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Status |
Public on Dec 31, 2022 |
Title |
Structural and Genome-wide Analysis Support a Role for SETMAR in Transcriptional Regulation |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Approximately 50 million years ago, the Hsmar1 transposon entered the primate lineage giving rise to a new protein, a chimeric fusion of a SET domain and the Hsmar1 transposase. This protein, SETMAR or Metnase, is broadly expressed in human tissues and has been shown to retain its ancestral sequence-specific binding to Hsmar1 terminal inverted repeat (TIR) sequences found at the ends of the transposons. Despite the fact that there were estimated to be anywhere from 1500-7000 TIR sites within the human genome, the relevance of SETMAR-TIR interactions was unknown. Here, we report the crystal structure of the SETMAR DNA-binding domain (DBD) complexed with TIR DNA at 2.37 Å. The DBD structure includes two helix-turn-helix motifs (HTH1 and HTH2), which dimerize through HTH1, and confer sequence-specific recognition of the TIR through nucleobase-specific interactions with R371 in HTH1 and R417, H427, S428, and R432 in HTH2. The extent of genome-wide binding was determined by chromatin immunoprecipitation sequencing (ChIP-seq) analysis yielding a total of 7457 SETMAR bound sites. The effect of SETMAR on the transcriptome was assessed by RNA-seq analysis; among the 177 differentially regulated transcripts, a cluster of histones on chromosome 6 were found to be repressed. The dimeric SETMAR structure with each DBD bound to TIR DNA, the presence of eleven TIR sites within the histone gene cluster, and previously reported DNA looping activity are consistent with a direct regulatory mechanism in which SETMAR represses mRNA expression for specific genes through chromatin looping.
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Overall design |
HEK293T cells were transfected with either empty vector or vector containing full length wild type SETMAR gene and differential gene expression was determined by Next Gen RNA sequencing
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Contributor(s) |
Georgiadis M, Bates A |
Citation missing |
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Submission date |
Aug 24, 2017 |
Last update date |
Dec 31, 2022 |
Contact name |
Millie Georgiadis |
E-mail(s) |
mgeorgia@iu.edu
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Organization name |
Indiana University School of Medicine
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Department |
Biochemistry and Molecular Biology
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Lab |
Dr. Millie Georgiadis
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Street address |
635 Barnhill Drive
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City |
Indianapolis |
State/province |
Indiana |
ZIP/Postal code |
46202 |
Country |
USA |
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Platforms (1) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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Samples (8)
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Relations |
BioProject |
PRJNA400164 |
SRA |
SRP116225 |