Spt4 facilitates the movement of RNA polymerase II through the +2 nucleosomal barrier

Ulku Uzun; Thomas Brown; Harry Fishcl; Andrew Angel; Jane Mellor

doi:10.1016/j.celrep.2021.109755

Spt4 facilitates the movement of RNA polymerase II through the +2 nucleosomal barrier

Ulku Uzun
, Thomas Brown
, Harry Fishcl
, Andrew Angel
, Jane Mellor^*

^*Corresponding author for this work

University of Oxford

Research output: Contribution to journal › Article › peer-review

16 Citations (Scopus)

6 Downloads (Pure)

Abstract

Spt4 is a transcription elongation factor with homologs in organisms with nucleosomes. Structural and in vitro studies implicate Spt4 in transcription through nucleosomes, and yet the in vivo function of Spt4 is unclear. Here, we assess the precise position of Spt4 during transcription and the consequences of the loss of Spt4 on RNA polymerase II (RNAPII) dynamics and nucleosome positioning in Saccharomyces cerevisiae. In the absence of Spt4, the spacing between gene-body nucleosomes increases and RNAPII accumulates upstream of the nucleosomal dyad, most dramatically at nucleosome +2. Spt4 associates with elongating RNAPII early in transcription, and its association dynamically changes depending on nucleosome positions. Together, our data show that Spt4 regulates early elongation dynamics, participates in co-transcriptional nucleosome positioning, and promotes RNAPII movement through the gene-body nucleosomes, especially the +2 nucleosome.

Original language	English
Pages (from-to)	4064-4075
Number of pages	12
Journal	Cell Reports
Volume	36
Issue number	13
DOIs	https://doi.org/10.1016/j.celrep.2021.109755
Publication status	Published - 28 Sept 2021
Externally published	Yes

Bibliographical note

We thank Frank Holstege for providing the S.cerevisiae Anchor Away strains, Lidia Vasilieva for Rpb9 FLAG-tagged S.pombe strain, Sabrina Liberatori and Shabaz Mohammed for proteomics, and Micron Oxford for imaging support.

Data Availability Statement

The datasets generated during this study are available at GEO:GSE159291. The PRO-seq (GEO:GSE76142) and paf1Δ NET-seq (ArrayExpress: E-MTAB-4568) datasets were downloaded and reanalyzed as part of this study.
The original code for mathematical model is provided at https://github.com/aangel-code/spt4_transcription_simulation.
Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Funding

This work was supported by a Cancer Research UK (CRUK) grant (C5255/A23225), a CRUK Oxford Centre Prize DPhil Studentship to Ü.U., an EPSRC studentship to T.B. (EP/F500394/10), a Royal Society University Research Fellowship to A.A. (UF120327), and BBSRC grants to J.M. (BB/S009035/1 for A.A. and BB/P00296X/1 for H.F).

Funders	Funder number
Cancer Research UK	C5255/A23225
Engineering & Physical Sciences Research Council (EPSRC)	EP/F500394/10
The Royal Society	UF120327
Biotechnology and Biological Sciences Research Council	BB/S009035/1, BB/P00296X/1

Keywords

spt4
spt5
transcriptional elongation
RNAPII
Saccharomyces cerevisiae
Nucleosome
NET-seq
TEF-seq
MNase-seq

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Uzun_etal_CR_Spt4_Facilitates_the_Movement_VOR
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Final published version, 22.8 MBLicence: CC BY

Cite this

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title = "Spt4 facilitates the movement of RNA polymerase II through the +2 nucleosomal barrier",

abstract = "Spt4 is a transcription elongation factor with homologs in organisms with nucleosomes. Structural and in vitro studies implicate Spt4 in transcription through nucleosomes, and yet the in vivo function of Spt4 is unclear. Here, we assess the precise position of Spt4 during transcription and the consequences of the loss of Spt4 on RNA polymerase II (RNAPII) dynamics and nucleosome positioning in Saccharomyces cerevisiae. In the absence of Spt4, the spacing between gene-body nucleosomes increases and RNAPII accumulates upstream of the nucleosomal dyad, most dramatically at nucleosome +2. Spt4 associates with elongating RNAPII early in transcription, and its association dynamically changes depending on nucleosome positions. Together, our data show that Spt4 regulates early elongation dynamics, participates in co-transcriptional nucleosome positioning, and promotes RNAPII movement through the gene-body nucleosomes, especially the +2 nucleosome.",

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author = "Ulku Uzun and Thomas Brown and Harry Fishcl and Andrew Angel and Jane Mellor",

note = "We thank Frank Holstege for providing the S.cerevisiae Anchor Away strains, Lidia Vasilieva for Rpb9 FLAG-tagged S.pombe strain, Sabrina Liberatori and Shabaz Mohammed for proteomics, and Micron Oxford for imaging support.",

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doi = "10.1016/j.celrep.2021.109755",

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AU - Angel, Andrew

AU - Mellor, Jane

N1 - We thank Frank Holstege for providing the S.cerevisiae Anchor Away strains, Lidia Vasilieva for Rpb9 FLAG-tagged S.pombe strain, Sabrina Liberatori and Shabaz Mohammed for proteomics, and Micron Oxford for imaging support.

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N2 - Spt4 is a transcription elongation factor with homologs in organisms with nucleosomes. Structural and in vitro studies implicate Spt4 in transcription through nucleosomes, and yet the in vivo function of Spt4 is unclear. Here, we assess the precise position of Spt4 during transcription and the consequences of the loss of Spt4 on RNA polymerase II (RNAPII) dynamics and nucleosome positioning in Saccharomyces cerevisiae. In the absence of Spt4, the spacing between gene-body nucleosomes increases and RNAPII accumulates upstream of the nucleosomal dyad, most dramatically at nucleosome +2. Spt4 associates with elongating RNAPII early in transcription, and its association dynamically changes depending on nucleosome positions. Together, our data show that Spt4 regulates early elongation dynamics, participates in co-transcriptional nucleosome positioning, and promotes RNAPII movement through the gene-body nucleosomes, especially the +2 nucleosome.

AB - Spt4 is a transcription elongation factor with homologs in organisms with nucleosomes. Structural and in vitro studies implicate Spt4 in transcription through nucleosomes, and yet the in vivo function of Spt4 is unclear. Here, we assess the precise position of Spt4 during transcription and the consequences of the loss of Spt4 on RNA polymerase II (RNAPII) dynamics and nucleosome positioning in Saccharomyces cerevisiae. In the absence of Spt4, the spacing between gene-body nucleosomes increases and RNAPII accumulates upstream of the nucleosomal dyad, most dramatically at nucleosome +2. Spt4 associates with elongating RNAPII early in transcription, and its association dynamically changes depending on nucleosome positions. Together, our data show that Spt4 regulates early elongation dynamics, participates in co-transcriptional nucleosome positioning, and promotes RNAPII movement through the gene-body nucleosomes, especially the +2 nucleosome.

KW - spt4

KW - spt5

KW - transcriptional elongation

KW - RNAPII

KW - Saccharomyces cerevisiae

KW - Nucleosome

KW - NET-seq

KW - TEF-seq

KW - MNase-seq

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DO - 10.1016/j.celrep.2021.109755

M3 - Article

SN - 2211-1247

VL - 36

SP - 4064

EP - 4075

JO - Cell Reports

JF - Cell Reports

IS - 13

ER -

Spt4 facilitates the movement of RNA polymerase II through the +2 nucleosomal barrier

Abstract

Bibliographical note

Data Availability Statement

Funding

Keywords

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