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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...-by-one testing limitation of these classic reporter assays, MPRAs add a DNA barcode that is transcribed if the sequence has regulatory activity and can be measured via RNA-sequencing (RNA-seq), providing a way to examine the functional effects of thousands of sequences in parallel (Patwardhan et al. 2009; Inoue...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...-seq in their respective tissue types (Supplemental Fig. S3B; Supplemental Table S2). This observation was further supported by our analysis of nucleosome-free regions (NFRs) (Tarbell and Liu 2019), which covered >48% of MHBs in 14 out of 17 tissue types (Supplemental Fig. S3C).Segmented DNA methylation states...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...the transcription start site [TSS]) exhibited similar signal intensities before and after injury globally (Supplemental Fig. S3E,F). This signal stability at the promoter regions suggests that the promoters of RRGs remain largely accessible, and other regulatory mechanisms may influence gene activation...
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Method: Identification and dynamic quantification of regulatory elements using total RNA
- Sascha H. Duttke,
- Max W. Chang,
- Sven Heinz,
- and Christopher Benner
Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
...et al. 2018), DNA topology (Teves and Henikoff 2014), and chromatin states (Santos-Rosa et al. 2002). It is therefore critical to assay active promoter and distal regulatory elements in a quantitative and sensitive manner when investigating biological phenomena, gene regulation, or regulatory...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...–dependent repair of erroneously incorporated nucleotides during pol α-dependent initiation of DNA replication of Okazaki fragments (Reijns et al. 2015), or of nucleotide excision repair (Sabarinathan et al. 2016), at sites where proteins, including TFs, bind DNA. In agreement with this hypothesis...
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Research: Genome-wide determinants of sequence-specific DNA binding of general regulatory factors
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. April 2018 28: 497-508; Published in Advance March 21, 2018, doi:10.1101/gr.229518.117
...IP-exo → WhIP-exo → PB-exo), site-specific protein-DNA interactions were altered that are manifested in quantitative and qualitative changes in the exonuclease stop sites.Promiscuous sites-specific binding on nucleosome-free DNAAbf1, Mcm1, Rap1, Cbf1, and Pho4 were assayed by PB-exo and ChIP-exo and analyzed...
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Method: Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data
- Shuze Wang,
- Mary P. Lee,
- Scott Jones,
- Jie Liu,
- and Joerg Waldhaus
Genome Res. October 2021 31: 1885-1899; Published in Advance April 9, 2021, doi:10.1101/gr.271080.120
...identifies accessible chromatin regions, which potentially harbor regulatory elements that can be used to characterize -wide DNA/TF interactions (Buenrostro et al. 2013). In combination, single-cell RNA-seq (scRNA-seq) and scATAC-seq technologies offer the potential to resolve dynamic changes...
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Method: Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
- Alicia N. Schep,
- Jason D. Buenrostro,
- Sarah K. Denny,
- Katja Schwartz,
- Gavin Sherlock,
- and William J. Greenleaf
Genome Res. November 2015 25: 1757-1770; Published in Advance August 27, 2015, doi:10.1101/gr.192294.115
..., Stanford, California 94305, USA Corresponding author: wjg@stanford.edu Abstract Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase...
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Research: DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome
- Leslie Y. Beh,
- Manuel M. Müller,
- Tom W. Muir,
- Noam Kaplan,
- and Laura F. Landweber
Genome Res. November 2015 25: 1727-1738; Published in Advance September 1, 2015, doi:10.1101/gr.188516.114
...DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic Leslie Y. Beh,1 Manuel M. Müller,2 Tom W. Muir,2 Noam Kaplan,3 and Laura F. Landweber1 1Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA; 2Department...
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Research: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters
- Suhn Kyong Rhie,
- Lijun Yao,
- Zhifei Luo,
- Heather Witt,
- Shannon Schreiner,
- Yu Guo,
- Andrew A. Perez,
- and Peggy J. Farnham
Genome Res. March 2018 28: 310-320; Published in Advance February 2, 2018, doi:10.1101/gr.228809.117
...that it is a DNA binding transcriptional activator that is expressed at high levels in many different types of cancers, ZFX binding sites have not yet been mapped in cancer cells. To understand the mechanism by which ZFX may regulate the cancer transcriptome, we performed ChIP-seq, NOMe-seq, and RNA-seq assays...
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