DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Van

被引:8
作者
Hope, C. Matthew [1 ]
Rebay, Ilaria [2 ,3 ]
Reinitz, John [2 ,4 ,5 ]
机构
[1] Univ Chicago, Dept Biochem & Mol Biophys, Chicago, IL 60637 USA
[2] Univ Chicago, Dept Mol Genet & Cell Biol, Chicago, IL 60637 USA
[3] Univ Chicago, Ben May Dept Canc Res, Chicago, IL 60637 USA
[4] Univ Chicago, Dept Ecol & Evolut, Chicago, IL 60637 USA
[5] Univ Chicago, Dept Stat, Chicago, IL 60637 USA
基金
美国国家卫生研究院;
关键词
PROTEIN INTERACTIONS; SELF-ASSOCIATION; GENE-EXPRESSION; REPRESSOR YAN; SAM DOMAIN; TEL ETV6; BINDING; DROSOPHILA; MOTIF; MODENCODE;
D O I
10.1016/j.bpj.2016.11.901
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
Transcription factors use both protein-DNA and protein-protein interactions to assemble appropriate complexes to regulate gene expression. Although most transcription factors operate as monomers or dimers, a few, including the E26 transformation-specific family repressors Drosophila melanogasterYan and its human homolog TEL/ETV6, can polymerize. Although polymerization is required for both the normal and oncogenic function of Yan and TEL/ETV6, the mechanisms by which it influences the recruitment, organization, and stability of transcriptional complexes remain poorly understood. Further, a quantitative description of the DNA occupancy of a polymerizing transcription factor is lacking, and such a description would have broader applications to the conceptually related area of polymerizing chromatin regulators. To expand the theoretical basis for understanding how the oligomeric state of a transcriptional regulator influences its chromatin occupancy and function, we leveraged the extensive biochemical characterization of E26 transformation-specific factors to develop a mathematical model of Yan occupancy at chemical equilibrium. We find that spreading condensation from a specific binding site can take place in a path-independent manner given reasonable values of the free energies of specific and non-specific DNA binding and protein protein cooperativity. Our calculations show that polymerization confers upon a transcription factor the unique ability to extend occupancy across DNA regions far from specific binding sites. In contrast, dimerization promotes recruitment to clustered binding sites and maximizes discrimination between specific and non-specific sites. We speculate that the association with non-specific DNA afforded by polymerization may enable regulatory behaviors that are well-suited to transcriptional repressors but perhaps incompatible with precise activation.
引用
收藏
页码:180 / 192
页数:13
相关论文
共 42 条
[1]   Animal Transcription Networks as Highly Connected, Quantitative Continua [J].
Biggin, Mark D. .
DEVELOPMENTAL CELL, 2011, 21 (04) :611-626
[2]   The human L(3)MBT polycomb group protein is a transcriptional repressor and interacts physically and functionally with TEL (ETV6) [J].
Boccuni, P ;
MacGrogan, D ;
Scandura, JM ;
Nimer, SD .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2003, 278 (17) :15412-15420
[3]   Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness [J].
Crocker, Justin ;
Abe, Namiko ;
Rinaldi, Lucrezia ;
McGregor, Alistair P. ;
Frankel, Nicolas ;
Wang, Shu ;
Alsawadi, Ahmad ;
Valenti, Philippe ;
Plaza, Serge ;
Payre, Francois ;
Mann, Richard S. ;
Stern, David L. .
CELL, 2015, 160 (1-2) :191-203
[4]   Properties of developmental gene regulatory networks [J].
Davidson, Eric H. ;
Levine, Michael S. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (51) :20063-20066
[5]   ETV6 fusion genes in hematological malignancies: A review [J].
De Braekeleer, Etienne ;
Douet-Guilbert, Nathalie ;
Morel, Frederic ;
Le Bris, Marie-Josee ;
Basinko, Audrey ;
De Braekeleer, Marc .
LEUKEMIA RESEARCH, 2012, 36 (08) :945-961
[6]   Steric Mechanism of Auto-Inhibitory Regulation of Specific and Non-Specific DNA Binding by the ETS Transcriptional Repressor ETV6 [J].
Del, Soumya ;
Chan, Anson C. K. ;
Coyne, H. Jerome, III ;
Bhachech, Niraja ;
Hermsdorf, Ulrike ;
Okon, Mark ;
Murphy, Michael E. P. ;
Graves, Barbara J. ;
McIntosh, Lawrence P. .
JOURNAL OF MOLECULAR BIOLOGY, 2014, 426 (07) :1390-1406
[7]   SPARKLING INSIGHTS INTO ENHANCER STRUCTURE, FUNCTION, AND EVOLUTION [J].
Evans, Nicole C. ;
Swanson, Christina I. ;
Barolo, Scott .
TRANSCRIPTIONAL SWITCHES DURING DEVELOPMENT, 2012, 98 :97-120
[8]  
Funnell APW, 2012, ADV EXP MED BIOL, V747, P105, DOI 10.1007/978-1-4614-3229-6_7
[9]   THE HELIX-LOOP-HELIX DOMAIN - A COMMON MOTIF FOR BRISTLES, MUSCLES AND SEX [J].
GARRELL, J ;
CAMPUZANO, S .
BIOESSAYS, 1991, 13 (10) :493-498
[10]   Dimerization of Nuclear Receptors [J].
Germain, Pierre ;
Bourguet, William .
RECEPTOR-RECEPTOR INTERACTIONS, 2013, 117 :21-41