ABSTRACT
Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA. By mutational analysis and uncoupling of ISW1a's dinucleosome specificity, we find that dinucleosome recognition is required by ISW1a for proper chromatin organization at promoters; as well as transcription regulation in combination with the histone acetyltransferase NuA4 and histone H2A.Z exchanger SWR1.
Subject(s)
Adenosine Triphosphatases/metabolism , Chromatin Assembly and Disassembly , DNA-Binding Proteins/metabolism , Nucleosomes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Transcription Factors/chemistry , Animals , Gene Expression Regulation , Histone Acetyltransferases/metabolism , Histones/metabolism , Saccharomyces cerevisiae/metabolism , Salmon , Transcription Factors/metabolism , XenopusABSTRACT
The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes.
Subject(s)
Adenosine Triphosphatases/metabolism , Chromosomal Proteins, Non-Histone/metabolism , DNA-Binding Proteins/metabolism , Models, Biological , Nucleosomes/physiology , Saccharomyces cerevisiae Proteins/metabolism , Transcription Factors/metabolism , Chromatin Assembly and Disassembly/physiology , DNA/chemistry , Optical Tweezers , Plasmids/genetics , Transcription Factors/geneticsABSTRACT
Small GTPase Rho signaling pathways regulate the growth, motility, invasion and metastasis of breast cancer cells. Aberrant Rho signaling, as results from alterations in the levels of Rho GTPase proteins, the status of activation, and the abundance of effector proteins, is found in breast cancers. Alterations of Rho signaling particularly impact the cytoskeleton, whose organization and reorganization underpin the motility of breast cancer cells during the invasive growth and metastasis of breast cancer. Progress is being made to elucidate the underlying mechanisms by which Rho GTPases activate the downstream signaling effectors. Further investigations are required for development of novel tumor therapeutic strategies targeting the Rho GTPase signaling pathways to treat breast cancer.
