Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome

AbstractR-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere homeostasis, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localisation was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the intergenic regions of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination, most T. brucei R-loops act in a novel role, promoting RNA Pol II movement or mRNA processing. Finally, we show there is little evidence for correlation between R-loop localisation and mapped sites of DNA replication initiation.

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Intronic heterochromatin prevents cryptic transcription initiation in Arabidopsis

10.1101/610832 ◽

2019 ◽

Author(s):

Jincong Zhou ◽

Liangyu Liu ◽

Qin Li ◽

Wei Xu ◽

Kuan Li ◽

...

Keyword(s):

Transcription Initiation ◽

Common Mechanism ◽

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide ◽

Chimeric Transcripts ◽

Genes Expression ◽

Cryptic Transcription ◽

Eukaryotic Genomes ◽

Host Genes

ABSTRACTIntronic transposable elements (TEs) comprise a large proportion in eukaryotic genomes, but how they regulate the host genes remains to be explored. Our forward genetic screen disclosed the plant specific RNA polymerases IV and V in suppressing intronic TE-mediated cryptic transcription initiation of a chimeric transcripts at FLC (FLCTE). Initiation of FLCTE transcription is blocked by the locally formed intronic heterochromatin, which is directly associated with RNA Pol V to inhibit the entry of RNA Pol II and the occupancy of H3K4 methylation. Genome-wide Pol II Ser5p native elongation transcription sequencing revealed that this is a common mechanism among intronic heterochromatin-containing genes. This study sheds light on deeply understanding the function of intronic heterochromatin on host genes expression in eukaryotic genome.

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Genome replication affects transcription factor binding mediating the cascade of herpes simplex virus transcription

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1818463116 ◽

2019 ◽

Vol 116 (9) ◽

pp. 3734-3739 ◽

Cited By ~ 8

Author(s):

Sarah E. Dremel ◽

Neal A. DeLuca

Keyword(s):

Transcription Factor ◽

Herpes Simplex Virus ◽

Dna Replication ◽

Herpes Simplex ◽

Gene Transcription ◽

Transcription Initiation ◽

Genome Replication ◽

Pol Ii ◽

Factor Binding ◽

Simplex Virus

In herpes simplex virus type 1 (HSV-1) infection, the coupling of genome replication and transcription regulation has been known for many years; however, the underlying mechanism has not been elucidated. We performed a comprehensive transcriptomic assessment and factor-binding analysis for Pol II, TBP, TAF1, and Sp1 to assess the effect genome replication has on viral transcription initiation and elongation. The onset of genome replication resulted in the binding of TBP, TAF1, and Pol II to previously silent late promoters. The viral transcription factor, ICP4, was continuously needed in addition to DNA replication for activation of late gene transcription initiation. Furthermore, late promoters contain a motif that closely matches the consensus initiator element (Inr), which robustly bound TAF1 postreplication. Continued DNA replication resulted in reduced binding of Sp1, TBP, and Pol II to early promoters. Therefore, the initiation of early gene transcription is attenuated following DNA replication. Herein, we propose a model for how viral DNA replication results in the differential utilization of cellular factors that function in transcription initiation, leading to the delineation of kinetic class in HSV-productive infection.

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Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq

Nucleic Acids Research ◽

10.1093/nar/gkq775 ◽

2010 ◽

Vol 39 (1) ◽

pp. 190-201 ◽

Cited By ~ 37

Author(s):

Hao Sun ◽

Jiejun Wu ◽

Priyankara Wickramasinghe ◽

Sharmistha Pal ◽

Ravi Gupta ◽

...

Keyword(s):

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide ◽

Mouse Tissues ◽

Promoter Usage ◽

Rna Pol Ii Promoter

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Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

eLife ◽

10.7554/elife.55667 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 5

Author(s):

Anand Ranjan ◽

Vu Q Nguyen ◽

Sheng Liu ◽

Jan Wisniewski ◽

Jee Min Kim ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Single Molecule ◽

Transcription Initiation ◽

General Mechanism ◽

Pol Ii ◽

Promoter Escape ◽

Genome Wide ◽

A Genome ◽

Particle Imaging

The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription at yeast promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.

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NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution

10.1101/246827 ◽

2018 ◽

Author(s):

Constantine Mylonas ◽

Peter Tessarz

Keyword(s):

Splicing Factors ◽

Elongation Factors ◽

Single Nucleotide ◽

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide ◽

Regulatory Complexity ◽

Pol Ii Pausing ◽

Nucleotide Resolution ◽

The Impact

ABSTRACTThe advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. However, little is known, at such high resolution, how transcription factors directly influence RNA Pol II pausing and directionality. To map the impact of transcription/elongation factors on transcription dynamics genome-wide at base pair resolution, we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). Application of NET-prism on elongation factors (Spt6, Ssrp1), splicing factors (Sf1), and components of the pre-initiation complex (PIC) (TFIID, and Mediator) reveals their inherent command on transcription dynamics, with regards to directionality and pausing over promoters, splice sites, and enhancers/super-enhancers. NET-prism will be broadly applicable as it exposes transcription factor/Pol II dependent topographic specificity and thus, a new degree of regulatory complexity during gene expression.

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