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Research: Systematic interrogation of human promoters
- Shira Weingarten-Gabbay,
- Ronit Nir,
- Shai Lubliner,
- Eilon Sharon,
- Yael Kalma,
- Adina Weinberger,
- and Eran Segal
Genome Res. February 2019 29: 171-183; Published in Advance January 8, 2019, doi:10.1101/gr.236075.118
...Cherry. In the last step, we used deep sequencing to determine the distribution of reads across the different bins for each oligo. For each designed promoter, we computed its activity levels from the mean of the reads distribution and cell-to-cell variability (noise) from the standard deviation (see Methods...
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Research: The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters
- Sachin Pundhir,
- Jinyu Su,
- Marta Tapia,
- Anne Meldgaard Hansen,
- James Seymour Haile,
- Klaus Hansen,
- and Bo Torben Porse
Genome Res. March 2023 33: 332-345; Published in Advance March 16, 2023, doi:10.1101/gr.277089.122
.... Here we show that SWI/SNF and NuRD are in a tug-of-war to regulate PRC2 occupancy at lowly expressed and bivalent genes in mouse embryonic stem cells (mESCs). In contrast, at promoters of average or highly expressed genes, SWI/SNF and NuRD antagonistically modulate RNA polymerase II (Pol II) release...
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Research: Clustering of Drosophila housekeeping promoters facilitates their expression
- Marc Corrales,
- Aránzazu Rosado,
- Ruggero Cortini,
- Joris van Arensbergen,
- Bas van Steensel,
- and Guillaume J. Filion
Genome Res. July 2017 27: 1153-1161; Published in Advance April 18, 2017, doi:10.1101/gr.211433.116
..., we show that the activity of Drosophila housekeeping gene promoters depends on the expression of their neighbors. By measuring the expression of ∼85,000 reporters integrated in Kc167 cells, we identified the best predictors of expression as chromosomal contacts with the promoters and terminators...
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Research: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
- Kaia Mattioli,
- Pieter-Jan Volders,
- Chiara Gerhardinger,
- James C. Lee,
- Philipp G. Maass,
- Marta Melé,
- and John L. Rinn
Genome Res. March 2019 29: 344-355; Published in Advance January 25, 2019, doi:10.1101/gr.242222.118
..., Colorado 80301, USA ↵12 These authors contributed equally to this work. Corresponding author: marta.mele.messeguer@gmail.comAbstractTranscription initiates at both coding and noncoding genomic elements, including mRNA and long noncoding RNA (lncRNA) core promoters and enhancer RNAs (eRNAs). However, each...
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Method: Probing the effect of promoters on noise in gene expression using thousands of designed sequences
- Eilon Sharon,
- David van Dijk,
- Yael Kalma,
- Leeat Keren,
- Ohad Manor,
- Zohar Yakhini,
- and Eran Segal
Genome Res. October 2014 24: 1698-1706; Published in Advance July 16, 2014, doi:10.1101/gr.168773.113
...may also affect its level of expression noise (Batenchuk et al. 2011). One way to isolate this effect is to integrate the tested promoter upstream of a reporter gene and within a fixed genomic context. Moreover, since the sequence of native promoters differs by many parameters, mutated versions...
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Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
- Rui Yokomori,
- Kotaro Shimai,
- Koki Nishitsuji,
- Yutaka Suzuki,
- Takehiro G. Kusakabe,
- and Kenta Nakai
Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
...; Okamura et al. 2011), at the −1,0 position, where the zero position represents the representative TSS. Although it is unclear whether these two types of 1-bp-width TSCs are noise or atypical promoters, we removed them in both C. intestinalis and human as well to increase the reliability of our data set...
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Research: Recurrent epimutations activate gene body promoters in primary glioblastoma
- Raman P. Nagarajan,
- Bo Zhang,
- Robert J.A. Bell,
- Brett E. Johnson,
- Adam B. Olshen,
- Vasavi Sundaram,
- Daofeng Li,
- Ashley E. Graham,
- Aaron Diaz,
- Shaun D. Fouse,
- Ivan Smirnov,
- Jun Song,
- Pamela L. Paris,
- Ting Wang,
- and Joseph F. Costello
Genome Res. May 2014 24: 761-774; Published in Advance April 7, 2014, doi:10.1101/gr.164707.113
...recurrent TERT promoter mutations, potentially generating binding sites for ETS/TCF transcription factors and presumably mediating increased TERT transcription, have recently been reported in GBM, low grade glioma, hereditary and sporadic melanoma, and other cancers (Horn et al. 2013; Huang et al. 2013...
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Research: Noise in gene expression is coupled to growth rate
- Leeat Keren,
- David van Dijk,
- Shira Weingarten-Gabbay,
- Dan Davidi,
- Ghil Jona,
- Adina Weinberger,
- Ron Milo,
- and Eran Segal
Genome Res. December 2015 25: 1893-1902; Published in Advance September 9, 2015, doi:10.1101/gr.191635.115
...cerevisiae promoters across four environmental conditions using flow cytometry, and find that gene expression noise is tightly coupled to the environment and is generally higher at lower growth rates. Nutrient-poor conditions, which support lower growth rates, display elevated levels of noise for most...
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Research: Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
- Danny Zeevi,
- Shai Lubliner,
- Maya Lotan-Pompan,
- Eran Hodis,
- Rita Vesterman,
- Adina Weinberger,
- and Eran Segal
Genome Res. December 2014 24: 1991-1999; Published in Advance October 7, 2014, doi:10.1101/gr.179259.114
...did not observe any change in promoter activity above our experimental noise in the species that lost the site. Variation of core promoter sequence is highly correlated to variation in promoter activity Since sequence variation of the entire promoter as well as in TF binding sites does not correlate...
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Research: TATA is a modular component of synthetic promoters
- Ilaria Mogno,
- Francesco Vallania,
- Robi D. Mitra,
- and Barak A. Cohen
Genome Res. October 2010 20: 1391-1397; Published in Advance July 13, 2010, doi:10.1101/gr.106732.110
...into cells (Volfson et al. 2006), or by mutating the TATA box at a particular promoter (Raser and O’Shea 2004; Blake et al. 2006). Here, rather than measuring single promoters or single proteins, we extend these studies by analyzing noise in libraries of promoters with different strength TATA boxes...

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