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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...lymphoma (DLBCL) data set in which we integrate SWATH-MS-based proteomics with transcriptomic and phenotypic data.State-of-the-art proteomic approaches such as liquid chromatography coupled to quadrupole-time of flight tandem mass spectrometry (LC-QTOF-MS/MS) facilitate the high-throughput characterization...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...structure analyses, genetic diversity evaluation, and ancestry estimation (Kennedy et al. 2003; Zimmerman et al. 2020). Simultaneously, the latest advances in SNP high-throughput arrays and WGS facilitate the SNPs applied in the usual genetic analyses. However, compared with WGS, SNP arrays were primarily...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
..., we perform capture STARR-sequencing of over 70,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We select candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWASs. Over 8000 regions demonstrate...
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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...of PSM SEs and incorporating SE profiling with multiomics data, and high-throughput screening for DNA variants affecting enhancer activity (Fig. 1). We first performed cleavage under targets and tagmentation (CUT&Tag) (Kaya-Okur et al. 2019) to profile H3K27ac and identify SEs in PSM samples across...
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Method: High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation
- Matthew A. Lalli,
- Denis Avey,
- Joseph D. Dougherty,
- Jeffrey Milbrandt,
- and Robi D. Mitra
Genome Res. September 2020 30: 1317-1331; Published in Advance September 4, 2020, doi:10.1101/gr.262295.120
...studies in discovering thousands of disease-associated genes necessitates developing novel high-throughput functional genomics approaches to elucidate the molecular mechanisms of these genes. Here, we have coupled multiplexed repression of neurodevelopmental disease–associated genes to single...
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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
...that is responsible for this genetic association.DiscussionHere, we have characterized the differences between lncRNA, mRNA, and eRNA core promoter sequences by combining computational predictions and experimental testing using high-throughput assays. Because many lncRNAs are thought to arise from enhancers (Marques...
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Method: High-throughput characterization of genetic effects on DNA–protein binding and gene transcription
- Cynthia A. Kalita,
- Christopher D. Brown,
- Andrew Freiman,
- Jenna Isherwood,
- Xiaoquan Wen,
- Roger Pique-Regi,
- and Francesca Luca
Genome Res. November 2018 28: 1701-1708; Published in Advance September 25, 2018, doi:10.1101/gr.237354.118
...that allow for higher throughput. Recently, high-throughput assays have been used to assess the enhancer function of genomic regions (Arnold et al. 2013; Wang et al. 2017), the allelic effects on gene expression for naturally occurring variation in 104 regulatory regions (Vockley et al. 2015), fine...
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Research: Enhancer–silencer transitions in the human genome
- Di Huang and
- Ivan Ovcharenko
Genome Res. March 2022 32: 437-448; Published in Advance February 1, 2022, doi:10.1101/gr.275992.121
..., (specific) REs acting in HPCs but not in T cells. (**) P < 10−5.DiscussionAdvances in high-throughput sequencing and MPRAs vastly increase the knowledge of gene regulation in human cells. However, the detection and functional characterization of active silencers remain challenging (Della Rosa and Spivakov...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...features at commonly and less frequently bound ESR1 sites. For this, we first evaluated chromatin conformation behavior of common and more patient-unique sites by means of high-throughput chromatin conformation analyses (Hi-C), which illustrated a direct positive association of long-range chromatin...
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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...the utility of this approach to identify promoter and enhancer shifts across ancestral and single-species branches, as well as connect these lineage-specific innovations with candidate tissue-specific processes rewired in mole-rats.MethodsChIP and high-throughput sequencingWe performed ChIP experiments...
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