15 papers · ranked by Valyu relevance
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…
Frédéric Flamant, Romain Guyot
When bound to thyroid hormone, the nuclear receptor TRα1 activates the transcription of a number of genes in many cell types. It mainly acts by binding DNA as an heterodimer with RXRs at specific response elements related to the DR4 consensus sequence. However, the number of DR4-like elements in the genome exceed by…
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…
Seth Weaver, Craig B Lowe, Harmit Malik
Gene regulatory innovation underlies many phenotypic transitions. Transposable elements are an established mechanism for creating families of cis-acting elements with shared sequence features and the potential to establish co-regulatory networks. To understand additional mechanisms by which co-regulatory networks form…
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…
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…
Ting-Ya Chang, David J Waxman
Growth hormone (GH) regulates sexual dimorphic programs in liver gene expression impacting lipid metabolism, bile acid synthesis and xenobiotic processing, which contribute to sex differences in metabolic dysfunction-associated steatotic liver disease (MASLD). Despite extensive knowledge of sex-biased transcriptomes…
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…
Ting-Ya Chang, David J. Waxman
Paired-end sequence reads, each 150 base pairs long, were generated for the STARR-seq plasmid, DNA and RNA libraries. Raw FASTQ files were input to a custom pipeline that produces quality control metrics, including FASTQC reports (FASTX Toolkit, version 0.0.13.2), identifies and removes contaminating adapter sequences…
Pengyu Ni, Siwen Wu, Zhengchang Su
Self-transcribing active regulatory region sequencing (STARR-seq) and its variants have been widely used to characterize enhancers. However, it has been reported that up to 87% of STARR-seq peaks are located in repressive chromatin and are not functional in the tested cells. While some of the STARR-seq peaks in…
Ya-Chien Chan, Eike Kienle, Martin Oti, Antonella Di Liddo + 10 more
'Maria Mendez-Lago' 'Dominik F. Aschauer' 'Manuel Peter' 'Michaela Pagani' 'Cosmas Arnold' 'Andreas Vonderheit' 'Christian Schön' 'Sebastian Kreuz' 'Alexander Stark' 'Simon Rumpel'] Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations 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…
Adrian Forsythe, Emile Gluck-Thaler, Aaron Vogan
Starships are a recently discovered superfamily of extremely large mobile genetic element (MGE)s in fungi that encode diverse gene sequences, many of unknown function. Starships are widespread throughout filamentous Ascomycetes (Pezizomycotina), but relatively little is known about their fine-grained distributions at…
Laura Puente-Santamaría, Luis del Peso
Single-cell transcriptomics techniques, such as scRNA-seq, attempt to characterize gene expression profiles in each cell of a heterogeneous sample individually. Due to growing amounts of data generated and the increasing complexity of the computational protocols needed to process the resulting datasets, the demand for…
Sheng Xu, Junkang Wei, Yu Li
Single-strand breaks (SSBs) are the major DNA damage in the genome arising spontaneously as the outcome of genotoxins and intermediates of DNA transactions. SSBs play a crucial role in various biological processes and show a non-random distribution in the genome. Several SSB detection approaches such as S1 END-seq and…