein products that cause atrophy. Using ChIP-sequencing we found that Bcl-3, an NF-kB transcriptional activator required for atrophy, binds to the promoters of a number of genes whose collective function describes two major aspects of muscle wasting. By means of bioinformatics analysis of ChIP-sequencing data we found Bcl-3 to be directing transcription networks of proteolysis and energy metabolism. The proteolytic arm of the Bcl-3 networks includes many E3 ligases associated with proteasomal protein degradation, including that of the N-end rule pathway. The metabolic arm appears to be involved in organizing the change from oxidative phosphorylation to glycolysis in atrophying muscle. For one gene, MuRF1, ChIP-sequencing data identified the location of Bcl-3 and p50 binding in the promoter region which directed the creation of deletant and base-substitution mutations of MuRF1 promoter constructs to determine the effect on gene transcription. The results provide the first direct confirmation that the NF-kB binding site is involved in the muscle unloading regulation of MuRF1. Finally, we have combined the ChIP-sequencing results with gene expression microarray data from unloaded muscle to map several direct targets of Bcl-3 that are transcription factors whose own targets describe a set of indirect targets for NF-kB in atrophy. ChIP-sequencing provides the first molecular explanation for the finding that Bcl3 knockout mice are resistant to disuse muscle atrophy. Mapping the transcriptional regulation of muscle atrophy requires an unbiased analysis of the whole genome, which we show is now possible with ChIP-sequencing.
AuthorsRobert W Jackman, Chia-Ling Wu, Susan C Kandarian
JournalPloS one (PLoS One) Vol. 7 Issue 12 Pg. e51478 ( 2012) ISSN: 1932-6203 [Electronic] United States
PMID23251550 (Publication Type: Journal Article, Research Support, N.I.H., Extramural)
Chemical References
  • B-Cell Lymphoma 3 Protein
  • BCL3 protein, human
  • Bcl3 protein, mouse
  • Muscle Proteins
  • Proto-Oncogene Proteins
  • Transcription Factors
  • Tripartite Motif Proteins
  • Luciferases
  • TRIM63 protein, human
  • Ubiquitin-Protein Ligases
Topics
  • Animals
  • B-Cell Lymphoma 3 Protein
  • Chromatin Immunoprecipitation
  • Female
  • Gene Expression Regulation
  • Gene Regulatory Networks (genetics)
  • Genes, Reporter
  • Genetic Loci (genetics)
  • Genome
  • Hindlimb Suspension
  • Luciferases (metabolism)
  • Mice
  • Mice, Inbred C57BL
  • Molecular Sequence Annotation
  • Muscle Proteins (genetics)
  • Muscle, Skeletal (metabolism, pathology, physiopathology)
  • Muscular Atrophy (genetics, pathology, physiopathology)
  • Polymerase Chain Reaction
  • Promoter Regions, Genetic (genetics)
  • Protein Binding (genetics)
  • Proteolysis
  • Proto-Oncogene Proteins (genetics)
  • Sequence Analysis, DNA
  • Transcription Factors (genetics)
  • Transcription Initiation Site
  • Tripartite Motif Proteins
  • Ubiquitin-Protein Ligases (genetics)
  • Weight-Bearing

Join CureHunter, for free Research Interface BASIC access!

Take advantage of free CureHunter research engine access to explore the best drug and treatment options for any disease. Find out why thousands of doctors, pharma researchers and patient activists around the world use CureHunter every day.
Realize the full power of the drug-disease research graph!


Choose Username:
Email:
Password:
Verify Password:
Enter Code Shown: