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Research: Promoter architecture of mouse olfactory receptor genes
- Charles Plessy,
- Giovanni Pascarella,
- Nicolas Bertin,
- Altuna Akalin,
- Claudia Carrieri,
- Anne Vassalli,
- Dejan Lazarevic,
- Jessica Severin,
- Christina Vlachouli,
- Roberto Simone,
- Geoffrey J. Faulkner,
- Jun Kawai,
- Carsten O. Daub,
- Silvia Zucchelli,
- Yoshihide Hayashizaki,
- Peter Mombaerts,
- Boris Lenhard,
- Stefano Gustincich,
- and Piero Carninci
Genome Res. March 2012 22: 486-497; Published in Advance December 22, 2011, doi:10.1101/gr.126201.111
...binding site motifs are overrepresented in the promoters of Class II OR genes, providing a molecular basis for the selective loss of this receptor class in Lhx2 knockout mice (Hirota et al. 2007). We also show that approximately half of the expressed OR loci contain antisense transcripts, with themajority...
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Research: The landscape of genomic imprinting across diverse adult human tissues
- Yael Baran,
- Meena Subramaniam,
- Anne Biton,
- Taru Tukiainen,
- Emily K. Tsang,
- Manuel A. Rivas,
- Matti Pirinen,
- Maria Gutierrez-Arcelus,
- Kevin S. Smith,
- Kim R. Kukurba,
- Rui Zhang,
- Celeste Eng,
- Dara G. Torgerson,
- Cydney Urbanek,
- the GTEx Consortium,
- Jin Billy Li,
- Jose R. Rodriguez-Santana,
- Esteban G. Burchard,
- Max A. Seibold,
- Daniel G. MacArthur,
- Stephen B. Montgomery,
- Noah A. Zaitlen,
- and Tuuli Lappalainen
Genome Res. July 2015 25: 927-936; Published in Advance May 7, 2015, doi:10.1101/gr.192278.115
...detect stage-specific or tissue-specific imprinting patterns. Genome-wide scans for epigenetic signatures of imprinting, such as chromatin marks (Nag et al. 2013) and DNA methylation (Court et al. 2014) have provided valuable information of imprinted loci, but the relationship between parental epigenetic...
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ARTICLE: Complex Evolution of 7E Olfactory Receptor Genes in Segmental Duplications
- Tera Newman and
- Barbara J. Trask
Genome Res. May 1, 2003 13: 781-793; doi:10.1101/gr.769003
...Complex Evolution of 7E Olfactory Receptor Genes in Segmental Duplications Tera Newman and Barbara J. Trask 1 Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Department of Genome Sciences, University...
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Research: The genomic landscape of cohesin-associated chromatin interactions
- Laura E. DeMare,
- Jing Leng,
- Justin Cotney,
- Steven K. Reilly,
- Jun Yin,
- Richard Sarro,
- and James P. Noonan
Genome Res. August 2013 23: 1224-1234; Published in Advance May 23, 2013, doi:10.1101/gr.156570.113
...al. 2012). Previous ChIA-PET studies have been performed in mouse and human cell culture to capture interactions involving transcription factor estrogen receptor-a, CTCF, and RNAPII (Fullwood et al. 2009; Handoko et al. 2011; Li et al. 2012). However, cohesin is recruited to both insulators...
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REPORT: Characterization of Clustered MHC-Linked Olfactory Receptor Genes in Human and Mouse
- Ruth M. Younger,
- Claire Amadou,
- Graeme Bethel,
- Anke Ehlers,
- Kirsten Fischer Lindahl,
- Simon Forbes,
- Roger Horton,
- Sarah Milne,
- Andrew J. Mungall,
- John Trowsdale,
- Armin Volz,
- Andreas Ziegler,
- and Stephan Beck
Genome Res. April 1, 2001 11: 519-530; Published in Advance March 13, 2001, doi:10.1101/gr.160301
...Abstract Olfactory receptor (OR) loci frequently cluster and are present on most human chromosomes. They are members of the seven transmembrane receptor (7-TM) superfamily and, as such, are part of one of the largest mammalian multigene families, with an estimated copy number of up to 1000 ORs per haploid...
