The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

Felipe Beckedorff; Ezra Blumenthal; Lucas Ferreira daSilva; Yuki Aoi; Pradeep Reddy Cingaram; Jingyin Yue; Anda Zhang; Sadat Dokaneheifard; Monica Guiselle Valencia; Gabriel Gaidosh; Ali Shilatifard; Ramin Shiekhattar

doi:10.1016/j.celrep.2020.107917

The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

Felipe Beckedorff, Ezra Blumenthal, Lucas Ferreira daSilva, Yuki Aoi, Pradeep Reddy Cingaram, Jingyin Yue, Anda Zhang, Sadat Dokaneheifard, Monica Guiselle Valencia, Gabriel Gaidosh, Ali Shilatifard, Ramin Shiekhattar^*

^*Corresponding author for this work

Biochemistry and Molecular Genetics

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

69 Scopus citations

Abstract

Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanisms controlling transcription at promoters and enhancers remain enigmatic. Here, we demonstrate that Integrator subunit 11 (INTS11), the catalytic subunit of the Integrator complex, regulates transcription at these loci through its endonuclease activity. Promoters of genes require INTS11 to cleave nascent transcripts associated with paused RNAPII and induce their premature termination in the proximity of the +1 nucleosome. The turnover of RNAPII permits the subsequent recruitment of an elongation-competent RNAPII complex, leading to productive elongation. In contrast, enhancers require INTS11 catalysis not to evict paused RNAPII but rather to terminate enhancer RNA transcription beyond the +1 nucleosome. These findings are supported by the differential occupancy of negative elongation factor (NELF), SPT5, and tyrosine-1-phosphorylated RNAPII. This study elucidates the role of Integrator in mediating transcriptional elongation at human promoters through the endonucleolytic cleavage of nascent transcripts and the dynamic turnover of RNAPII.

Original language	English (US)
Article number	107917
Journal	Cell reports
Volume	32
Issue number	3
DOIs	https://doi.org/10.1016/j.celrep.2020.107917
State	Published - Jul 21 2020

Funding

We thank the Shiekhattar lab for constructive discussions and suggestions for experimental design. We thank Lucia Speroni for technical help. We thank the Oncogenomics core facility at Sylvester Comprehensive Cancer Center for performing high-throughput sequencing. This work was supported by funding from the University of Miami Miller School of Medicine , the Sylvester Comprehensive Cancer Center , and the National Institutes of Health (grants R01 GM078455 , GM105754 , and DP1 CA228041 to R.S.). Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under award number P30CA240139 . The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Keywords

RNA polymerase II
RNA processing
elongation
enhancers
integrator
pause-release
promoters
termination
transcription
traveling ratio

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.1016/j.celrep.2020.107917

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Beckedorff, F., Blumenthal, E., daSilva, L. F., Aoi, Y., Cingaram, P. R., Yue, J., Zhang, A., Dokaneheifard, S., Valencia, M. G., Gaidosh, G., Shilatifard, A., & Shiekhattar, R. (2020). The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts. Cell reports, 32(3), Article 107917. https://doi.org/10.1016/j.celrep.2020.107917

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abstract = "Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanisms controlling transcription at promoters and enhancers remain enigmatic. Here, we demonstrate that Integrator subunit 11 (INTS11), the catalytic subunit of the Integrator complex, regulates transcription at these loci through its endonuclease activity. Promoters of genes require INTS11 to cleave nascent transcripts associated with paused RNAPII and induce their premature termination in the proximity of the +1 nucleosome. The turnover of RNAPII permits the subsequent recruitment of an elongation-competent RNAPII complex, leading to productive elongation. In contrast, enhancers require INTS11 catalysis not to evict paused RNAPII but rather to terminate enhancer RNA transcription beyond the +1 nucleosome. These findings are supported by the differential occupancy of negative elongation factor (NELF), SPT5, and tyrosine-1-phosphorylated RNAPII. This study elucidates the role of Integrator in mediating transcriptional elongation at human promoters through the endonucleolytic cleavage of nascent transcripts and the dynamic turnover of RNAPII.",

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AU - Beckedorff, Felipe

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AU - Aoi, Yuki

AU - Cingaram, Pradeep Reddy

AU - Yue, Jingyin

AU - Zhang, Anda

AU - Dokaneheifard, Sadat

AU - Valencia, Monica Guiselle

AU - Gaidosh, Gabriel

AU - Shilatifard, Ali

AU - Shiekhattar, Ramin

N1 - Funding Information: We thank the Shiekhattar lab for constructive discussions and suggestions for experimental design. We thank Lucia Speroni for technical help. We thank the Oncogenomics core facility at Sylvester Comprehensive Cancer Center for performing high-throughput sequencing. This work was supported by funding from the University of Miami Miller School of Medicine , the Sylvester Comprehensive Cancer Center , and the National Institutes of Health (grants R01 GM078455 , GM105754 , and DP1 CA228041 to R.S.). Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under award number P30CA240139 . The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Publisher Copyright: © 2020 The Author(s)

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N2 - Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanisms controlling transcription at promoters and enhancers remain enigmatic. Here, we demonstrate that Integrator subunit 11 (INTS11), the catalytic subunit of the Integrator complex, regulates transcription at these loci through its endonuclease activity. Promoters of genes require INTS11 to cleave nascent transcripts associated with paused RNAPII and induce their premature termination in the proximity of the +1 nucleosome. The turnover of RNAPII permits the subsequent recruitment of an elongation-competent RNAPII complex, leading to productive elongation. In contrast, enhancers require INTS11 catalysis not to evict paused RNAPII but rather to terminate enhancer RNA transcription beyond the +1 nucleosome. These findings are supported by the differential occupancy of negative elongation factor (NELF), SPT5, and tyrosine-1-phosphorylated RNAPII. This study elucidates the role of Integrator in mediating transcriptional elongation at human promoters through the endonucleolytic cleavage of nascent transcripts and the dynamic turnover of RNAPII.

AB - Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanisms controlling transcription at promoters and enhancers remain enigmatic. Here, we demonstrate that Integrator subunit 11 (INTS11), the catalytic subunit of the Integrator complex, regulates transcription at these loci through its endonuclease activity. Promoters of genes require INTS11 to cleave nascent transcripts associated with paused RNAPII and induce their premature termination in the proximity of the +1 nucleosome. The turnover of RNAPII permits the subsequent recruitment of an elongation-competent RNAPII complex, leading to productive elongation. In contrast, enhancers require INTS11 catalysis not to evict paused RNAPII but rather to terminate enhancer RNA transcription beyond the +1 nucleosome. These findings are supported by the differential occupancy of negative elongation factor (NELF), SPT5, and tyrosine-1-phosphorylated RNAPII. This study elucidates the role of Integrator in mediating transcriptional elongation at human promoters through the endonucleolytic cleavage of nascent transcripts and the dynamic turnover of RNAPII.

KW - RNA polymerase II

KW - RNA processing

KW - elongation

KW - enhancers

KW - integrator

KW - pause-release

KW - promoters

KW - termination

KW - transcription

KW - traveling ratio

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SN - 2211-1247

VL - 32

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JF - Cell reports

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The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

Abstract

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Keywords

ASJC Scopus subject areas

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