A Unified View of the Sequence and Functional Organization of the Human RNA Polymerase II Promoter

Luse, Donal S.; Parida, Mrutyunjaya; Spector, Benjamin M.; Nilson, Kyle A.; Price, David

doi:10.2139/ssrn.3492116

Cited by 5 publications

(21 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Cap analysis of gene expression sequencing (CAGE-seq) tracks visualized as layered track of 7 ENCODE cell lines and from GM12878 and K562 cells (44). Precision run on sequencing (PRO-seq) track from HeLa cells visualizes amplified regions of Pol II binding and thus transcription initiation sites (23). RNA annotation and mapping of promoters for the analysis of gene expression (RAMPAGE) sourced from 7 ENCODE cell lines (44).…”

Section: Resultsmentioning

confidence: 99%

“…RNA annotation and mapping of promoters for the analysis of gene expression (RAMPAGE) sourced from 7 ENCODE cell lines (44). (B) Initiation site from PRO-seq analyses (23) suggest start site at 87,863,624 for canonical PTEN TSS, 87,862,418 for furthest-upstream novel TSS, and 87,862,565 for second novel TSS. The canonical TSS mirrors the consensus initiator sequence of BBCA +1 BW, supporting the PRO-seq data.…”

Section: Resultsmentioning

confidence: 99%

“…Since initial Run On Sequencing data support the existence of two upstream promoters for PTEN , we sought to map the transcription initation to a specific initiator (Inr) sequence. To do so, we visualized Precision Run On Sequencing (PRO-seq) and RNA annotation and mapping of promoters for analysis of gene expression (RAMPAGE) from HeLa cells and a layering of seven cell lines, respectively (23, 44). We were therefore able to directly compare the DNA sequence of canonical and upstream initation sites to the consensus Inr sequences of CA +1 GT (23) and BBCA +1 BW (51), where B represents an A, C, or T and W is an A or T. An exact Inr sequence was found to match the PRO-seq peak within the Sheng promoter of CTCA +1 GT, with the +1 site 846 bp upstream of the canonical ATG translation start codon (Figure 2B).…”

Section: Resultsmentioning

confidence: 99%

“…Subsequently, through a combination of publicly available NGS data and in-house experiments, we demonstrated that there are two novel PTEN TSRs upstream of the Sheng promoter (Figure 2,3,4). These novel PTEN TSRs, located within the KLLN CDS and 5’UTR, are identifiable by an Inr sequence at −2052 and a non-canonical Inr at −1907, respectively (Figure 2) (23, 51, 54, 55). Moreover, the upstream TSRs maintains a unique TF profile compared to the Sheng promoter (Figure 5).…”

Section: Discussionmentioning

confidence: 99%

“…Many high-throughput assays have been developed that expand our understanding of global transcriptional regulation. Here, we present comprehensive alignments of multiple forms of NGS data (23, 40–45) using the UCSC Genome Browser (46), followed by empirical validation studies that led to identification of two novel TSRs for PTEN , upstream of the current clinically-relevant promoter region.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Redefining thePTENPromoter: Identification of Two Upstream Transcription Start Regions

Grencewicz

Romigh

Thacker

et al. 2021

Preprint

View full text Add to dashboard Cite

Germline mutation of PTEN is causally observed in Cowden syndrome (CS) and is one of the most common genetic causes of autism spectrum disorder (ASD). However, the majority of individuals who present with CS-like clinical features are found to be PTEN-mutation negative. Reassessment of PTEN promoter regulation may help explain abnormal PTEN dosage, as only the minimal promoter and coding regions are currently included in diagnostic PTEN mutation analysis. We reanalyzed the architecture of the PTEN promoter using next-generation sequencing datasets. Specifically, run-on sequencing assays identified two additional TSRs at -2052 and -1907 basepairs from the start of PTEN, thus redefining the PTEN promoter and extending the PTEN 5-UTR. The upstream TSRs described are active in cancer cell lines and human cancer and normal tissue. Further, these TSRs can produce novel PTEN transcripts due to the introduction of new splice sites. Evaluation of transcription factor binding specific to the upstream TSRs shows overrepresentation of TFs involved in inflammatory processes. Together, these data suggest that potentially clinically relevant promoter variants upstream of the known promoter may be overlooked in indivduals considered PTEN germline mutation-negative and may also explain lack of PTEN expression in sporadic neoplasias without PTEN somatic structural defects.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Redefining thePTENPromoter: Identification of Two Upstream Transcription Start Regions

Grencewicz

Romigh

Thacker

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

A PICture is worth a thousand words (and ten references)

Kaplan

Arndt

2021

Cell

View full text Add to dashboard Cite

Ssl2/TFIIH function in Transcription Start Site Scanning by RNA Polymerase II in Saccharomyces cerevisiae

Zhao

Vvedenskaya

Lai

et al. 2021

Preprint

View full text Add to dashboard Cite

Ssl2, as an essential subunit of the RNA Polymerase II (Pol II) general transcription factor TFIIH, promotes melting of promoter DNA through its ATPase-dependent DNA translocase activity within the Pol II pre-initiation complex. In Saccharomyces cerevisiae, after DNA melting, Ssl2 is proposed to drive Pol II scanning downstream for usable transcription start sites (TSSs) through this same ATP-dependent DNA translocase activity. However, how Pol II catalytic activity or activities of other general transcription factors integrate with Ssl2/TFIIH activity for promoter scanning and what ways Ssl2 modulates TSS selection by scanning have not been well studied. Here, we report the identification of ssl2 alleles conferring phenotypes in vivo consistent with altered Pol II initiation. We find that these ssl2 alleles alter TSS selection by scanning in ways that are distinct from how changes to Pol II or other GTF activities alter TSS selection by scanning. Specific predictions arise for interactions among initiation mutants depending on whether they function in promoter scanning through modulating initiation at an individual TSS or if they control the probability that a TSS is reached during the scanning process (scanning processivity). We test these predictions genetically and through analysis of transcription output at ADH1 and at promoters across the genome. Our data support a model whereby ssl2 alleles alter Ssl2 processivity and therefore the probability that TSSs are scanned. Examination of TSS usage genome-wide finds global effects of ssl2 alleles on TSS usage and the potential coupling of Pol II activity and Ssl2/TFIIH processivity during scanning. We propose that the initiation by promoter scanning is determined by the interaction of two functional networks, one controlling initiation efficiency and one controlling the processivity of scanning.

show abstract

A Unified View of the Sequence and Functional Organization of the Human RNA Polymerase II Promoter

Cited by 5 publications

References 0 publications

Redefining thePTENPromoter: Identification of Two Upstream Transcription Start Regions

Redefining thePTENPromoter: Identification of Two Upstream Transcription Start Regions

A PICture is worth a thousand words (and ten references)

Ssl2/TFIIH function in Transcription Start Site Scanning by RNA Polymerase II in Saccharomyces cerevisiae

Contact Info

Product

Resources

About