Robin Dowell
Boulder, Broomfield
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Articles by Robin Dowell
The chemotherapy-induced senescence-associated secretome promotes cell detachment and metastatic dissemination through metabolic reprogramming
Abstract Cellular senescence is a consequence of many chemotherapeutics that plays context-dependent roles in cancer. Senescent cells secrete an array of factors collectively known as the senescence-associated secretory phenotype (SASP). Here we show that the cisplatin-induced SASP enhances the detachment of high-grade serous ovarian cancer (HGSOC) cells in vitro and dissemination in vivo.
Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages - BMC Genomics
Detailed methods can be found in the Supplementary Methods, which includes technical details, full citations for all data utilized, and version numbers for all software utilized. Mouse samples were mapped to the mm10 reference genome and human samples to the hg38 genome. Nascent RNA sequencing experiments were manually curated from the Gene Expression Omnibus (GEO) [25, 26] and the Sequence Read Archive (SRA) [27]. All treatment conditions were annotated with reference to the cell harvest time.
TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks | Genome Biology | Full Text
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The stand-alone TF Profiler application can be found on github (https://github.com/Dowell-Lab/TF_profiler) and Zenodo [76]. TF Profiler takes an annotation file for bidirectional regions from a nascent sequencing experiment and derives a TF activity profile. This includes generating simulated sequences based on the base composition of the regions provided, scanning for PSSM hits within the genome and statistically assessing TF enrichment and depletion.
By Taylor Jones Verified, Rutendo F. Sigauke, Lynn Sanford, Dylan J. Taatjes, Mary Allen, Robin Dowell
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Genome Biology
Verified
Enhancer RNA transcription pinpoints functional genetic variants linked to asthma - Nature Communications
Abstract Bidirectional enhancer RNA (eRNA) transcription is a widespread response to environmental signals and glucocorticoids. We investigated whether single nucleotide polymorphisms (SNPs) within dynamically regulated eRNA-transcribing regions contribute to genetic variation in asthma.
The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation - Nature Communications
Abstract Numerous studies have now demonstrated that lncRNAs can influence gene expression programs leading to cell and organismal phenotypes. Typically, lncRNA perturbations and concomitant changes in gene expression are measured on the timescale of many hours to days. Thus, we currently lack a temporally grounded understanding of the primary, secondary, and tertiary relationships of lncRNA-mediated transcriptional and epigenetic regulation—a prerequisite to elucidating lncRNA mechanisms.
Rapid P-TEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy - Nature Communications
Abstract Dynamic regulation of gene expression is fundamental for cellular adaptation to exogenous stressors. P-TEFb-mediated pause-release of RNA polymerase II (Pol II) is a conserved regulatory mechanism for synchronous transcriptional induction in response to heat shock, but this pro-survival role has not been examined in the applied context of cancer therapy.
Single nucleus RNA-sequencing reveals transcriptional synchrony across different relationships
Abstract Relationships are shaped by reciprocal interaction and feedback between individuals. As relationships mature, pairs share common goals, improve their ability to work together, and experience coordinated emotions. However, the neural underpinnings responsible for this unique, pair-specific experience remain largely unexplored.
Deconvolution of Nascent Sequencing Data Using Transcriptional Regulatory Elements
Abstract The problem of microdissection of heterogeneous tissue samples is of great interest for both fundamental biology and biomedical research. Until now, microdissection in the form of supervised deconvolution of mixed sequencing samples has been limited to assays measuring gene expression (RNA-seq) or chromatin accessibility (ATAC-seq).
Transcription dosage compensation does not occur in Down syndrome
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Characterizing Primary transcriptional responses to short term heat shock in paired fraternal lymphoblastoid lines with and without Down syndrome.
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Characterizing Primary transcriptional responses to short term heat shock in paired fraternal lymphoblastoid lines with and without Down syndrome.
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Competition between PRC2.1 and 2.2 subcomplexes regulates PRC2 chromatin occupancy in human stem cells
Highlights • Mutations in the SUZ12 subunit of PRC2 coerce formation of PRC2.1 or 2.2 • PRC2.1 and 2.2 display high and low affinity for PRC2 target genes, respectively • Human stem cells expressing solely PRC2.1 gain H3K27me3 at polycomb target sites • Cancer mutations in SUZ12 force PRC2.1 formation and increase chromatin occupancy Summary Polycomb repressive complex 2 (PRC2) silences expression of developmental transcription factors in pluripotent stem cells by methylating lysine 27 on...
Correction: Discriminating between HuR and TTP binding sites using the k-spectrum kernel method
The following information is missing from the Funding section of the paper: Publication of this article was funded by the University of Colorado Boulder Libraries Open Access Fund. Citation: Bhandare S, Goldberg DS, Dowell R (2017) Correction: Discriminating between HuR and TTP binding sites using the k-spectrum kernel method. PLoS ONE 12(4): e0175988. https://doi.org/10.1371/journal.pone.0175988 Copyright: © 2017 Bhandare et al.
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