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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
...regulation. By critically examining both established tools and emerging techniques such as editing, synthetic chromosomes, and high-resolution imaging, we provide a practical framework for investigators seeking to uncover direct regulators of specific genes. Our goal is to guide the design of experiments...
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Research: Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers
- Yumeng Wang,
- Xiaoyan Xu,
- Shuangxing Yu,
- Kang Jin Jeong,
- Zhicheng Zhou,
- Leng Han,
- Yiu Huen Tsang,
- Jun Li,
- Hu Chen,
- Lingegowda S. Mangala,
- Yuan Yuan,
- A. Karina Eterovic,
- Yiling Lu,
- Anil K. Sood,
- Kenneth L. Scott,
- Gordon B. Mills,
- and Han Liang
Genome Res. July 2017 27: 1112-1125; Published in Advance April 14, 2017, doi:10.1101/gr.219741.116
...events alter the growthof cancer cells and also selectively change drug sensitivity in cell lines consistent with therapeutic relevance in patients. In addition to protein-coding genes, RNA editing can occur in noncoding genes, such as lncRNAs and microRNAs (miRNAs) (Gong et al. 2014, 2017).miRNAs are∼22...
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Resource: Identification of the long, edited dsRNAome of LPS-stimulated immune cells
- Matthew G. Blango and
- Brenda L. Bass
Genome Res. June 2016 26: 852-862; Published in Advance April 21, 2016, doi:10.1101/gr.203992.116
...-to-U RNA editing is enriched at 3′UTRs and microRNA target sites in multiple mouse tissues. PLoS One 7: e33720. ↵Hambleton J, Weinstein SL, Lem L, DeFranco AL. 1996. Activation of c-Jun N-terminal kinase in bacterial...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...).Dysregulation of APA could be associated with human diseases, including cancer. It has been shown that APA-mediated 3′ UTR shortening could activate oncogene expression via escaping from microRNA regulation, whereas RNA transcripts with shortened 3′ UTRs could also inhibit other transcripts from tumor...
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Method: Infernape uncovers cell type–specific and spatially resolved alternative polyadenylation in the brain
- Bowei Kang,
- Yalan Yang,
- Kaining Hu,
- Xiangbin Ruan,
- Yi-Lin Liu,
- Pinky Lee,
- Jasper Lee,
- Jingshu Wang,
- and Xiaochang Zhang
Genome Res. October 2023 33: 1774-1787; Published in Advance October 31, 2023, doi:10.1101/gr.277864.123
...) critically regulate gene expression, but their cell type–specific usage and spatial distribution in the brain have not been systematically characterized. Here, we present Infernape, which infers and quantifies PA usage from single-cell and spatial transcriptomic data and show its application in the mouse...
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Resource: Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9
- Yonghua Sun,
- Bo Zhang,
- Lingfei Luo,
- De-Li Shi,
- Han Wang,
- Zongbin Cui,
- Honghui Huang,
- Ying Cao,
- Xiaodong Shu,
- Wenqing Zhang,
- Jianfeng Zhou,
- Yun Li,
- Jiulin Du,
- Qingshun Zhao,
- Jun Chen,
- Hanbing Zhong,
- Tao P. Zhong,
- Li Li,
- Jing-Wei Xiong,
- Jinrong Peng,
- Wuhan Xiao,
- Jian Zhang,
- Jihua Yao,
- Zhan Yin,
- Xianming Mo,
- Gang Peng,
- Jun Zhu,
- Yan Chen,
- Yong Zhou,
- Dong Liu,
- Weijun Pan,
- Yiyue Zhang,
- Hua Ruan,
- Feng Liu,
- Zuoyan Zhu,
- Anming Meng,
- and The ZAKOC Consortium
Genome Res. January 2020 30: 118-126; Published in Advance December 12, 2019, doi:10.1101/gr.248559.119
...Systematic editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9 Yonghua Sun1, Bo Zhang2, Lingfei Luo3, De-Li Shi4, Han Wang5, Zongbin Cui1, Honghui Huang3, Ying Cao6, Xiaodong Shu7, Wenqing Zhang8, Jianfeng Zhou9, Yun Li9, Jiulin Du10, Qingshun Zhao11, Jun Chen12, Hanbing Zhong13, Tao P...
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Research: Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
- Eugene Berezikov,
- Nicolas Robine,
- Anastasia Samsonova,
- Jakub O. Westholm,
- Ammar Naqvi,
- Jui-Hung Hung,
- Katsutomo Okamura,
- Qi Dai,
- Diane Bortolamiol-Becet,
- Raquel Martin,
- Yongjun Zhao,
- Phillip D. Zamore,
- Gregory J. Hannon,
- Marco A. Marra,
- Zhiping Weng,
- Norbert Perrimon,
- and Eric C. Lai
Genome Res. February 2011 21: 203-215; Published in Advance December 22, 2010, doi:10.1101/gr.116657.110
...Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence Eugene Berezikov 1 , Nicolas Robine 2 , Anastasia Samsonova 3 , Jakub O. Westholm 2 , Ammar Naqvi 2 , Jui-Hung Hung...
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Resource: A biochemical landscape of A-to-I RNA editing in the human brain transcriptome
- Masayuki Sakurai,
- Hiroki Ueda,
- Takanori Yano,
- Shunpei Okada,
- Hideki Terajima,
- Toutai Mitsuyama,
- Atsushi Toyoda,
- Asao Fujiyama,
- Hitomi Kawabata,
- and Tsutomu Suzuki
Genome Res. March 2014 24: 522-534; Published in Advance January 9, 2014, doi:10.1101/gr.162537.113
...A biochemical landscape of A-to-I RNA editing in the human brain transcriptome Masayuki Sakurai 1 , 4 , Hiroki Ueda 1 , 4 , Takanori Yano 1 , Shunpei Okada 1 , Hideki Terajima 1 , Toutai Mitsuyama 2 , Atsushi Toyoda 3...
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Method: Accurate identification of A-to-I RNA editing in human by transcriptome sequencing
- Jae Hoon Bahn,
- Jae-Hyung Lee,
- Gang Li,
- Christopher Greer,
- Guangdun Peng,
- and Xinshu Xiao
Genome Res. January 2012 22: 142-150; Published in Advance September 29, 2011, doi:10.1101/gr.124107.111
...fromahumangrade IV glioma, one of themost deadly types of brain cancer. The of this cell line was sequenced recently using Figure 1. Identification of RNA editing sites. (A) Generative process of the pipeline. (B) Evaluation of mapping bias using simulated data. Histogram shows the distribution of relative ratios...
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Research: Deep sequencing the circadian and diurnal transcriptome of Drosophila brain
- Michael E. Hughes,
- Gregory R. Grant,
- Christina Paquin,
- Jack Qian,
- and Michael N. Nitabach
Genome Res. July 2012 22: 1266-1281; Published in Advance April 3, 2012, doi:10.1101/gr.128876.111
...editing, and provide a novel, genome-wide map of splicing in Drosophila brain. Footnotes ↵ 3 Corresponding author E-mail michael.nitabach@yale.edu [Supplemental material is available for this article.] Article published online before print. Article, supplemental...

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