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Transient genome-wide adaptations of nascent RNAPII transcription triggered by low temperature

ABSTRACT: Transient genome-wide adaptations of nascent RNAPII transcription triggered by low temperature

PROVIDER: PRJNA544565 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9117170_1.fastq.gz	Fastqsanger.gz
	SRR9117170_2.fastq.gz	Fastqsanger.gz
	SRR9117180_1.fastq.gz	Fastqsanger.gz
	SRR9117180_2.fastq.gz	Fastqsanger.gz
	SRR9117190_1.fastq.gz	Fastqsanger.gz

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Transient genome-wide adaptations of nascent RNAPII transcription triggered by low temperature

Project description:We determined RNA polymerase (RNAPII) transcription at single-nucleotide resolution in Arabidopsis during early stages of exposure to low temperature. Our data inform on the dynamics of RNAPII transcription and detect thousands of often short-lived uncharacterized transcripts. We demonstrate that low temperature triggers transient genome-wide effects on RNAPII activity, in particular the stalling of RNAPII at both gene ends and the distance of read-through transcription.

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Slow RNAPII transcription elongation rate, low levels of RNAPII pausing, and elevated histone H1 content at promoters associate with higher m6A deposition on nascent mRNAs

Project description:N6-methyladenosine modification (m6A) fine-tunes RNA fate in a variety of ways, thus regulating multiple fundamental biological processes. m6A writers bind to chromatin and interact with RNA polymerase II (RNAPII) during transcription. To evaluate how the dynamics of the transcription process impact m6A deposition, we studied RNAPII elongation rates in mouse embryonic stem cells with altered chromatin configurations, due to reductions in linker histone H1 content. We found that genes transcribed at slow speed are preferentially methylated and display unique signatures at their promoter region, namely high levels of histone H1, together with marks of bivalent chromatin and low RNAPII pausing. They are also highly susceptible to m6A loss upon histone H1 reduction. These results indicate that RNAPII velocity links chromatin structure and the deposition of m6A, highlighting the intricate relationship between different regulatory layers on nascent mRNA molecules.

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Effect of HDAC inhibition on nascent transcription by RNAPII in fission yeast

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Project description:Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter-proximal RNAPII stalling in predisposing genes for transcriptional activation during plant-environment interactions. At gene 3'-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.

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

Project description: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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Project description:The carboxy-terminal domain (CTD) of the largest subunit of RNA Polymerase II (RNAPII) consists of multiple tandem repeats of the heptapeptide consensus Y1-S2-P3-T4-S5-P6-S7. RNAPII CTD is intrinsically disordered and has been shown to promote liquid-liquid phase-separation (LLPS) of RNAPII in vivo. However, understanding the precise role of the conserved heptad residues in LLPS has been hampered by the lack of direct characterization of the biochemical properties of the CTD. Here, we generated a systematic array of RNAPII CTD variants to unravel the sequence-encoded molecular grammar underlying LLPS of the human CTD.

2024-09-19 | PXD049700 | Pride

Slow RNAPII transcription elongation rate, low levels of RNAPII pausing, and elevated histone H1 content at promoters associate with higher m6A deposition on nascent mRNAs

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