Processing and evaluating the quality of genome-wide nascent transcription profiling libraries

Scott, Thomas G.; Martins, André L.; Guertin, Michael J.

doi:10.1101/2022.12.14.520463

Cited by 7 publications

(9 citation statements)

References 41 publications

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“…A degradation ratio score is also reported at the top of each plot. Degradation ratios for C.elegans and A.thaliana were computed manually using the scripts in ( 43 ).…”

Section: Figure Legendsmentioning

confidence: 99%

Evolution of promoter-proximal pausing enabled a new layer of transcription control

Chivu

Abuhashem

Barshad

et al. 2023

Preprint

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Promoter-proximal pausing of RNA polymerase II (Pol II) is a key regulatory step during transcription. To understand the evolution and function of pausing, we analyzed transcription in 20 organisms across the tree of life. Unicellular eukaryotes have a slow acceleration of Pol II near transcription start sites that matured into a longer and more focused pause in metazoans. Increased pause residence time coincides with the evolution of new subunits in the NELF and 7SK complexes. In mammals, depletion of NELF reverts a focal pause to a proto-paused-like state driven in part by DNA sequence. Loss of this focal pause compromises transcriptional activation for a set of heat shock genes. Overall, we discovered how pausing evolved and increased regulatory complexity in metazoans.

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“…A degradation ratio score is also reported at the top of each plot. Degradation ratios for C.elegans and A.thaliana were computed manually using the scripts in ( 43 ).…”

Section: Figure Legendsmentioning

confidence: 99%

Evolution of promoter-proximal pausing enabled a new layer of transcription control

Chivu

Abuhashem

Barshad

et al. 2023

Preprint

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“…Quality control and read alignment were performed as described previously (Scott et al 2022). We used cutadapt to remove adapters from our reads (Martin 2011), and to deduplicate our libraries with the 3′ UMIs (Martins and Guertin 2018).…”

Section: Methodsmentioning

confidence: 99%

ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes

Dong,

Scott,

Mukherjee

et al. 2024

Preprint

Self Cite

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Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle. ZNF143 facilitates RNA Polymerase initiation and activates gene expression. ZNF143 binds the promoter of nearly all its activated target genes. ZNF143 also binds near the site of genic transcription initiation to directly repress a subset of genes. Although ZNF143 stimulates initiation at ZNF143-repressed genes (i.e. those that increase expression upon ZNF143 depletion), the molecular context of binding leads to cis repression. ZNF143 competes with other more efficient activators for promoter access, physically occludes transcription initiation sites and promoter-proximal sequence elements, and acts as a molecular roadblock to RNA Polymerases during early elongation. The term context specific is often invoked to describe transcription factors that have both activation and repression functions. We define the context and molecular mechanisms of ZNF143-mediated cis activation and repression.

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“…As an orthogonal readout of RE activity, we measured bidirectional transcription around TRPS1 binding sites using precision genomic run-on with sequencing (PRO-seq) [38]. Our libraries were of high quality using several quality control metrics (S5 Fig) [39]. Using a window centered on each summit of TRPS1 ChIP-seq intensity, we observed an increase in bidirectional transcription 30 minutes after TRPS1 depletion (Fig 3G).…”

Section: Trps1 Directly Represses Regulatory Element Activitymentioning

confidence: 99%

“…Based on the correlation between cancer cell line sensitivity to TRPS1 knockout and ESR1 knockout (Fig 1B ), the enrichment of an ER binding motif in both increased and decreased ATAC-seq peaks (Fig 3D ), and the over-representation of estrogen response gene sets in the genes repressed by TRPS1 depletion (Fig 4D ), we focused on ER target genes to explore a possible mechanism by which TRPS1 indirectly activates transcription. We first defined direct ER target genes using our previously-generated PRO-seq data from parental T47D cells that were hormone starved for three days and then acutely stimulated with estrogen or a DMSO vehicle control for 90 minutes (S8 Fig) [39]. We exclusively focused on estrogen-activated genes because ER directly activates these genes [8,42,43].…”

Section: Trps1 Redistributes Er Binding To Modulate Er Target Gene Tr...mentioning

confidence: 99%

TRPS1 modulates chromatin accessibility to regulate estrogen receptor alpha (ER) binding and ER target gene expression in luminal breast cancer cells

Scott,

Sathyan,

Gioeli

et al. 2024

PLoS Genet

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Common genetic variants in the repressive GATA-family transcription factor (TF) TRPS1 locus are associated with breast cancer risk, and luminal breast cancer cell lines are particularly sensitive to TRPS1 knockout. We introduced an inducible degron tag into the native TRPS1 locus within a luminal breast cancer cell line to identify the direct targets of TRPS1 and determine how TRPS1 mechanistically regulates gene expression. We acutely deplete over 80 percent of TRPS1 from chromatin within 30 minutes of inducing degradation. We find that TRPS1 regulates transcription of hundreds of genes, including those related to estrogen signaling. TRPS1 directly regulates chromatin structure, which causes estrogen receptor alpha (ER) to redistribute in the genome. ER redistribution leads to both repression and activation of dozens of ER target genes. Downstream from these primary effects, TRPS1 depletion represses cell cycle-related gene sets and reduces cell doubling rate. Finally, we show that high TRPS1 activity, calculated using a gene expression signature defined by primary TRPS1-regulated genes, is associated with worse breast cancer patient prognosis. Taken together, these data suggest a model in which TRPS1 modulates the genomic distribution of ER, both activating and repressing transcription of genes related to cancer cell fitness.

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Processing and evaluating the quality of genome-wide nascent transcription profiling libraries

Cited by 7 publications

References 41 publications

Evolution of promoter-proximal pausing enabled a new layer of transcription control

Evolution of promoter-proximal pausing enabled a new layer of transcription control

ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes

TRPS1 modulates chromatin accessibility to regulate estrogen receptor alpha (ER) binding and ER target gene expression in luminal breast cancer cells

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