Results 51 to 60 of about 122 (91)

Comprehensive Mapping of Functional Enhancers in Chinese Hamster Ovary Cells

Biotechnology and Bioengineering, Volume 123, Issue 1, Page 196-211, January 2026.
In this study, the authors identified regions with enhancer activity in the CHO cell genome using genome‐wide and targeted STARR‐seq. The analysis revealed thousands of newly identified enhancer sequences, where some of the most active sequences could drive transgene expression at levels similar to or higher than strong viral enhancers.
María Santos, Yusuf B. Johari, Laura Biggins, Natalie C. Elliott, Stefan Schoenfelder, Mounika Boddireddy, Daniel K. Fabian, Michael Anbar, Peter M. O'Callaghan, Peter J. Rugg‐Gunn   +9 more
wiley   +1 more source

Genome‐Wide Silencer Screening Reveals Key Silencer Modulating Reprogramming Efficiency in Mouse Induced Pluripotent Stem Cells

Advanced Science
The majority of the mouse genome is composed of non‐coding regions, which harbor numerous regulatory sequences essential for gene regulation. While extensive research focuses on enhancers that activate gene expression, the role of silencers that repress ...
Xiusheng Zhu, Lei Huang, Guoli Li, Biao Deng, Xiaoxiao Wang, Hu Yang, Yuanyuan Zhang, Qiuhan Wen, Chao Wang, Jingshu Zhang, Yunxiang Zhao, Kui Li, Yuwen Liu   +12 more
doaj   +1 more source

Additional file 1 of STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

, 2020
Additional file 1: Supplementary Figure S1. Comparison of STARR-seq output coverage calculated using the center of the fragment to using the start position of the sequencing read. (A) Distribution of shift in final peak locations resulting from using two alternative coverage counting schemes in HepG2. Comparison of (B) overall fold enrichment level, (C)
Lee, Donghoon, Shi, Manman, Moran, Jennifer, Wall, Martha, Zhang, Jing, Liu, Jason, Fitzgerald, Dominic, Kyono, Yasuhiro, Ma, Lijia, White, Kevin P., Gerstein, Mark   +10 more
openaire   +1 more source

Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability

Nature Communications
The 3’ end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the ...
Sayeh Gorjifard, Tobias Jores, Jackson Tonnies, Nicholas A. Mueth, Kerry Bubb, Travis Wrightsman, Edward S. Buckler, Stanley Fields, Josh T. Cuperus, Christine Queitsch   +9 more
doaj   +1 more source

Abundant repressor binding sites in human enhancers are associated with the fine-tuning of gene regulation

iScience
Summary: The regulation of gene expression relies on the coordinated action of transcription factors (TFs) at enhancers, including both activator and repressor TFs.
Wei Song, Ivan Ovcharenko
doaj   +1 more source

Additional file 10 of STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

, 2020
Additional file 10. Review history.
Lee, Donghoon, Shi, Manman, Moran, Jennifer, Wall, Martha, Zhang, Jing, Liu, Jason, Fitzgerald, Dominic, Kyono, Yasuhiro, Ma, Lijia, White, Kevin P., Gerstein, Mark   +10 more
openaire   +1 more source

STARR-seq Screening protocol [PDF]

Protocol Exchange, 2017
Felix Muerdter, Felix Muerdter, Łukasz M. Boryń, Ashley R. Woodfin, Christoph Neumayr, Martina Rath, Muhammad A. Zabidi, Michaela Pagani, Vanja Haberle, Tomáš Kazmar, Rui R. Catarino, Katharina Schernhuber, Cosmas D. Arnold, Alexander Stark   +13 more
openaire   +1 more source

High‐throughput quantitative assessment of ABA‐responsive elements at single‐nucleotide resolution

Quantitative Biology
Abscisic acid (ABA)‐responsive elements (ABREs) are the major cis‐regulatory elements in ABA‐induced gene expression. However, the impact of sequence variations on ABRE function is not yet well‐understood.
Fangnan Sun, Yaxin Deng, Weihua Zhao, Yixue Xiong, Lingxia Zhao, Lida Zhang   +5 more
doaj   +1 more source

Evolutionarily conserved enhancer-associated features within the MYEOV locus suggest a regulatory role for this non-coding DNA region in cancer

Frontiers in Cell and Developmental Biology
The myeloma overexpressed gene (MYEOV) has been proposed to be a proto-oncogene due to high RNA transcript levels found in multiple cancers, including myeloma, breast, lung, pancreas and esophageal cancer.
Brigid S. A. Davidson, Juliana Estefania Arcila-Galvis, Marco Trevisan-Herraz, Aneta Mikulasova, Chris A. Brackley, Lisa J. Russell, Daniel Rico, Daniel Rico   +7 more
doaj   +1 more source

Plant STARR-seq: von der DNA-Sequenz zur Funktion pflanzlicher Genregulation

BIOspektrum
Abstract Cis -regulatory elements are promising targets for genome editing in crop improvement. However, our understanding of their activity is limited. Plant STARR-seq enables the quantitative, systematic, high-throughput measurement of regulatory activity. In combination with machine learning,
Julia Macholl, Sebastian Triesch, Tobias Jores   +2 more
openaire   +1 more source