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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...that these ERVs also function as enhancers. To test this proposal, from the 1170 ERV loci potentially regulated by KZFPs, we first selected 286 ERV loci based on their transcripts and the adjacent gene transcripts being detected by RNA-seq either in KIT+ SGs or in PSs. Whereas expression of intergenic ERVs...
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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
...in zebrafish are located on the long arm of Chromosome 4 (Chr 4q), a region previously noted for its enrichment in TEs, ZNFs, and immunity genes, as well as a wide variety of RNA-encoding loci (Howe et al. 2013, 2016). This physical colocalization of FZNFs superficially resembles that of KZNF genes, which form...
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Resource: Multiparameter functional diversity of human C2H2 zinc finger proteins
- Frank W. Schmitges,
- Ernest Radovani,
- Hamed S. Najafabadi,
- Marjan Barazandeh,
- Laura F. Campitelli,
- Yimeng Yin,
- Arttu Jolma,
- Guoqing Zhong,
- Hongbo Guo,
- Tharsan Kanagalingam,
- Wei F. Dai,
- Jussi Taipale,
- Andrew Emili,
- Jack F. Greenblatt,
- and Timothy R. Hughes
Genome Res. December 2016 26: 1742-1752; Published in Advance November 16, 2016, doi:10.1101/gr.209643.116
..., Deplancke B, Trono D. 2013. Global and stage specific patterns of Krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells. PLoS One 8: e56721. de Amorim RC, Hennig C. 2015. Recovering the number of clusters in data sets with noise features using feature rescaling...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...is a conserved small RNA-based mechanism regulating TE activity (Lau et al. 2006; Brennecke et al. 2007; Houwing et al. 2007; Grimson et al. 2008). piRNAs are 23- to 32-nucleotide RNAs produced from discrete loci called piRNA clusters (piCs) that guide effector Piwi proteins to silence TEs (Ozata et al. 2019...
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Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
...(Antunez-Sanchez et al. 2020), we assessed whether gene pairs connected through reSLs showed similar transcriptional shifts between ref6-5 and WT. We found a significant enrichment of corepressed reSL-paired gene loci among the 546 plotted couples (P-value = 4 × 10−10) (Fig. 4F; Supplemental Fig. S12...
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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
...that the host ZF response is lagging behind a recent burst of LTR retroelement activity. Alternative explanations of thismouse result are considered in the Discussion. If the major function of ZF genes is to transcriptionally repress LTR retroelements, then the sequence diversity of LTR retroelements should...
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Research: Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
- Iris Zhu and
- David Landsman
Genome Res. October 2023 33: 1662-1672; Published in Advance October 26, 2023, doi:10.1101/gr.278130.123
..., in each cell type are likely to “attract” more TFs, and these sites become effective enhancers. Because each cell type has a specific repertoire and expression pattern of TFs, the enhancers occur at cell type–specific loci, even if they target the same genes.A simplified schematic explanation is presented...
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LETTER: Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes
- Aaron T. Hamilton,
- Stuart Huntley,
- Mary Tran-Gyamfi,
- Daniel M. Baggott,
- Laurie Gordon,
- and Lisa Stubbs
Genome Res. May 2006 16: 584-594; Published in Advance April 10, 2006, doi:10.1101/gr.4843906
..., divergence, and loss that have continued in each mammalian group. One such family encodes KRAB-zinc finger (KRAB-ZNF) proteins, which function as transcriptional repressors. One particular subfamily of KRAB-ZNF genes, including ZNF91, has expanded specifically in primates to comprise more than 110 loci...
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Research: Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity
- Angela Jimeno-Martín,
- Erick Sousa,
- Rebeca Brocal-Ruiz,
- Noemi Daroqui,
- Miren Maicas,
- and Nuria Flames
Genome Res. March 2022 32: 459-473; Published in Advance January 24, 2022, doi:10.1101/gr.275623.121
...) tyrosine. (B) Schematic representation of unc-62 and vab-3 gene loci and alleles used in the analysis. (C,D) Endogenous dat-1 and cat-2 dopamine pathway gene reporter expression analysis in unc-62(e971) and vab-3(ot346) alleles. For cat-2 and dat-1 analysis, disorganization of vab-3(ot346) head neurons...
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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
...-binding sites gradually accumulated at some genomic loci (Fig. 4A), we identified 188 Nanog-binding clusters (NBCs) containing Nanog-binding sites since the 256-cell stage. Compared to that of other pre-MBT targets, the inferred putative pre-MBT target genes of NBCs showed much higher functional enrichment...

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