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Method: Identification and dynamic quantification of regulatory elements using total RNA
- Sascha H. Duttke,
- Max W. Chang,
- Sven Heinz,
- and Christopher Benner
Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
...the molecular complexes necessary to start transcription. Annotation of genes and regulatory elements and the analysis of the underlying molecular mechanisms regulating transcription therefore depend on the identification of TSSs and the measurement of their activity -wide.The advent of nascent RNA sequencing...
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Research: Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
- Anish Dattani,
- Damian Kao,
- Yuliana Mihaylova,
- Prasad Abnave,
- Samantha Hughes,
- Alvina Lai,
- Sounak Sahu,
- and A. Aziz Aboobaker
Genome Res. October 2018 28: 1543-1554; Published in Advance August 24, 2018, doi:10.1101/gr.239848.118
...pluripotency requires bivalent chromatin, planarian adult stem cells or neoblasts represent another possible scenario in which poised promoters could have an important role in invertebrates, if this regulatory feature is conserved. Planarian NBs are a population of adult dividing cells that collectively...
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Research: Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
- Manuel Irimia,
- Juan J. Tena,
- Maria S. Alexis,
- Ana Fernandez-Miñan,
- Ignacio Maeso,
- Ozren Bogdanović,
- Elisa de la Calle-Mustienes,
- Scott W. Roy,
- José L. Gómez-Skarmeta,
- and Hunter B. Fraser
Genome Res. December 2012 22: 2356-2367; Published in Advance June 21, 2012, doi:10.1101/gr.139725.112
...features, we provide extensive evidence that many conserved ancient linkages involve (1) the coordinated transcription of neighboring genes, or (2) genomic regulatory blocks (GRBs) in which transcriptional enhancers controlling developmental genes are contained within nearby bystander genes. In addition...
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Research: Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis
- Paola Cornejo-Páramo,
- Kathrein Roper,
- Sandie M. Degnan,
- Bernard M. Degnan,
- and Emily S. Wong
Genome Res. March 2022 32: 474-487; Published in Advance January 19, 2022, doi:10.1101/gr.275864.121
...arose before the divergence of sponge and vertebrate lineages some 700 million years ago and has been maintained in conserved genomic regulatory blocks.Advances in sequencing technology have enabled the mapping and characterization of the metazoan gene regulatory landscape during embryogenesis...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...and Martindale 2017b); and the target genes of developmentally significant TFs are at least partially conserved across the two clades (Münder et al. 2010; Gufler et al. 2018; Hartl et al. 2019). However, beyond these general similarities, little is known about cnidarian gene regulatory networks...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...; Schultz et al. 2023; Lin et al. 2024). This conservation of chromosome-scale gene linkages, known as macrosynteny, is intriguing, as the selective pressures maintaining it and its significance for function remain largely unexplored.The persistence of gene linkages enables the identification of orthologous...
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Research: Cnidarian microRNAs frequently regulate targets by cleavage
- Yehu Moran,
- David Fredman,
- Daniela Praher,
- Xin Z. Li,
- Liang Meng Wee,
- Fabian Rentzsch,
- Phillip D. Zamore,
- Ulrich Technau,
- and Hervé Seitz
Genome Res. April 2014 24: 651-663; Published in Advance March 18, 2014, doi:10.1101/gr.162503.113
...and biological activity of miRNAs in the sea anemone Nematostella vectensis , a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella , increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting...
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Research: The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer
- Lei Li,
- Chabane Tibiche,
- Cong Fu,
- Tomonori Kaneko,
- Michael F. Moran,
- Martin R. Schiller,
- Shawn Shun-Cheng Li,
- and Edwin Wang
Genome Res. July 2012 22: 1222-1230; Published in Advance December 22, 2011, doi:10.1101/gr.128819.111
...that the development of complex regulatory systems, such as molecular networks that are mediated by tyrosine phosphorylation, plays an important role in the appearance of multicellularity and the coordination of complex morphogenetic events in eumetazoans (Weiss and Littman 1994; Tan et al. 2009b). Therefore...

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