Transcribe this way: Rap1 confers promoter directionality by repressing divergent transcription

Wu, Andrew; Werven, Folkert J. van

doi:10.1080/21541264.2019.1608716

Cited by 6 publications

(4 citation statements)

References 70 publications

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“…cryptic transcripts), for example widespread divergent lncRNA transcription from gene promoter NDRs in the opposite direction respective to the mRNA 7 . Transcription in each direction of gene promoter NDRs is also selectively controlled at the level of initiation by chromatin-based mechanisms 14,15 and sequence-specific transcription factors 16 . Binding sites for the spliceosomal small nuclear RNA (snRNA) U1 selectively promote elongation of mRNA transcription over divergent lncRNA transcription 17 .…”

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confidence: 99%

Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis

et al. 2020

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RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.

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confidence: 99%

Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis

et al. 2020

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“…On the other hand, ScRap1-mediated telomeric silencing depends on its recruitment of Sir proteins to RAP1 homologs' functions in gene transcription regulation appear more divergent (Figure 3). ScRap1's transcription activation function depends on its binding to the ribosomal protein gene promoter [97], and ScRap1 also represses cryptic or divergent transcription to ensure the transcription goes in the correct direction [302,303]. On the other hand, ScRap1-mediated telomeric silencing depends on its recruitment of Sir proteins to the telomere and a heterochromatic telomere structure [41].…”

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confidence: 99%

Unwrap RAP1’s Mystery at Kinetoplastid Telomeres

2024

Biomolecules

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Although located at the chromosome end, telomeres are an essential chromosome component that helps maintain genome integrity and chromosome stability from protozoa to mammals. The role of telomere proteins in chromosome end protection is conserved, where they suppress various DNA damage response machineries and block nucleolytic degradation of the natural chromosome ends, although the detailed underlying mechanisms are not identical. In addition, the specialized telomere structure exerts a repressive epigenetic effect on expression of genes located at subtelomeres in a number of eukaryotic organisms. This so-called telomeric silencing also affects virulence of a number of microbial pathogens that undergo antigenic variation/phenotypic switching. Telomere proteins, particularly the RAP1 homologs, have been shown to be a key player for telomeric silencing. RAP1 homologs also suppress the expression of Telomere Repeat-containing RNA (TERRA), which is linked to their roles in telomere stability maintenance. The functions of RAP1s in suppressing telomere recombination are largely conserved from kinetoplastids to mammals. However, the underlying mechanisms of RAP1-mediated telomeric silencing have many species-specific features. In this review, I will focus on Trypanosoma brucei RAP1’s functions in suppressing telomeric/subtelomeric DNA recombination and in the regulation of monoallelic expression of subtelomere-located major surface antigen genes. Common and unique mechanisms will be compared among RAP1 homologs, and their implications will be discussed.

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“…Consequently, the looping-defective sua7-1 mutant of TFIIB exhibits loss of promoter directionality (Tan-Wong et al 2012;Agarwal and Ansari 2016). TFIIB is not the only transcription factor to play a role in promoter directionality, as the transcription factor Rap1 has also been implicated in repressing divergent transcription in yeast (Wu and Van Werven 2019;Rossi et al 2021). A recent study in plants also implicated gene looping in promoter directionality similar to that in yeast (Gagliardi et al 2019).…”

Section: Potential Role Of Tfiib In Promoter Directionalitymentioning

confidence: 98%