title: Combinatorial control of DNase I-hypersensitive site formation and erasure by immunoglobulin heavy chain enhancer-binding proteins.
abstract: DNase I-hypersensitive sites in cellular chromatin are usually believed to be nucleosome-free regions generated by transcription factor binding. Using a cell-free system we show that hypersensitivity does not simply correlate with the number of DNA-bound proteins. Specifically, the leucine zipper containing basic helix-loop-helix protein TFE3 was sufficient to induce a DNase I-hypersensitive site at the immunoglobulin heavy chain micro enhancer in vitro. TFE3 enhanced binding of an ETS protein PU.1 to the enhancer. However, PU.1 binding erased the DNase I-hypersensitive site without abolishing TFE3 binding. Furthermore, TFE3 binding enhanced transcription in the presence and absence of a hypersensitive site, whereas endonuclease accessibility correlated strictly with DNase I hypersensitivity. We infer that chromatin constraints for transcription and nuclease sensitivity can differ.
authors.affiliation: Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454, USA.
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Ishii
authors.forename: Ranjan
authors.initials: R
authors.lastname: Sen
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Pazin
mesh_terms: D000818:Animals; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; D001665:Binding Sites; D015139:Blotting, Southern; D002474:Cell-Free System; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry; D003850:Deoxyribonuclease I / Q000737:chemistry*; D019281:Dimerization; D004330:Drosophila; D004742:Enhancer Elements, Genetic; D005803:Genes, Immunoglobulin / Q000235:genetics*; D005982:Glutathione Transferase / Q000378:metabolism; D016350:Leucine Zippers; D010957:Plasmids / Q000378:metabolism; D011485:Protein Binding; D011518:Proto-Oncogene Proteins / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000378:metabolism; D015534:Trans-Activators / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry; D014158:Transcription, Genetic; D000099232:Proto-Oncogene Protein Spi-1
chemical_list: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; D002843:Chromatin; D004268:DNA-Binding Proteins; D003850:Deoxyribonuclease I; D005982:Glutathione Transferase; D011518:Proto-Oncogene Proteins; D011993:Recombinant Fusion Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D000099232:Proto-Oncogene Protein Spi-1; C069203:TFE3 protein, human