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LETTER: Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
- Ines Hellmann,
- Yuan Mang,
- Zhiping Gu,
- Peter Li,
- Francisco M. de la Vega,
- Andrew G. Clark,
- and Rasmus Nielsen
Genome Res. July 2008 18: 1020-1029; Published in Advance April 14, 2008, doi:10.1101/gr.074187.107
...: 10.1371/journal.pbio.0020286 . ↵ Aloni, R. , Olender, T. , Lancet, D. ( 2006 ) Ancient genomic architecture for mammalian olfactory receptor clusters . Genome Biol. 7 : R88 , doi: 10.1186/gb-2006-7-10-r88 . ↵ Altshuler, D. , Pollara, V.J. , Cowles, C.R. , Van Etten, W.J. , Baldwin, J. , Linton, L...
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LETTER: Genomic regions exhibiting positive selection identified from dense genotype data
- Christopher S. Carlson,
- Daryl J. Thomas,
- Michael A. Eberle,
- Johanna E. Swanson,
- Robert J. Livingston,
- Mark J. Rieder,
- and Deborah A. Nickerson
Genome Res. November 2005 15: 1553-1565; doi:10.1101/gr.4326505
...genes to this CRTR are RAG1 and RAG2 (chr11, 36,546,150–36,557,871, and chr11, 36,570,070–36,576,362, respectively), which are essential for adaptive immunity through the rearrangement of T Cell Receptor genes ( Fugmann 2001 ). Therefore, it is possible that long-range regulatory elements affecting...
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LETTER: G Protein-Coupled Receptor Genes in the FANTOM2 Database
- Yuka Kawasawa,
- Louise M. McKenzie,
- David P. Hill,
- Hidemasa Bono,
- RIKEN GER Group,
- GSL Members,
- and Masashi Yanagisawa
Genome Res. June 2003 13: 1466-1477; doi:10.1101/gr.1087603
....T., Campbell, N.F., and Bourgeois, S. 1991 . Identification of a gene induced by glucocorticoids in murine T-cells: A potential G protein-coupled receptor. Mol. Endocrinol. 5 : 1331 -1338. ↵ Hewes, R.S. and Taghert, P.H. 2001 . Neuropeptides and neuropeptide receptors in the Drosophila melanogaster . Genome...
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LETTER: Transcriptional Regulation of the Stem Cell Leukemia Gene (SCL) — Comparative Analysis of Five Vertebrate SCL Loci
- Berthold Göttgens,
- Linda M. Barton,
- Michael A. Chapman,
- Angus M. Sinclair,
- Bjarne Knudsen,
- Darren Grafham,
- James G.R. Gilbert,
- Jane Rogers,
- David R. Bentley,
- and Anthony R. Green
Genome Res. May 1, 2002 12: 749-759; doi:10.1101/gr.45502
...with mammalian, chicken, and pufferfish sequences. Our data show conserved synteny between zebrafish and mammalian SCL and MAP17 loci, thus suggesting the likely genomic domain necessary for the conserved pattern of SCL expression. Long-range comparative sequence analysis/phylogenetic footprinting was used...
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LETTER: Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas
- Neerja Karnani,
- Christopher Taylor,
- Ankit Malhotra,
- and Anindya Dutta
Genome Res. June 2007 17: 865-876; doi:10.1101/gr.5427007
...of origin ( Simon et al. 1999 ), genes encoding olfactory receptors ( Chess et al. 1994 ), genes on the female X-chromosome ( Avner and Heard 2001 ; Boumil and Lee 2001 ), and immunoglobulin and T-cell receptor genes ( Mostoslavsky et al. 2001 ). We will test in the future whether all the pan-S segments...
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