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1.
Methods Mol Biol ; 2366: 43-66, 2021.
Article in English | MEDLINE | ID: mdl-34236632

ABSTRACT

Nuclear factor-kappa B (NF-κB) transcription factors coordinate gene expression in response to a broad array of cellular signals. In vertebrates, there are five NF-κB proteins (c-Rel, RelA/p65, RelB, p50, and p52) that can form various dimeric combinations exhibiting both common and dimer-specific DNA-binding specificity. In this chapter, we describe the use of the nuclear extract protein-binding microarray (nextPBM), a high-throughput method to characterize the DNA binding of transcription factors present in cell nuclear extracts. NextPBMs allow for sensitive analysis of the DNA binding of NF-κB dimers and their interactions with cell-specific cofactors.


Subject(s)
Protein Array Analysis , Animals , DNA/genetics , DNA/metabolism , NF-kappa B/metabolism , NF-kappa B p50 Subunit/genetics , NF-kappa B p50 Subunit/metabolism , Plant Extracts , Protein Binding , Signal Transduction , Transcription Factor RelA/genetics , Transcription Factor RelA/metabolism
2.
Am J Hum Genet ; 102(4): 696-705, 2018 04 05.
Article in English | MEDLINE | ID: mdl-29606302

ABSTRACT

AEBP1 encodes the aortic carboxypeptidase-like protein (ACLP) that associates with collagens in the extracellular matrix (ECM) and has several roles in development, tissue repair, and fibrosis. ACLP is expressed in bone, the vasculature, and dermal tissues and is involved in fibroblast proliferation and mesenchymal stem cell differentiation into collagen-producing cells. Aebp1-/- mice have abnormal, delayed wound repair correlating with defects in fibroblast proliferation. In this study, we describe four individuals from three unrelated families that presented with a unique constellation of clinical findings including joint laxity, redundant and hyperextensible skin, poor wound healing with abnormal scarring, osteoporosis, and other features reminiscent of Ehlers-Danlos syndrome (EDS). Analysis of skin biopsies revealed decreased dermal collagen with abnormal collagen fibrils that were ragged in appearance. Exome sequencing revealed compound heterozygous variants in AEBP1 (c.1470delC [p.Asn490_Met495delins(40)] and c.1743C>A [p.Cys581∗]) in the first individual, a homozygous variant (c.1320_1326del [p.Arg440Serfs∗3]) in the second individual, and a homozygous splice site variant (c.1630+1G>A) in two siblings from the third family. We show that ACLP enhances collagen polymerization and binds to several fibrillar collagens via its discoidin domain. These studies support the conclusion that bi-allelic pathogenic variants in AEBP1 are the cause of this autosomal-recessive EDS subtype.


Subject(s)
Alleles , Carboxypeptidases/genetics , Collagen/metabolism , Connective Tissue/pathology , Ehlers-Danlos Syndrome/genetics , Mutation/genetics , Repressor Proteins/genetics , Adult , Amino Acid Sequence , Carboxypeptidases/chemistry , Child , Child, Preschool , Female , Fibroblasts/metabolism , Fibroblasts/pathology , Humans , Male , Protein Domains , RNA, Messenger/genetics , RNA, Messenger/metabolism , Repressor Proteins/chemistry , Skin/pathology , Skin/ultrastructure , Young Adult
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