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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...that balance biological relevance, sensitivity, and interpretability to ultimately answer a deceptively simple question: What TFs directly regulate the expression of my GOI?Cellular processes are regulated by transcription machinery binding the promoters and enhancers of target genes to activate gene...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...to the expression of its target gene. Epigenetic repression with dCas9KRAB (CRISPRi) or activation with VP64dCas9VP64 (CRISPRa) at regulatory elements can alter gene expression when delivered to the enhancer of a target gene (McCutcheon et al. 2023). We transduced iPSC-CMs with lentivirus-expressing dCas9KRAB...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...with predicted target genes and disrupted transcription factor binding sites. CaQTLs identify threefold more GWAS colocalizations than liver expression QTLs (eQTLs) in a larger sample size, suggesting that caQTLs can detect mechanisms missed by eQTLs. At a GWAS signal colocalized with a caQTL and an e...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
...the 22 impact of HIV-1 promoter activity on host chromatin accessibility downstream of the integration site, we used 23 sgRNA targeting HIV-1 promoter versus nontargeting controls (NT) with CRISPR-activation (CRISPRa) and 24 CRISPR-inhibition (CRISPRi) cell line clones. We examined whether activation...
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Research: Sequence determinants of improved CRISPR sgRNA design
- Han Xu,
- Tengfei Xiao,
- Chen-Hao Chen,
- Wei Li,
- Clifford A. Meyer,
- Qiu Wu,
- Di Wu,
- Le Cong,
- Feng Zhang,
- Jun S. Liu,
- Myles Brown,
- and X. Shirley Liu
Genome Res. August 2015 25: 1147-1157; Published in Advance June 10, 2015, doi:10.1101/gr.191452.115
...(CRISPRi) and activation (CRISPRa) screens. (A) Distribution of phenotype scores (Gilbert et al. 2014) for sgRNAs targeting the top 500 essential genes and the control sgRNAs in CRISPRi experiments. The dashed line represents the threshold chosen to determine efficient and inefficient sgRNAs. (B) A bar...
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Method: Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
- Arshad H. Khan,
- Andy Lin,
- Richard T. Wang,
- Joshua S. Bloom,
- Kenneth Lange,
- and Desmond J. Smith
Genome Res. October 2020 30: 1458-1467; Published in Advance September 2, 2020, doi:10.1101/gr.262204.120
...and Griffiths-Jones 2014; Frankish et al. 2015; Liu et al. 2017).Gene expression can be manipulated in a targeted fashion using CRISPR interference (CRISPRi) or CRISPR activation (CRISPRa), in which a catalytically dead Cas9 (dCas9) protein is fused with a transcriptional repressor or activator domain...
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Method: Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives
- Hyun-Hwan Jeong,
- Seon Young Kim,
- Maxime W.C. Rousseaux,
- Huda Y. Zoghbi,
- and Zhandong Liu
Genome Res. June 2019 29: 999-1008; Published in Advance April 23, 2019, doi:10.1101/gr.245571.118
...with a catalytically inactive Cas9 fused to the transcriptional repressor KRAB, which results in gene repression). These benchmark data sets (CRISPRn-RT112, CRISPRn-UMUC3, and CRISPRi-RT112) were constructed based on 46 genes that are essential for cell survival and 47 genes that are nonessential. We first tested...
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Research: Sense–antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit
- Yulong Song,
- Lishi Li,
- Wenbing Yang,
- Qiang Fu,
- Wanying Chen,
- Zeng Fang,
- Wen Li,
- Nannan Gu,
- and Rui Zhang
Genome Res. May 2020 30: 661-672; Published in Advance May 18, 2020, doi:10.1101/gr.257121.119
...RNAs. Through examining the unstranded targeted RNA-seq libraries covering all miRNA loci in 25 types of human tissues, we identified 7275 editing events located in 81% of the antisense strand of the miRNA loci, thus uncovering the previously unknown prevalent antisense transcription of the miRNAs. We found...
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Perspective: Linking RNA biology to lncRNAs
- Loyal A. Goff and
- John L. Rinn
Genome Res. October 2015 25: 1456-1465; doi:10.1101/gr.191122.115
...RNA transcription rates. CRISPR-inhibition and activation (CRISPRi and CRISPRa, respectively) are two examples of Cas9-mediated activities to directly modulate gene transcription levels (Gilbert et al. 2013, 2014; Qi et al. 2013; Zalatan et al. 2015). These applications involve the coupling...
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