16 papers · ranked by Valyu relevance
Tianran Peng, Yanan Zhai, Yaser Atlasi, Menno ter Huurne + 3 more
'Hendrik Marks' 'Hendrik G. Stunnenberg' 'Wout Megchelenbrink'] Background Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a complex network of enhancers, that…
Christoph Neumayr, Michaela Pagani, Alexander Stark, Cosmas D. Arnold
'Cosmas D. Arnold'] Title: Abstract The identification of transcriptional enhancers and the quantitative assessment of enhancer activities is essential to understanding how regulatory information for gene expression is encoded in animal and human genomes. Further, it is key to understanding how sequence variants affect…
Donghoon Lee, Manman Shi, Jennifer Moran, Martha Wall + 7 more
'Jason Liu' 'Dominic Fitzgerald' 'Yasuhiro Kyono' 'Lijia Ma' 'Kevin P. White' 'Mark Gerstein'] STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is non-uniform…
Donghoon Lee, Manman Shi, Jennifer Moran, Martha Wall + 7 more
High-throughput reporter assays, such as self-transcribing active regulatory region sequencing (STARR-seq), allow for unbiased and quantitative assessment of enhancers at a genome-wide level. Recent advances in STARR-seq technology have employed progressively more complex genomic libraries and increased sequencing…
Maitreya Das, Ayaan Hossain, Deepro Banerjee, Craig Alan Praul + 1 more
High-throughput methods such as RNA-seq, ChIP-seq and ATAC-seq have well-established guidelines, commercial kits, and analysis pipelines that enable consistency and wider adoption for understanding genome function and regulation. STARR-seq, a popular assay for directly quantifying activity of thousands of enhancer…
Amin Safaeesirat, Hoda Taeb, Emirhan Tekoglu, Tunc Morova + 2 more
One of the primary regulatory processes in cells is transcription, during which RNA polymerase II (Pol-II) transcribes DNA into RNA. The binding of Pol-II to its site is regulated through interactions with transcription factors (TFs) that bind to DNA at enhancer cis-regulatory elements. Measuring the enhancer activity…
Longjian Niu, Jing Wan, Jialei Sun, Yingzhang Huang + 3 more
STARR-seq assesses millions of fragments in parallel measuring enhancer activity quantitatively. Here we show that STARR-seq is critically flawed with a systematic error in the cells of Arabidopsis thaliana (A. thaliana). Large amount of self-transcripts (STs) is lost during reverse transcription because these STs are…
Young-Sook Kim, Graham D. Johnson, Jungkyun Seo, Alejandro Barrera + 4 more
High-throughput reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq) have made it possible to measure genome-wide regulatory element activity across the human genome. The assays, however, also present substantial analytical challenges. Here, we identify technical biases that explain…
Kurtis Stefan, Artem Barski
Cis-regulatory elements (CRE) are critical for coordinating gene expression programs that dictate cell-specific differentiation and homeostasis. Recently developed self-transcribing active regulatory region sequencing (STARR-Seq) has allowed for genome-wide annotation of functional CREs. Despite this, STARR-Seq assays…
María Santos, Yusuf B. Johari, Laura Biggins, Natalie C. Elliott + 6 more
Chinese hamster ovary (CHO) cells are the leading mammalian system for recombinant therapeutic protein production. However, optimizing transgene expression remains challenging due to the limited understanding of the regulatory mechanisms controlling gene expression in CHO cells. Towards overcoming this barrier, here we…
Drew T. Bergman, Thouis R. Jones, Vincent Liu, Layla Siraj + 8 more
Gene regulation in the human genome is controlled by distal enhancers that activate specific nearby promoters. One model for the specificity of enhancer-promoter regulation is that different promoters might have sequence-encoded preferences for distinct classes of enhancers, for example mediated by interacting sets of…
S. Weber, Joseph Pallas, Gary M. Olson, David W. Love + 5 more
Medicine Authors: ['S. Weber' 'Joseph Pallas' 'Gary M. Olson' 'David W. Love' 'Sanjay Malunjkar' 'Srinivasan Boosi' 'Erwin Loh' 'Sudip Kumar Datta' 'Timothy Ferris'] STARR (STAnford Research Repository) is a clinical research support ecosystem that supports basic science research, population health research and…
Felipe Victoria-Muñoz, Norberto Sánchez-Cruz, José L. Medina-Franco, Fabian López-Vallejo
Transcription factors associated with quorum sensing in P. aeruginosa are promising targets for developing new adjuvants against infection by this pathogen. Regulation of these transcription factors offers the possibility of controlling multiple virulence factors related to them, as the development of biofilm…
William T. Ireland, Suzannah M. Beeler, Emanuel Flores-Bautista, Nathan M. Belliveau + 4 more
'Nathan M. Belliveau' 'Michael J. Sweredoski' 'Annie Moradian' 'Justin B. Kinney' 'Rob Phillips'] Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium Escherichia coli, for ≈ 65% of the promoters we remain completely ignorant of…
Nick Schurch, Christian Cole, Alexander Sherstnev, Junfang Song + 6 more
'Céline Duc' 'Kate G. Storey' 'W.H. Irwin McLean' 'Sara Brown' 'Gordon G. Simpson' 'Geoffrey J. Barton'] The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments…
Priyanka Ghosh, Kjiersten Fagnan, Ryan Connor, Ravinder Pannu + 34 more
'Travis J. Wheeler' 'Mihai Pop' 'C. Titus Brown' 'Tessa Pierce-Ward' 'Rob Patro' 'Jacquelyn S. Michaelis' 'Thomas L. Madden' 'Christiam Camacho' 'Olaitan I. Awe' 'Arianna I. Krinos' 'René KM Xavier' 'Rodrigo Ortega Polo' 'Jack W. Roddy' 'Adelaide Rhodes' 'Alexander Sweeten' 'Adrian Viehweger' 'Bariş Ekim' 'Harihara…