Transcriptional control of transglutaminase 2 expression in mouse apoptotic thymocytes.
Transglutaminase 2 (TGM2) is a ubiquitously expressed multifunctional protein, which participates in various biological processes including thymocyte apoptosis. As a result, the transcriptional regulation of the gene is complex and must depend on the cell type. Previous studies from our laboratory have shown that in dying thymocytes the expression of Tgm2 is induced by external signals derived from engulfing macrophages, such as retinoids, transforming growth factor (TGF)-β and adenosine, the latter triggering the adenylate cyclase signaling pathway. The existence of TGF-β and retinoid responsive elements in the promoter region of Tgm2 has already been reported, but the intergenic regulatory elements participating in the regulation of Tgm2 have not yet been identified. Here we used publicly available results from DNase I hypersensitivity analysis followed by deep sequencing and chromatin immunoprecipitation followed by deep sequencing against CCCTC-binding factor (CTCF), H3K4me3, H3K4me1 and H3K27ac to map a putative regulatory element set for Tgm2 in thymocytes. By measuring eRNA expressions of these putative enhancers in retinoid, rTGF-β or dibutiryl cAMP-exposed thymocytes we determined which of them are functional. By applying ChIP-qPCR against SMAD4, retinoic acid receptor, retinoid X receptor, cAMP response element binding protein, P300 and H3K27ac under the same conditions, we identified two enhancers of Tgm2, which seem to act as integrators of the TGF-β, retinoid and adenylate cyclase signaling pathways in dying thymocytes. Our study describes a novel strategy to identify and characterize the signal-specific functional enhancer set of a gene by integrating genome-wide datasets and measuring the production of enhancer specific RNA molecules.
Division of Dental Biochemistry, Signaling and Apoptosis Research Group, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., Debrecen H-4012, Hungary.
Katalin
K
Sándor
Nuclear Receptor Research Group, Research Center of Molecular Medicine, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt. 98, Debrecen H-4012, Hungary.
Bence
B
Daniel
Division of Dental Biochemistry, Signaling and Apoptosis Research Group, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., Debrecen H-4012, Hungary.
Bea
B
Kiss
Division of Dental Biochemistry, Signaling and Apoptosis Research Group, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., Debrecen H-4012, Hungary.
Fruzsina
F
Kovács
Division of Dental Biochemistry, Signaling and Apoptosis Research Group, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., Debrecen H-4012, Hungary. Electronic address: szondy@med.unideb.hu.
Zsuzsa
Z
Szondy
D000818:Animals; D017209:Apoptosis / Q000235:genetics*; D003994:Bucladesine / Q000494:pharmacology; D000076246:CCCTC-Binding Factor; D017362:Cyclic AMP Response Element-Binding Protein / Q000235:genetics / Q000378:metabolism; D050881:E1A-Associated p300 Protein / Q000235:genetics / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D019204:GTP-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D005786:Gene Expression Regulation; D006657:Histones / Q000235:genetics / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism; D061251:Primary Cell Culture; D011401:Promoter Regions, Genetic; D000091345:Protein Glutamine gamma Glutamyltransferase 2; D018168:Receptors, Retinoic Acid / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D047488:Retinoid X Receptors / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D051901:Smad4 Protein / Q000235:genetics / Q000378:metabolism; D060168:Thymocytes / Q000166:cytology / Q000187:drug effects / Q000378:metabolism*; D014158:Transcription, Genetic; D016212:Transforming Growth Factor beta / Q000494:pharmacology; D011503:Transglutaminases / Q000235:genetics* / Q000378:metabolism; D014212:Tretinoin / Q000494:pharmacology
D000076246:CCCTC-Binding Factor; C000619698:Ctcf protein, mouse; D017362:Cyclic AMP Response Element-Binding Protein; D006657:Histones; D008565:Membrane Proteins; C498709:Pag1 protein, mouse; D010750:Phosphoproteins; D018168:Receptors, Retinoic Acid; D012097:Repressor Proteins; D047488:Retinoid X Receptors; D051901:Smad4 Protein; C490810:Smad4 protein, mouse; D016212:Transforming Growth Factor beta; D014212:Tretinoin; D003994:Bucladesine; D050881:E1A-Associated p300 Protein; C494361:Ep300 protein, mouse; D000091345:Protein Glutamine gamma Glutamyltransferase 2; D011503:Transglutaminases; D019204:GTP-Binding Proteins
Apoptosis; ChIP-seq; Enhancer RNA; Gene regulation; T cells; Transglutaminase 2