RESUMO
How chromatin remodelers cooperate to organize nucleosomes around the start and end of genes is not known. We determined the genome-wide binding of remodeler complexes SWI/SNF, RSC, ISW1a, ISW1b, ISW2, and INO80 to individual nucleosomes in Saccharomyces, and determined their functional contributions to nucleosome positioning through deletion analysis. We applied ultra-high-resolution ChIP-exo mapping to Isw2 to determine its subnucleosomal orientation and organization on a genomic scale. Remodelers interacted with selected nucleosome positions relative to the start and end of genes and produced net directionality in moving nucleosomes either away or toward nucleosome-free regions at the 5' and 3' ends of genes. Isw2 possessed a subnucleosomal organization in accord with biochemical and crystallographic-based models that place its linker binding region within promoters and abutted against Reb1-bound locations. Together, these findings reveal a coordinated position-specific approach taken by remodelers to organize genic nucleosomes into arrays.
Assuntos
Montagem e Desmontagem da Cromatina , Genoma Fúngico , Estudo de Associação Genômica Ampla , Nucleossomos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Adenosina Trifosfatases/metabolismo , Proteínas de Ligação a DNA/metabolismo , Exodesoxirribonucleases , Técnicas Genéticas , Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/metabolismoRESUMO
A canonical nucleosome architecture around promoters establishes the context in which proteins regulate gene expression. Whether gene regulatory proteins that interact with nucleosomes are selective for individual nucleosome positions across the genome is not known. Here, we examine on a genomic scale several protein-nucleosome interactions, including those that (1) bind histones (Bdf1/SWR1 and Srm1), (2) bind specific DNA sequences (Rap1 and Reb1), and (3) potentially collide with nucleosomes during transcription (RNA polymerase II). We find that the Bdf1/SWR1 complex forms a dinucleosome complex that is selective for the +1 and +2 nucleosomes of active genes. Rap1 selectively binds to its cognate site on the rotationally exposed first and second helical turn of nucleosomal DNA. We find that a transcribing RNA polymerase creates a delocalized state of resident nucleosomes. These findings suggest that nucleosomes around promoter regions have position-specific functions and that some gene regulators have position-specific nucleosomal interactions.
Assuntos
Regulação Fúngica da Expressão Gênica , Genoma Fúngico , Nucleossomos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Fatores de Transcrição/metabolismo , Transcrição Gênica , Adenosina Trifosfatases/genética , Adenosina Trifosfatases/metabolismo , Sítios de Ligação , Montagem e Desmontagem da Cromatina , DNA Polimerase II/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Fatores de Troca do Nucleotídeo Guanina/genética , Fatores de Troca do Nucleotídeo Guanina/metabolismo , Histona Acetiltransferases/genética , Histona Acetiltransferases/metabolismo , Histonas/metabolismo , Complexos Multiproteicos , Mutação , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Conformação de Ácido Nucleico , Regiões Promotoras Genéticas , Conformação Proteica , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Complexo Shelterina , Proteínas de Ligação a Telômeros/genética , Proteínas de Ligação a Telômeros/metabolismo , Fatores de Transcrição/genéticaRESUMO
Spiroplasma sp. strain GNAT3597T was isolated from the biting midge genus Atrichopogon (Diptera: Ceratopogonidae). It was serologically distinct from other Spiroplasma species, groups or subgroups. Dark-field microscopy of the cells revealed the classical helical shape and subsequent transmission electron microscopy revealed cells surrounded by only a cell membrane (i.e. lacking a cell wall). Growth of strain GNAT3597T occurred in M1D medium at 30 degrees C. Strain GNAT3597T catabolized both glucose and arginine, but did not hydrolyse urea. The DNA G+C content of strain GNAT3597T was 29+/-1 mol%. Only one strain, SMCAT (Spiroplasma mirum), is serologically related to strain GNAT3597T, although the relationship is weak (positive reaction to only a 1 : 80 dilution). It is therefore proposed that strain GNAT3597T (=ATCC BAA-520T=NBRC 100390T) represents a novel species, Spiroplasma atrichopogonis sp. nov. (class Mollicutes: order Entomoplasmatales: family Spiroplasmataceae).