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Research: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters
- Suhn Kyong Rhie,
- Lijun Yao,
- Zhifei Luo,
- Heather Witt,
- Shannon Schreiner,
- Yu Guo,
- Andrew A. Perez,
- and Peggy J. Farnham
Genome Res. March 2018 28: 310-320; Published in Advance February 2, 2018, doi:10.1101/gr.228809.117
...in MCF-7. (E) A model demonstrating the relationship of ZFX to other components of CpG island promoter structure. ZFX binds at +240 bp in the nucleosome-depleted region of CpG island promoters, between the general transcription preinitiation complex (PIC) and the first nucleosome in the transcribed...
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Research: The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes
- Daniel C. Kraushaar,
- Zuozhou Chen,
- Qingsong Tang,
- Kairong Cui,
- Junfang Zhang,
- and Keji Zhao
Genome Res. November 2018 28: 1646-1655; Published in Advance September 25, 2018, doi:10.1101/gr.236224.118
...the ZMYND8–NuRD chromatin remodeler to promote DNA repair. J Cell Biol 216: 1959–1974. ↵Gunther K, Rust M, Leers J, Boettger T, Scharfe M, Jarek M, Bartkuhn M, Renkawitz R. 2013. Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences. Nucleic Acids Res...
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Research: The mutational spectrum of non-CpG DNA varies with CpG content
- Jean-Claude Walser and
- Anthony V. Furano
Genome Res. July 2010 20: 875-882; Published in Advance May 24, 2010, doi:10.1101/gr.103283.109
.... 2005; Tyekucheva et al. 2008). A prevailing reasonable explanation for this odd result was that the non-CpG mutation rate and CpG content were joint manifestations of the chromosomal environment (Hellmann et al. 2005; Tyekucheva et al. 2008). We recently considered an alternative, that CpGs (i...
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Research: Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
- Sharmistha Pal,
- Ravi Gupta,
- Hyunsoo Kim,
- Priyankara Wickramasinghe,
- Valérie Baubet,
- Louise C. Showe,
- Nadia Dahmane,
- and Ramana V. Davuluri
Genome Res. August 2011 21: 1260-1272; Published in Advance June 28, 2011, doi:10.1101/gr.120535.111
...27me3, defined the use of alternative promoters, and we identified a combinatorial role of H3K4me3 and H3K27me3 in regulating the expression of transcripts, including transcript variants of a gene during development. We observed a strong bias of both H3K4me3 and H3K27me3 for CpG-rich promoters...
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LETTER: Suz12 binds to silenced regions of the genome in a cell-type-specific manner
- Sharon L. Squazzo,
- Henriette O’Geen,
- Vitalina M. Komashko,
- Sheryl R. Krig,
- Victor X. Jin,
- Sung-wook Jang,
- Raphael Margueron,
- Danny Reinberg,
- Roland Green,
- and Peggy J. Farnham
Genome Res. July 2006 16: 890-900; Published in Advance June 2, 2006, doi:10.1101/gr.5306606
...-containing transcription factors was very highly represented (see Supplemental Table S4 for a list of the set of 1076 F9 cell Suz12 target genes having known functions). We have also performed a ChIP-chip analysis of F9 cell Suz12 target genes using mouse CpG island arrays. We found identical categories of Suz12 target...
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ARTICLE: A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes
- Liora Z. Strichman-Almashanu,
- Richard S. Lee,
- Patrick O. Onyango,
- Elizabeth Perlman,
- Folke Flam,
- Matthew B. Frieman,
- and Andrew P. Feinberg
Genome Res. April 1, 2002 12: 543-554; Published in Advance March 20, 2002, doi:10.1101/gr.224102
...to expected ratio based on GC content) &gt;0.6 ( Gardiner-Garden and Frommer 1987 ). CpG islands have been estimated to constitute 1%–2% of the mammalian ( Antequera and Bird 1993 ), and are found in the promoters of all housekeeping genes, as well as in a less conserved position in 40% of genes showing...
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LETTER: Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
- Kouichi Kimura,
- Ai Wakamatsu,
- Yutaka Suzuki,
- Toshio Ota,
- Tetsuo Nishikawa,
- Riu Yamashita,
- Jun-ichi Yamamoto,
- Mitsuo Sekine,
- Katsuki Tsuritani,
- Hiroyuki Wakaguri,
- Shizuko Ishii,
- Tomoyasu Sugiyama,
- Kaoru Saito,
- Yuko Isono,
- Ryotaro Irie,
- Norihiro Kushida,
- Takahiro Yoneyama,
- Rie Otsuka,
- Katsuhiro Kanda,
- Takahide Yokoi,
- Hiroshi Kondo,
- Masako Wagatsuma,
- Katsuji Murakawa,
- Shinichi Ishida,
- Tadashi Ishibashi,
- Asako Takahashi-Fujii,
- Tomoo Tanase,
- Keiichi Nagai,
- Hisashi Kikuchi,
- Kenta Nakai,
- Takao Isogai,
- and Sumio Sugano
Genome Res. January 2006 16: 55-65; Published in Advance December 12, 2005, doi:10.1101/gr.4039406
...PPR) promoters with respect to the frequencies of basic promoter elements, namely, TATA boxes and CpG islands. As shown in Figure 3 , the frequencies of the TATA box-containing ( Fig. 2B ) and the CpG island-containing ( Fig. 3A ) promoters were 17% and 58% for the PAP-less promoters, respectively...
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LETTER: An Abundance of Bidirectional Promoters in the Human Genome
- Nathan D. Trinklein,
- Shelley Force Aldred,
- Sara J. Hartman,
- Diane I. Schroeder,
- Robert P. Otillar,
- and Richard M. Myers
Genome Res. January 2004 14: 62-66; doi:10.1101/gr.1982804
...promoters have a median GC-content of 66% compared to 53% for nonbidirectional promoters. Furthermore, 77% of the bidirectional promoters are located within a CpG island, compared to 38% of nonbidirectional promoters. We found no difference in the length and sequence characteristics of the CpG islands...
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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
...are available for predicting the presence of CpG islands in DNA sequences. Examples include the CpGplot tool from the European Molecular Biology Open Software Suite (EMBOSS) (Rice et al. 2000), the CpG Island Searcher (Takai and Jones 2003), CpGProD (Ponger and Mouchiroud 2002), and CpGPAP (Chuang et al. 2012...
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Method: A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma
- Jan Müller,
- Christina Hartwig,
- Mirko Sonntag,
- Lisa Bitzer,
- Christopher Adelmann,
- Yevhen Vainshtein,
- Karolina Glanz,
- Sebastian O. Decker,
- Thorsten Brenner,
- Georg F. Weber,
- Arndt von Haeseler,
- and Kai Sohn
Genome Res. August 2024 34: 1185-1195; Published in Advance September 13, 2024, doi:10.1101/gr.279326.124
...to be an essential regulator of gene activity and is associated with transcription factor binding and thus, potentially, DNA footprint signals. Consequently, we classified CpG islands (CpGis) into methylated and unmethylated CpGis based on the signal strength of cell-free methyl-CpG-binding domain sequencing (cf...
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