RNA polymerases reshape chromatin architecture and couple transcription on individual fibers.

Tullius, Thomas W; Isaac, R Stefan; Dubocanin, Danilo; Ranchalis, Jane; Churchman, L Stirling; Stergachis, Andrew B

Tullius, Thomas W; Isaac, R Stefan; Dubocanin, Danilo; Ranchalis, Jane; Churchman, L Stirling; Stergachis, Andrew B.

Afiliación

Tullius TW; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Isaac RS; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Dubocanin D; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
Ranchalis J; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
Churchman LS; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: churchman@genetics.med.harvard.edu.
Stergachis AB; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA. Electronic address: absterga@uw.edu.

Mol Cell ; 84(17): 3209-3222.e5, 2024 Sep 05.

Article en En | MEDLINE | ID: mdl-39191261

ABSTRACT

ABSTRACT

RNA polymerases must initiate and pause within a complex chromatin environment, surrounded by nucleosomes and other transcriptional machinery. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies. To address this, we employed long-read chromatin fiber sequencing (Fiber-seq) in Drosophila to visualize RNA polymerase (Pol) within its native chromatin context with single-molecule precision along up to 30 kb fibers. We demonstrate that Fiber-seq enables the identification of individual Pol II, nucleosome, and transcription factor footprints, revealing Pol II pausing-driven destabilization of downstream nucleosomes. Furthermore, we demonstrate pervasive direct distance-dependent transcriptional coupling between nearby Pol II genes, Pol III genes, and transcribed enhancers, modulated by local chromatin architecture. Overall, transcription initiation reshapes surrounding nucleosome architecture and couples nearby transcriptional machinery along individual chromatin fibers.

Asunto(s)

Cromatina; Drosophila melanogaster; Nucleosomas; Transcripción Genética; Animales; Nucleosomas/metabolismo; Nucleosomas/genética; Cromatina/metabolismo; Cromatina/genética; Drosophila melanogaster/genética; Drosophila melanogaster/enzimología; ARN Polimerasa II/metabolismo; ARN Polimerasa II/genética; Proteínas de Drosophila/genética; Proteínas de Drosophila/metabolismo; Ensamble y Desensamble de Cromatina; ARN Polimerasa III/metabolismo; ARN Polimerasa III/genética; Factores de Transcripción/metabolismo; Factores de Transcripción/genética; ARN Polimerasas Dirigidas por ADN/metabolismo; ARN Polimerasas Dirigidas por ADN/genética

Palabras clave

Fiber-seq; RNA Pol II; RNA Pol III; chromatin; nucleosome; promoter proximal pausing; single-molecule; transcription initiation

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Transcripción Genética / Cromatina / Nucleosomas / Drosophila melanogaster Límite: Animals Idioma: En Revista: Mol Cell Asunto de la revista: BIOLOGIA MOLECULAR Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos

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