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Resource: The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program
- Olivier Tassy,
- Delphine Dauga,
- Fabrice Daian,
- Daniel Sobral,
- François Robin,
- Pierre Khoueiry,
- David Salgado,
- Vanessa Fox,
- Danièle Caillol,
- Renaud Schiappa,
- Baptiste Laporte,
- Anne Rios,
- Guillaume Luxardi,
- Takehiro Kusakabe,
- Jean-Stéphane Joly,
- Sébastien Darras,
- Lionel Christiaen,
- Magali Contensin,
- Hélène Auger,
- Clément Lamy,
- Clare Hudson,
- Ute Rothbächer,
- Michael J. Gilchrist,
- Kazuhiro W. Makabe,
- Kohji Hotta,
- Shigeki Fujiwara,
- Nori Satoh,
- Yutaka Satou,
- and Patrick Lemaire
Genome Res. October 2010 20: 1459-1468; Published in Advance July 20, 2010, doi:10.1101/gr.108175.110
...the automatic inference of gene regulatory interactions, the identification of inducing signals, and the discovery and explanation of novel asymmetric divisions. Footnotes ↵ 23 Corresponding author. E-mail lemaire@ibdml.univ-mrs.fr . [Supplemental material is available online at http...
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LETTER: Experimental validation of predicted mammalian erythroid cis-regulatory modules
- Hao Wang,
- Ying Zhang,
- Yong Cheng,
- Yuepin Zhou,
- David C. King,
- James Taylor,
- Francesca Chiaromonte,
- Jyotsna Kasturi,
- Hanna Petrykowska,
- Brian Gibb,
- Christine Dorman,
- Webb Miller,
- Louis C. Dore,
- John Welch,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2006 16: 1480-1492; Published in Advance October 12, 2006, doi:10.1101/gr.5353806
...Multiple alignments of sequences are helpful guides to functional analysis, but predicting cis -regulatory modules (CRMs) accurately from such alignments remains an elusive goal. We predict CRMs for mammalian genes expressed in red blood cells by combining two properties gleaned from aligned, noncoding...
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PERSPECTIVE: Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
- Michael Freeling and
- Brian C. Thomas
Genome Res. July 2006 16: 805-814; doi:10.1101/gr.3681406
...base that makes specific predictions as to gene content changes following different types of gene duplication. Genomic data from both chordate and angiosperm genomes fit these predictions: Each type of duplication provides a one-way injection of a biased set of genes into the gene pool. Tetraploidies...
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Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
- Rui Yokomori,
- Kotaro Shimai,
- Koki Nishitsuji,
- Yutaka Suzuki,
- Takehiro G. Kusakabe,
- and Kenta Nakai
Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
...). These data will be useful for deciphering transcriptional regulatory codes controlling tissue-specific expression in chordates. Discussion In this study, we identified candidate TSSs at the -wide level in C. intestinalis by applying TSS-seq to a total of five samples. The candidate TSSs were clustered...
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Resource: Toward the human cellular microRNAome
- Matthew N. McCall,
- Min-Sik Kim,
- Mohammed Adil,
- Arun H. Patil,
- Yin Lu,
- Christopher J. Mitchell,
- Pamela Leal-Rojas,
- Jinchong Xu,
- Manoj Kumar,
- Valina L. Dawson,
- Ted M. Dawson,
- Alexander S. Baras,
- Avi Z. Rosenberg,
- Dan E. Arking,
- Kathleen H. Burns,
- Akhilesh Pandey,
- and Marc K. Halushka
Genome Res. October 2017 27: 1769-1781; Published in Advance September 6, 2017, doi:10.1101/gr.222067.117
...novelmicroRNAs. Of these, 226 (55%) overlapped with a known microRNA seed sequence. This indicates the potential for more shared regulatory control of genes often in a more cell-specific manner. We then validated nine novel microRNAs from six different cell types or tissue by PCR (Fig. 3C). As an example...
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Perspective: Insights into neural crest development and evolution from genomic analysis
- Marcos Simões-Costa and
- Marianne E. Bronner
Genome Res. July 2013 23: 1069-1080; doi:10.1101/gr.157586.113
..., synergistic activity of different regulatory modules can bring a level of robustness to transcriptional control, particularly in the case of genes downstream from signaling pathways (Garnett et al. 2012). Tissue-specific enhancers for neural crest derivatives have also been identified. For example...
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Research: Sequence features that drive human promoter function and tissue specificity
- Jane M. Landolin,
- David S. Johnson,
- Nathan D. Trinklein,
- Shelly F. Aldred,
- Catherine Medina,
- Hennady Shulha,
- Zhiping Weng,
- and Richard M. Myers
Genome Res. July 2010 20: 890-898; Published in Advance May 25, 2010, doi:10.1101/gr.100370.109
...annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2: e162. doi: 10.1371/journal.pbio.0020162. Johnson DS, Zhou Q, Yagi K, Satoh N, Wong W, Sidow A. 2005. De novo discovery of a tissue-specific gene regulatory module in a chordate. Genome Res 15: 1315–1324. Johnson DS, Mortazavi...
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Research: Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification
- Megan Rothstein and
- Marcos Simoes-Costa
Genome Res. January 2020 30: 35-48; Published in Advance December 17, 2019, doi:10.1101/gr.249680.119
...modules (Simões-Costa and Bronner 2015), allowing for the progressive commitment to a neural crest fate. This feature of the gene regulatory network affords us with a tractable platform to explore the context-specific functions of developmental genes.A number of factors participate in multiple network...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
...binding sites in vertebrate genomes. Precise detection of these elements is a prerequisite to deciphering the complex regulatory networks that direct tissue specific and lineage specific patterns of gene expression. This review summarizes approaches for in silico, in vitro, and in vivo identification...
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