Distinct transcription kinetics of pluripotent cell states

Shao, Rui; Kumar, B. Mohana; Lidschreiber, Katja; Lidschreiber, Michael; Cramer, Patrick; Elsässer, Simon J.

doi:10.15252/msb.202110407

Cited by 9 publications

(3 citation statements)

References 109 publications

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“…To study antisense transcription beyond annotated genes, we first assembled a nascent transcriptome annotation for each time point from scratch (Fig. 3A, see methods for details), as done previously for such data (Shao et al , 2022). We segmented the genome into transcribed and non-transcribed 200 bp fragments for each strand.…”

Section: Resultsmentioning

confidence: 99%

Antisense transcription can induce expression memory via stable promoter repression

Mutzel,

Schwämmle,

Oeverdieck

et al. 2024

Preprint

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The capacity of cells to retain a memory of previous signals enables them to adopt unique cell fates and adjust to their surrounding environment. The underlying gene expression memory can arise from mutual repression of two genes, forming a toggle switch. Such mutual repression may occur at antisense loci, where two convergently oriented genes repress each other in cis. Under which conditions antisense transcription can generate expression memory remains poorly understood. To address this question, we combine mathematical modeling, genomics and a synthetic biology approach. Through simulations we show that stable memory can emerge, if both genes in an antisense pair transcribe through the convergent promoter and induce a stable repressive chromatin state. Genome-wide analysis of nascent transcription further supports antisense-mediated promoter repression with promoter-overlapping antisense gene pairs exhibiting mutually exclusive expression. Through constructing a synthetic antisense locus in mouse embryonic stem cells (mESCs) we then show that such a locus architecture can indeed maintain a memory of a transient stimulus. Mutual repression and the capacity for memory formation are elevated, when mESCs differentiate, showing that epigenetic memory is a cell type-specific property. Our finding that stem cells adapt their ability to remember stimuli as they differentiate might help to elucidate how stemness is maintained.

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Section: Resultsmentioning

confidence: 99%

Antisense transcription can induce expression memory via stable promoter repression

Mutzel,

Schwämmle,

Oeverdieck

et al. 2024

Preprint

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show abstract

“…In mammalian single-cell sequencing studies, RNA spike-ins have demonstrated the presence of hypertranscription states, where cells undergo global transcriptional upregulation (Kim et al, 2023;Percharde et al, 2017). RNA spike-ins have also been successfully used to control for differences in transcriptome size, for example, in maturing oocytes (Wu, 2022) and pluripotent states (Shao et al, 2022). Further complicating single-cell RNA-Seq analysis, in mammalian cells, significant variation in the number of mRNA per cell is observed due to bursts of active transcription periods (Raj et al, 2006).…”

Section: The Implication Of Rna Spike-in Controls In Rna-seq Normaliz...mentioning

confidence: 99%

A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning‐expressed responses

Laosuntisuk,

Vennapusa,

Somayanda

et al. 2024

The Plant Journal

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SUMMARYRNA‐Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA‐Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike‐ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike‐ins as a normalization control produces differences in RNA‐Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike‐ins with 3' RNA‐Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.

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“…A transitional formative state that is germ cell competent can also be captured (42). It was recently reported that RNAPII elongates slower in 2i/LIF conditions (43). We passaged serum/LIF ESCs, in which all the preceding experiments were performed, into either 2i/LIF or formative conditions (fig.…”

Section: Escs Have Greater Rnapii Elongation As Compared To Somatic C...mentioning

confidence: 99%

DOT1L is a barrier to histone acetylation during reprogramming to pluripotency

Wille,

Zhang,

Haws

et al. 2023

Sci. Adv.

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Embryonic stem cells (ESCs) have transcriptionally permissive chromatin enriched for gene activation–associated histone modifications. A striking exception is DOT1L-mediated H3K79 dimethylation (H3K79me2) that is considered a positive regulator of transcription. We find that ESCs are depleted for H3K79me2 at shared locations of enrichment with somatic cells, which are highly and ubiquitously expressed housekeeping genes, and have lower RNA polymerase II (RNAPII) at the transcription start site (TSS) despite greater nascent transcription. Inhibiting DOT1L increases the efficiency of reprogramming of somatic to induced pluripotent stem cells, enables an ESC-like RNAPII pattern at the TSS, and functionally compensates for enforced RNAPII pausing. DOT1L inhibition increases H3K27 methylation and RNAPII elongation–enhancing histone acetylation without changing the expression of the causal histone-modifying enzymes. Only the maintenance of elevated histone acetylation is essential for enhanced reprogramming and occurs at loci that are depleted for H3K79me2. Thus, DOT1L inhibition promotes the hyperacetylation and hypertranscription pluripotent properties.

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Distinct transcription kinetics of pluripotent cell states

Cited by 9 publications

References 109 publications

Antisense transcription can induce expression memory via stable promoter repression

Antisense transcription can induce expression memory via stable promoter repression

A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning‐expressed responses

DOT1L is a barrier to histone acetylation during reprogramming to pluripotency

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