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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
...FANTOM5 (Kawaji et al. 2014) or DBTSS (Suzuki et al. 2015). However, for genes expressed at a low level, whole- experiments might not have enough coverage to reliably pinpoint TSS(s).Several databases provide comprehensive DNA methylation data derived from high-throughput sequencing, including single...
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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
...-RNAi shoot bases (Xu et al. 2020), suggesting a conserved effect of loss of Pol IV in different tissues of rice.In summary, the activity of RNA Pol IV and ensuing sRNAs are essential for regulating the expression of genes and repeats via DNA methylation, and loss of these processes results...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...generated by gene-poor and highly repetitive TCAST arrays. To reduce the suspected negative effects of TCAST satDNA on the assembly process, we performed an additional filtering step. In this step, the contigs that did not contain at least 1000 bp of unique gene-coding sequence were removed, resulting...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...of target mRNAs. For example, in mature B lymphocytes, a 3′ fragment derived from tRNAGlyGCC (referred to as 3′-tsRNAGlyGCC) has activities characteristic of a miRNA, including the capacity of binding to all four human AGOs and gene silencing via target sites in 3′ UTRs (Maute et al. 2013). In addition, ts...
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Research: Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing
- Florian Caiment,
- Carole Charlier,
- Tracy Hadfield,
- Noelle Cockett,
- Michel Georges,
- and Denis Baurain
Genome Res. December 2010 20: 1651-1662; Published in Advance October 13, 2010, doi:10.1101/gr.108787.110
...target the ORF of DLK1 , thereby causing the trans inhibition underlying polar overdominance. We highlight the limitations of high-throughput sequencing for digital gene expression profiling as a result of biased and inconsistent amplification of specific miRNAs. Footnotes ↵ 3...
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Method: ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens
- Diane D. Shao,
- Aviad Tsherniak,
- Shuba Gopal,
- Barbara A. Weir,
- Pablo Tamayo,
- Nicolas Stransky,
- Steven E. Schumacher,
- Travis I. Zack,
- Rameen Beroukhim,
- Levi A. Garraway,
- Adam A. Margolin,
- David E. Root,
- William C. Hahn,
- and Jill P. Mesirov
Genome Res. April 2013 23: 665-678; Published in Advance December 26, 2012, doi:10.1101/gr.143586.112
...in each reagent and thus enables the use of ATARiS in the selection of reagents for validation studies and as an aid in the design and refinement of RNAi libraries. Based on our work with these shRNAs, we anticipate that we lack more than one effective shRNA for a fraction of targeted genes. ATARi...
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Research: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes
- Joe R. Harman,
- Ross Thorne,
- Max Jamilly,
- Marta Tapia,
- Nicholas T. Crump,
- Siobhan Rice,
- Ryan Beveridge,
- Edward Morrissey,
- Marella F.T.R. de Bruijn,
- Irene Roberts,
- Anindita Roy,
- Tudor A. Fulga,
- and Thomas A. Milne
Genome Res. July 2021 31: 1159-1173; Published in Advance June 4, 2021, doi:10.1101/gr.268490.120
..., and RUNX1 regulating a gene target independent of KMT2A-AFF1) (Fig. 4E). FFLs can be classified as coherent (C1-FFL, C3-FFL, the same sign of effect) and incoherent (I1-FFL, I3-FFL, opposing signs), based on the regulatory effect (up- or down-regulation) on the target gene by RUNX1 and KMT2A-AFF1 (Mangan...
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Research: Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1–S6K pathway signaling
- Robert A. Lindquist,
- Kathleen A. Ottina,
- Douglas B. Wheeler,
- Peggy P. Hsu,
- Carson C. Thoreen,
- David A. Guertin,
- Siraj M. Ali,
- Shomit Sengupta,
- Yoav D. Shaul,
- Michael R. Lamprecht,
- Katherine L. Madden,
- Adam R. Papallo,
- Thouis R. Jones,
- David M. Sabatini,
- and Anne E. Carpenter
Genome Res. March 2011 21: 433-446; Published in Advance January 14, 2011, doi:10.1101/gr.111492.110
...list of 70 confirmednoncanonical genes (51 low and19 high) for which RNAi perturbs p-hS6, p-dS6K, or total dS6K is in Supplemental Table S2B. To characterize and categorize these genes’ effects on TORC1 signaling and cell proliferation under diverse nutrient conditions, we hierarchically clustered...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...identify the stress response gene P5CS in A. avenae nematodes. Aap5cs RNAi experiments demonstrate that knockdown of Aap5cs results in increased accumulation of reactive oxygen species under desiccation stress and reduced desiccation survival time, suggesting that Aap5cs plays a role in the stress response...
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Research: Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer
- Fátima Valdés-Mora,
- Jenny Z. Song,
- Aaron L. Statham,
- Dario Strbenac,
- Mark D. Robinson,
- Shalima S. Nair,
- Kate I. Patterson,
- David J. Tremethick,
- Clare Stirzaker,
- and Susan J. Clark
Genome Res. February 2012 22: 307-321; Published in Advance July 25, 2011, doi:10.1101/gr.118919.110
...of acH2A.Z at the TSS occurs with an overall decrease of H2A.Z levels, in concert with oncogene activation. Furthermore, deacetylation of H2A.Z at TSSs is increased with silencing of tumor suppressor genes. We also demonstrate that acH2A.Z anti-correlates with promoter H3K27me3 and DNA methylation. We...

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