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Research: Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome
- Masako Suzuki,
- Mayumi Oda,
- María-Paz Ramos,
- Marién Pascual,
- Kevin Lau,
- Edyta Stasiek,
- Frederick Agyiri,
- Reid F. Thompson,
- Jacob L. Glass,
- Qiang Jing,
- Richard Sandstrom,
- Melissa J. Fazzari,
- R. Scott Hansen,
- John A. Stamatoyannopoulos,
- Andrew S. McLellan,
- and John M. Greally
Genome Res. November 2011 21: 1833-1840; Published in Advance September 28, 2011, doi:10.1101/gr.116509.110
...of unmethylated Hha I sites. Proc Natl Acad Sci 85: 7657–7660. VogelMJ, Guelen L, deWit E, Peric-Hupkes D, LodenM, TalhoutW, Feenstra M, Abbas B, Classen AK, van Steensel B. 2006. Human heterochromatin proteins form large domains containing KRAB-ZNF genes. Genome Res 16: 1493–1504. Zeschnigk M, Martin M, Betzl G...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
.... 2019). Furthermore, they are frequently lineage-specific; for example, a survey of three great ape species and rhesus macaque found that ∼10% (213 out of 2253) of predicted KRAB-ZNFs (KZNFs) were species-specific, including seven from humans and 145 from orangutangs (Nowick et al. 2011). This rapid...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...as NRSF), and several members of the repressive KRAB-ZNF family, including ZNF334, ZFP14, and ZNF140. This is consistent with a model in which these factors localize to regulatory elements to directly or indirectly decrease transcription of nearby genes. Many of the other factors have not been described...
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RESOURCE: A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors
- Stuart Huntley,
- Daniel M. Baggott,
- Aaron T. Hamilton,
- Mary Tran-Gyamfi,
- Shan Yang,
- Joomyeong Kim,
- Laurie Gordon,
- Elbert Branscomb,
- and Lisa Stubbs
Genome Res. May 2006 16: 669-677; Published in Advance April 10, 2006, doi:10.1101/gr.4842106
..., California 94550, USA 3 ↵ 3 Present address: Louisiana State University, Baton Rouge, LA. Abstract Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
...). In addition, novel TE insertions can affect gene expression negatively through the induction of local heterochromatin mediated by KRAB zinc finger (KZNF) proteins and cofactors (Lippman et al. 2004; Rebollo et al. 2011; Jacobs et al. 2014). Thus, we can conclude that TE insertions can have a long...
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Research: Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program
- Vishnu Dileep,
- Ferhat Ay,
- Jiao Sima,
- Daniel L. Vera,
- William S. Noble,
- and David M. Gilbert
Genome Res. August 2015 25: 1104-1113; Published in Advance May 20, 2015, doi:10.1101/gr.183699.114
...of developmental early and late domains, whereas B2 and B3, which comprised mainly heterochromatin, were devoid of analyzed chromatin marks, and were enriched for constitutive late and developmental late RDs (Fig. 6C). B4, which consists of a small percentage of the and is heavily enriched for KRAB-ZNF genes...
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Method: Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo
- Luca Tosti,
- James Ashmore,
- Boon Siang Nicholas Tan,
- Benedetta Carbone,
- Tapan K. Mistri,
- Valerie Wilson,
- Simon R. Tomlinson,
- and Keisuke Kaji
Genome Res. April 2018 28: 592-605; Published in Advance March 23, 2018, doi:10.1101/gr.227124.117
...). The first successful DamID experiments in human cells were performed for heterochromatin binding protein CBX1 and LMNB1 (Vogel et al. 2006; Guelen et al. 2008). More recently, DamID-seq has been used to investigate LMNB1 binding even in single human cells (Kind et al. 2015). In contrast, TF DamID has been...
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Research: CBX3 regulates efficient RNA processing genome-wide
- Andrea Smallwood,
- Gary C. Hon,
- Fulai Jin,
- Ryan E. Henry,
- Joaquín M. Espinosa,
- and Bing Ren
Genome Res. August 2012 22: 1426-1436; Published in Advance June 8, 2012, doi:10.1101/gr.124818.111
...material is available for this article.] Once thought of as static components of heterochromatin, heterochromatin protein 1 family members (HP1s—CBX5, CBX1, and CBX3) are now known to function in a myriad of cellular processes, including DNA repair, gene regulation, and telomere function (Maison...
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Research: Coevolution of retroelements and tandem zinc finger genes
- James H. Thomas and
- Sean Schneider
Genome Res. November 2011 21: 1800-1812; Published in Advance July 22, 2011, doi:10.1101/gr.121749.111
...numbers of tandem C2H2 zinc finger (tandem ZF) transcription factor proteins. In mammals, most tandem ZF genes also encode a KRAB domain (KZNF proteins). Very little is known about what forces have driven the number and diversity of tandem ZF genes. Recent studies suggest that one role of KZNF proteins...
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Research: Unique DNA methylome profiles in CpG island methylator phenotype colon cancers
- Yaomin Xu,
- Bo Hu,
- Ae-Jin Choi,
- Banu Gopalan,
- Byron H. Lee,
- Matthew F. Kalady,
- James M. Church,
- and Angela H. Ting
Genome Res. February 2012 22: 283-291; Published in Advance October 11, 2011, doi:10.1101/gr.122788.111
...incubated randomly sheared genomic DNA from each sample with recombinantmethyl CpG-biding domain (MBD) proteins to capture methylatedDNA fragments for sequencing on the IlluminaGenome 6Corresponding author. E-mail tinga@ccf.org. Article published online before print. Article, supplemental material...

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