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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...conserved genomic clusters, which contain two or more maternally and paternally expressed genes in large regions of up to several megabases in size (Table 1; Fig. 1).View larger version: In this window In a new window Figure 1. Schematic representation of the genomic organization of the 10 largest imprinted...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...animals in our orthology analysis. These results indicate that Hydractinia’s stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...is attributed to sharing of two distinct features. The first is that each locus is enriched for CTCF binding motifs, which act to anchor loops resulting from chromatin extrusion to these regions in a polarity-dependent manner (Rao et al. 2014). Second, each of these loci are colocalized to the peri-nucleolar...
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LETTER: Transposon-free regions in mammalian genomes
- Cas Simons,
- Michael Pheasant,
- Igor V. Makunin,
- and John S. Mattick
Genome Res. February 2006 16: 164-172; Published in Advance December 19, 2005, doi:10.1101/gr.4624306
...Acids Res. 32 : D262 -D266. ↵ Cavaillé, J., Buiting, K., Kiefmann, M., Lalande, M., Brannan, I., Horsthemke, B., Bachellerie, J., Brosius, J., and Hüttenhofer, A. 2000 . Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl. Acad...
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LETTER: Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions
- Elfar Torarinsson,
- Zizhen Yao,
- Eric D. Wiklund,
- Jesper B. Bramsen,
- Claus Hansen,
- Jørgen Kjems,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. February 2008 18: 242-251; Published in Advance December 20, 2007, doi:10.1101/gr.6887408
...Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions Elfar Torarinsson 1 , 2 , Zizhen Yao 3 , Eric D. Wiklund 4 , Jesper B. Bramsen 4 , Claus Hansen 5 , Jørgen Kjems 4 , Niels Tommerup...
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ARTICLE: Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression
- Wei Deng,
- Xiaopeng Zhu,
- Geir Skogerbø,
- Yi Zhao,
- Zhuo Fu,
- Yudong Wang,
- Housheng He,
- Lun Cai,
- Hong Sun,
- Changning Liu,
- Biao Li,
- Baoyan Bai,
- Jie Wang,
- Dong Jia,
- Shiwei Sun,
- Hang He,
- Yan Cui,
- Yu Wang,
- Dongbo Bu,
- and Runsheng Chen
Genome Res. January 2006 16: 20-29; Published in Advance December 12, 2005, doi:10.1101/gr.4139206
...Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression Wei Deng 1 , Xiaopeng Zhu 1 , 5 , Geir Skogerbø 2 , Yi Zhao 2 , Zhuo Fu 1 , Yudong Wang 1 , Housheng He...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...universitaire de Sherbrooke (CRCHUS), Sherbrooke, Québec J1H 5N3, Canada; 3Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada Corresponding authors: michelle.scott@usherbrooke.ca, pierre-etienne.jacques@usherbrooke.caAbstractSmall nucleolar RNAs (sno...
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ARTICLE: Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray
- Heenam Kim,
- Erik C. Snesrud,
- Brian Haas,
- Foo Cheung,
- Christopher D. Town,
- and John Quackenbush
Genome Res. March 1, 2003 13: 327-340; doi:10.1101/gr.552003
...detected in all assays as well as those significantly up- or down-regulated in particular assays. In each graph, genes are arranged in the order they appear along the chromosome starting from the nucleolar organizer region on the short arm. Also shown is a plot of the average GC content 1 kb upstream...
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LETTER: Multimeric Threading-Based Prediction of Protein–Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome
- Long Lu,
- Adrian K. Arakaki,
- Hui Lu,
- and Jeffrey Skolnick
Genome Res. June 2003 13: 1146-1154; doi:10.1101/gr.1145203
...regions and share similar functional roles in telomeric silencing. DISCUSSION In the present work, we applied our recently developed multimeric threading algorithm, MULTIPROSPECTOR, to genomic-scale predictions of the protein–protein interactions in S. cerevisiae . This approach predicts 7321 interactions...
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LETTER: Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic Approach
- Eugene V. Koonin,
- Yuri I. Wolf,
- and L. Aravind
Genome Res. February 1, 2001 11: 240-252; doi:10.1101/gr.162001
...of the eukaryotic MUS308-like proteins in which the helicase is fused to a DNA Pol I domain ( Harris et al. 1996 ). The domain organization of these helicases also supports a function in DNA repair because they contain a carboxy-terminal DNA-binding helix-hairpin-helix (HhH) module that is shared with the Mus308...

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