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Method: Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN
- Xiangxiu Wang,
- Wen Wang,
- Yiman Wang,
- Jia Chen,
- Guifen Liu,
- and Yong Zhang
Genome Res. February 2022 32: 378-388; Published in Advance December 29, 2021, doi:10.1101/gr.275837.121
...). For DamID, the resolution of TF-binding sites was limited to their distribution at GATC sites, and the excessive methylation activity of the fused DNA adenine methyltransferase (Dam) may lead to false-positive enrichment (Aughey and Southall 2016). To date, only ChEC-seq applications to yeast have been...
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Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- Melissa J. Fullwood,
- Chia-Lin Wei,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
...cells ( Zhao et al. 2007 ). Variants of ChIP-PET have also been reported, such as paired-end genomic signature tags (PE-GST), which has been used to identify transcription factor binding sites and DNA methylation patterns ( Dunn et al. 2007 ). ChIP-chip and ChIP-PET methods agree well on strong binding...
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Research: Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication
- Eve Shinbrot,
- Erin E. Henninger,
- Nils Weinhold,
- Kyle R. Covington,
- A. Yasemin Göksenin,
- Nikolaus Schultz,
- Hsu Chao,
- HarshaVardhan Doddapaneni,
- Donna M. Muzny,
- Richard A. Gibbs,
- Chris Sander,
- Zachary F. Pursell,
- and David A. Wheeler
Genome Res. November 2014 24: 1740-1750; Published in Advance September 16, 2014, doi:10.1101/gr.174789.114
...Henninger Muzny, D Wheeler, David A KyleR Covington Chris Z.F. Pursell Kyle Muzny, Donna M Hsu Chao Nils, Weinhold ZacharyF Pursell DA Wheeler genome;gr.174789.114 10.1101/gr.174789.114 1549-5469 1088-9051 Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns...
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Letter: Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns
- Michael P. Schnetz,
- Cynthia F. Bartels,
- Kuntal Shastri,
- Dheepa Balasubramanian,
- Gabriel E. Zentner,
- Ravishankar Balaji,
- Xiaodong Zhang,
- Lingyun Song,
- Zhenghe Wang,
- Thomas LaFramboise,
- Gregory E. Crawford,
- and Peter C. Scacheri
Genome Res. April 2009 19: 590-601; Published in Advance February 27, 2009, doi:10.1101/gr.086983.108
...related to antibody specificity, we introduced DNA encoding a triple Flag epitope tag (3 × FLAG) into the CHD7 locus using a rAAV-mediated somatic cell knock-in approach ( Zhang et al. 2008 ), and then performed ChIP-chip analysis of Flag-tagged CHD7 using anti-Flag antibody. ChIP-chip results using...
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REVIEW: Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
- Albertha J.M. Walhout
Genome Res. December 2006 16: 1445-1454; Published in Advance October 19, 2006, doi:10.1101/gr.5321506
....J A Walhout Walhout Albertha JM Albertha Walhout 10.1101/gr.5321506 genome;gr.5321506 1088-9051 Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping Albertha J...
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LETTER: Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis
- Stewart J. Hinchliffe,
- Karen E. Isherwood,
- Richard A. Stabler,
- Michael B. Prentice,
- Alexander Rakin,
- Richard A. Nichols,
- Petra C.F. Oyston,
- Jason Hinds,
- Richard W. Titball,
- and Brendan W. Wren
Genome Res. September 2003 13: 2018-2029; doi:10.1101/gr.1507303
...in a limited number of conserved genes, rRNA/rDNA, or signature sequences. However, due to the acquisition of DNA through lateral gene transfer, the differences between closely related bacterial strains, particularly members of the enterobacteriaceae such as the yersiniae, can be significant. Genome...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...to be DEV1 and DEV2/3 (T12–T16).The ICOPa and ICOPb proteins had no other detectable domains but contained three amino acid residues, called the GxD signature (Fig. 1A–C; Aravind and Iyer 2012), within the WSD motif. The WSD motif is known to interact with linker DNA and the SLIDE domain in ISWI proteins...
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Research: Cancer-associated rs6983267 SNP and its accompanying long noncoding RNA CCAT2 induce myeloid malignancies via unique SNP-specific RNA mutations
- Maitri Y. Shah,
- Manuela Ferracin,
- Valentina Pileczki,
- Baoqing Chen,
- Roxana Redis,
- Linda Fabris,
- Xinna Zhang,
- Cristina Ivan,
- Masayoshi Shimizu,
- Cristian Rodriguez-Aguayo,
- Mihnea Dragomir,
- Katrien Van Roosbroeck,
- Maria Ines Almeida,
- Maria Ciccone,
- Daniela Nedelcu,
- Maria Angelica Cortez,
- Taghi Manshouri,
- Steliana Calin,
- Muharrem Muftuoglu,
- Pinaki P. Banerjee,
- Mustafa H. Badiwi,
- Jan Parker-Thornburg,
- Asha Multani,
- James William Welsh,
- Marcos Roberto Estecio,
- Hui Ling,
- Ciprian Tomuleasa,
- Delia Dima,
- Hui Yang,
- Hector Alvarez,
- M. James You,
- Milan Radovich,
- Elizabeth Shpall,
- Muller Fabbri,
- Katy Rezvani,
- Leonard Girnita,
- Ioana Berindan-Neagoe,
- Anirban Maitra,
- Srdan Verstovsek,
- Riccardo Fodde,
- Carlos Bueso-Ramos,
- Mihai Gagea,
- Guillermo Garcia Manero,
- and George A. Calin
Genome Res. April 2018 28: 432-447; Published in Advance March 22, 2018, doi:10.1101/gr.225128.117
...mice. The RNA transcribed from the SNP locus in malignant hematopoietic cells have different allelic composition from the corresponding genomic DNA, a phenomenon rarely observed in normal cells. Our findings provide fundamental insights into the functional role of rs6983267 SNP and CCAT2 in myeloid...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...a transposase domain derived from an Hsmar1 insertion conserved in primates, providing functional DNA-binding to target methylation (Cordaux et al. 2006). Such exaptation and domestication events can often be identified by the occurrence of chimeric transcripts, which are mRNAs with both gene- and TE...
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Methods: A Gateway-Compatible Yeast One-Hybrid System
- Bart Deplancke,
- Denis Dupuy,
- Marc Vidal,
- and Albertha J.M. Walhout
Genome Res. October 15, 2004 14: 2093-2101; doi:10.1101/gr.2445504
...: In this window In a new window Figure 7 Validation of Y1H-based protein-DNA interactions. Results of a representative experiment validating Y1H TF- Pfog-3 interactions by transient transfections and luciferase assays are shown. Negative controls include an empty GST-tag-containing vector and GST- php-3 . Values...

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