Enhancers predominantly regulate gene expression during differentiation via transcription initiation

Larke, Martin S.C.; Schweßinger, Ron; Nojima, Takayuki; Telenius, Jelena; Beagrie, Robert A.; Downes, Damien J.; Oudelaar, A. Marieke; Truch, Julia; Graham, Bryony; Bender, Michael A.; Proudfoot, Nick J.; Higgs, Douglas R.; Hughes, Jim R.

doi:10.1016/j.molcel.2021.01.002

Cited by 33 publications

(26 citation statements)

References 95 publications

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“…Therefore we were able to deduce that RNA synthesis decrease in the pluripotent state transitions is independent from elongation slowdown and neither controlled by pause release dynamics (Fig 3L,Fig EV3B). This result agrees with a recent study that transcription initiation dominates gene regulation in murine erythropoiesis differentiation over pause-release dynamics (Larke et al, 2021).…”

Section: Previous Estimates Of Transcription Elongation Kinetics Rely On Chemical Inhibition and Time-seriessupporting

confidence: 93%

Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States

Shao

Kumar

Liedschreiber

et al. 2021

Preprint

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Unique transcriptomes define naïve, primed and paused pluripotent states in mouse embryonic stem cells. Here we perform transient transcriptome sequencing (TT-seq) to de novo define and quantify coding and non-coding transcription units (TUs) in different pluripotent states. We observe a global reduction of RNA synthesis, total RNA amount and turnover rates in ground state naïve cells (2i) and paused pluripotency (mTORi). We demonstrate that elongation velocity can be reliably estimated from TT-seq nascent RNA and RNA polymerase II occupancy and observe a transcriptome-wide attenuation of elongation velocity in the two inhibitor-induced states. We also discover a relationship between elongation velocity and termination read-through distance. Our analysis suggests that steady-state transcriptomes in mouse ES cells are controlled predominantly on the level of RNA synthesis, and that signaling pathways governing different pluripotent states immediately control key parameters of transcription.

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Section: Previous Estimates Of Transcription Elongation Kinetics Rely On Chemical Inhibition and Time-seriessupporting

confidence: 93%

Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States

Shao

Kumar

Liedschreiber

et al. 2021

Preprint

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“…Promoter Capture Hi-C of primary human blood cells similarly shows that while promoter-promoter (P-P) interactions occur between only 10% of genes, nearly all promoters engage in cell-type-specific interactions, and 60% of promoters establish interactions that are invariant across cell types (Javierre et al, 2016). Furthermore, changes in transcription initiation rather than a release from pausing, have recently been observed in mammalian cells at developmentally regulated E-P contacts at the aand b-globin loci (Larke et al, 2021). Together, these observations suggest that a complex arrangement of promoter-interacting regions is required to achieve proper gene expression and the evidence supports that both stable and dynamic chromatin structures can contribute to gene expression.…”

Section: Regulatory Interactions As a Distinct Molecular Layer In Gene-regulatory Networkmentioning

confidence: 99%

Decoding the organization, dynamics, and function of the 4D genome

Aboelnour

Bonev

2021

Developmental Cell

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“…Monitoring nascent transcripts has improved the mapping of transcription start sites (TSS) (Tome et al 2018) and identified novel concepts such as promoter-proximal pausing (Core and Adelman 2019) and enhancer RNAs (eRNA) (Hou and Kraus 2021). Recent advances in nascent RNA technologies demonstrated how these processes are integral to gene regulation in eukaryotes (Laitem et al 2015; Nojima et al 2018; Core and Adelman 2019; Larke et al 2021) in response to a range of different conditions and during development. These techniques (see Supplemental Table 1) were successfully employed to monitor nascent transcription quantitatively e.g.…”

Section: Introductionmentioning

confidence: 99%

“…These techniques (see Supplemental Table 1) were successfully employed to monitor nascent transcription quantitatively e.g. TT-Seq (Schwalb et al 2016), PRO-Seq (Kwak et al 2013), GRO-Seq (Core and Lis 2008), NET-Seq (Churchman and Weissman 2011; Nojima et al 2015; Larke et al 2021), to assess elongation rates (TT-Seq), to identify and map promoter proximal pause sites (NET-Seq, PRO-Seq), and TSSs e.g. START-Seq, ScaRNA-Seq (Nechaev et al 2010; Scruggs et al 2015; Lavender et al 2016; Larke et al 2021) and CoPRO-Seq (Tome et al 2018).…”

Section: Introductionmentioning

confidence: 99%

“…TT-Seq (Schwalb et al 2016), PRO-Seq (Kwak et al 2013), GRO-Seq (Core and Lis 2008), NET-Seq (Churchman and Weissman 2011; Nojima et al 2015; Larke et al 2021), to assess elongation rates (TT-Seq), to identify and map promoter proximal pause sites (NET-Seq, PRO-Seq), and TSSs e.g. START-Seq, ScaRNA-Seq (Nechaev et al 2010; Scruggs et al 2015; Lavender et al 2016; Larke et al 2021) and CoPRO-Seq (Tome et al 2018). Whilst these methods have been extensively used and yielded the data to formulate and provided the basis to understand these new concepts, they are costly and each have limitations.…”

Section: Introductionmentioning

confidence: 99%

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Mapping Human Transient Transcriptomes Using Single Nucleotide Resolution 4sU Sequencing (SNU-Seq)

Mellor

Lorenz

Lamstaes

et al. 2021

Preprint

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Genomes are pervasively transcribed leading to stable and unstable transcripts that define functional regions of genomes and contribute to cellular phenotypes. Defining comprehensive nascent transcriptomes is pivotal to understand gene regulation, disease processes, and the impact of extracellular signals on cells. However, currently employed methods are laborious, technically challenging and costly. We developed single-nucleotide resolution 4sU-sequencing (SNU-Seq), involving pulse labelling, biotinylation and direct isolation of nascent transcripts. Artificial poly-(A)-tailing of the 3' most nucleotide of nascent transcripts ensures oligo-d(T) primer-based library preparation and sequencing using commercial 3' RNA-Seq kits. We show that SNU-Seq is a cost-effective new method generating even read profiles across transcription units. We used SNU-Seq to identify transcription elongation parameters, to map usage of polyadenylation (PAS) sites and novel enhancers. Remarkably, 4sU labelled nascent RNA accumulates short ~100nt transcripts that map to the 5' end of genes. We show that isolation of these short nascent RNA and sequencing the 5' and 3' ends using size-selected SNU-Seq (ssSNU-Seq) provides highly sensitive annotations of mapped and novel TSSs, promoter-proximal pause/termination sites. Thus, SNU-seq and ssSNU-seq combined yield comprehensive transcriptomics data at low cost with high spatial and temporal resolution.

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Enhancers predominantly regulate gene expression during differentiation via transcription initiation

Cited by 33 publications

References 95 publications

Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States

Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States

Decoding the organization, dynamics, and function of the 4D genome

Mapping Human Transient Transcriptomes Using Single Nucleotide Resolution 4sU Sequencing (SNU-Seq)

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