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Method: Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
- Shilin Zhang,
- Yichen Wang,
- Lin Jia,
- Xue Wen,
- Zhonghua Du,
- Cong Wang,
- Yajing Hao,
- Dehai Yu,
- Lei Zhou,
- Naifei Chen,
- Jingcheng Chen,
- Huiling Chen,
- Hui Zhang,
- Ilkay Celik,
- Günhan Gülsoy,
- Jianjun Luo,
- Baoming Qin,
- Xueling Cui,
- Zhonghui Liu,
- Songling Zhang,
- Miguel A. Esteban,
- Ferhat Ay,
- Wei Xu,
- Runsheng Chen,
- Wei Li,
- Andrew R. Hoffman,
- Ji-Fan Hu,
- and Jiuwei Cui
Genome Res. September 2019 29: 1521-1532; Published in Advance July 17, 2019, doi:10.1101/gr.244996.118
...noncoding RNAs in tumor-associated genes, including the proto-oncogene FLI1 and the fetal mitogen insulin-like growth factor II (IGF2). Because of the flexibility of gene-specific gRNAs, this CRIST-seq approach may be used broadly to map lncRNA interaction networks at target loci across the .Results...
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Research: Ligand-induced native G-quadruplex stabilization impairs transcription initiation
- Conghui Li,
- Honghong Wang,
- Zhinang Yin,
- Pingping Fang,
- Ruijing Xiao,
- Ying Xiang,
- Wen Wang,
- Qiuzi Li,
- Beili Huang,
- Jian Huang,
- and Kaiwei Liang
Genome Res. September 2021 31: 1546-1560; Published in Advance August 16, 2021, doi:10.1101/gr.275431.121
...with transcriptional regulatory elements carrying active epigenetic modifications. Drug-induced promoter-proximal RNA polymerase II pausing promotes nearby G4 formation. In contrast, G4 stabilization by G4-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis...
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Research: An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
- Zhizhuo Zhang,
- Kern Rei Chng,
- Shreyas Lingadahalli,
- Zikai Chen,
- Mei Hui Liu,
- Huy Hoang Do,
- Shaojiang Cai,
- Nicola Rinaldi,
- Huay Mei Poh,
- Guoliang Li,
- Ying Ying Sung,
- Charlie L. Heng,
- Leighton J. Core,
- Si Kee Tan,
- Xiaoan Ruan,
- John T. Lis,
- Manolis Kellis,
- Yijun Ruan,
- Wing-Kin Sung,
- and Edwin Cheung
Genome Res. February 2019 29: 223-235; Published in Advance January 3, 2019, doi:10.1101/gr.230243.117
...noncoding RNAs were found to be connected near protein-coding genes through AR-ERG looping. Finally, we found strong enrichment of prostate cancer -wide association study (GWAS) single nucleotide polymorphisms (SNPs) at AR-ERG co-binding sites participating in chromatin interactions and gene regulation...
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Research: Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells
- Luciano Pirola,
- Aneta Balcerczyk,
- Richard W. Tothill,
- Izhak Haviv,
- Antony Kaspi,
- Sebastian Lunke,
- Mark Ziemann,
- Tom Karagiannis,
- Stephen Tonna,
- Adam Kowalczyk,
- Bryan Beresford-Smith,
- Geoff Macintyre,
- Ma Kelong,
- Zhang Hongyu,
- Jingde Zhu,
- and Assam El-Osta
Genome Res. October 2011 21: 1601-1615; Published in Advance September 2, 2011, doi:10.1101/gr.116095.110
...the extracellular conditions to maintain primary human aortic endothelial cells. In this study we examined the immediate glucose-mediated transcriptional response and specifically determine histone and DNA methylation changes in primary aortic endothelial cells. We show that hyperglycemia induces changes in mRNA...
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Research: Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm
- Shan-Fu Wu,
- Haiying Zhang,
- and Bradley R. Cairns
Genome Res. April 2011 21: 578-589; Published in Advance March 7, 2011, doi:10.1101/gr.113167.110
...of the gene by the attraction of PRC2/H3K27 by the nascent RNAs produced (Zhao et al. 2008; Lee 2009; Tsai et al. 2010) and deacetylation through resident H3K36me3 and its recruitment of HDACs (Carrozza et al. 2005; Joshi and Struhl 2005; Keogh et al. 2005). The purpose of zebrafish sperm chromatin Loci...
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Research: Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures
- Federico Comoglio,
- Hyun Jung Park,
- Stefan Schoenfelder,
- Iros Barozzi,
- Daniel Bode,
- Peter Fraser,
- and Anthony R. Green
Genome Res. March 2018 28: 295-309; Published in Advance February 2, 2018, doi:10.1101/gr.227272.117
...spliced transcripts (Supplemental Fig. S1C). In addition, analysis of small nuclear and small cytoplasmic RNA gene loci revealed compartment-specific transcript localization, confirming the high enrichment of our RNA fractions (Supplemental Fig. S1D).We then analyzed the immediate early transcriptional...
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