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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
...for transcription located proximal to the protein-coding genes (PCGs) in the euchromatic domains (Hirsch and Springer 2017).The activity of RNA polymerase II (Pol II) on the euchromatic domains is regulated locally by transcription factors, chaperones, and chromatin remodeling enzymes that transduces the local...
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Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
- William K.M. Lai,
- Luca Mariani,
- Gerson Rothschild,
- Edwin R. Smith,
- Bryan J. Venters,
- Thomas R. Blanda,
- Prashant K. Kuntala,
- Kylie Bocklund,
- Joshua Mairose,
- Sarah N. Dweikat,
- Katelyn Mistretta,
- Matthew J. Rossi,
- Daniela James,
- James T. Anderson,
- Sabrina K. Phanor,
- Wanwei Zhang,
- Zibo Zhao,
- Avani P. Shah,
- Katherine Novitzky,
- Eileen McAnarney,
- Michael-C. Keogh,
- Ali Shilatifard,
- Uttiya Basu,
- Martha L. Bulyk,
- and B. Franklin Pugh
Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
...are not limited to): (1) the target TF was not expressed at sufficiently high levels or at sufficiently high nuclear concentrations in the assayed cells, (2) the epitope recognized by the antibody was not accessible in the chromatin context in the assayed cells, (3) the target TF was not occupying specific...
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Research: A chromatin link to caste identity in the carpenter ant Camponotus floridanus
- Daniel F. Simola,
- Chaoyang Ye,
- Navdeep S. Mutti,
- Kelly Dolezal,
- Roberto Bonasio,
- Jürgen Liebig,
- Danny Reinberg,
- and Shelley L. Berger
Genome Res. March 2013 23: 486-496; Published in Advance December 3, 2012, doi:10.1101/gr.148361.112
...factor (TF) binding sites that might explain the locus-specific recruitment of CBP (Supplemental Text 3). We identified binding sites for nine TFs including CREB, Mothers against dpp (Mad, a TGF-b receptor-SMAD),Medea (its coSMAD), Brinker (Mad repressor), and Trithorax-like (Trl, or GAGA factor) (FDR...
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Research: The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo
- Rahul Satija and
- Robert K. Bradley
Genome Res. April 2012 22: 656-665; Published in Advance January 13, 2012, doi:10.1101/gr.130682.111
...factor could help to explain the relationship between TAGteam motifs and overlapping binding. Intriguingly, after controlling for levels ofMedea binding, we observed little difference in binding of all factors between regions with and without TAGteammotifs (Supplemental Fig. 12A). Furthermore, ;80...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...in other aspects of plant development, such as imprinting by regulating MEDEA, a histone methyltransferase of the polycomb repressive complex 2 (PRC2) (Satyaki and Gehring 2017), in recombination patterns during meiosis, where mCHG limits heterochromatin rearrangements (Underwood et al. 2018...
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Research: Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
...in the Arabidopsis genus. Nat Plants 2: 16145. ↵Köhler C, Page DR, Gagliardini V, Grossniklaus U. 2005. The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat Genet 37: 28–30. ↵Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, et al...
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LETTER: Widespread balancing selection and pathogen-driven selection at blood group antigen genes
- Matteo Fumagalli,
- Rachele Cagliani,
- Uberto Pozzoli,
- Stefania Riva,
- Giacomo P. Comi,
- Giorgia Menozzi,
- Nereo Bresolin,
- and Manuela Sironi
Genome Res. February 2009 19: 199-212; Published in Advance November 7, 2008, doi:10.1101/gr.082768.108
...Bresolin 1 , 3 and Manuela Sironi 1 , 4 1 Scientific Institute IRCCS E. Medea, Bioinformatic Lab, 23842 Bosisio Parini (LC), Italy; 2 Bioengineering Department, Politecnico di Milano, 20133 Milan, Italy; 3 Dino Ferrari Centre, Department...
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Research: Drosophila poised enhancers are generated during tissue patterning with the help of repression
- Nina Koenecke,
- Jeff Johnston,
- Qiye He,
- Samuel Meier,
- and Julia Zeitlinger
Genome Res. January 2017 27: 64-74; Published in Advance November 14, 2016, doi:10.1101/gr.209486.116
...that repressors play a central role in preventing the inappropriate activation of accessible enhancers. Below, we discuss a number of reasons why this is not only plausible but also an attractive model. Based on ChIP-seq data, regions of open chromatin are surprisingly susceptible to unspecific transcription...
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LETTER: Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25
- Mario Ventura,
- Jonathan M. Mudge,
- Valeria Palumbo,
- Sally Burn,
- Elisabeth Blennow,
- Mauro Pierluigi,
- Roberto Giorda,
- Orsetta Zuffardi,
- Nicoletta Archidiacono,
- Michael S. Jackson,
- and Mariano Rocchi
Genome Res. September 2003 13: 2059-2068; Published in Advance January 1, 2003, doi:10.1101/gr.1155103
...Ricovero e Cura a Carattere Scientifico Eugenio Medea, Bosisio Parini, Lecco, Italy 6 Dip. Patol. Umana ed Ereditaria, Sezione Biologia Generale, 27100 Pavia, Italy Abstract The existence of latent centromeres has been proposed as a possible explanation for the ectopic...

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