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Research: Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control
- Miguel L. Soares,
- Carol A. Edwards,
- Frances L. Dearden,
- Sacri R. Ferrón,
- Scott Curran,
- Jennifer A. Corish,
- Rebecca C. Rancourt,
- Sarah E. Allen,
- Marika Charalambous,
- Malcolm A. Ferguson-Smith,
- Willem Rens,
- David J. Adams,
- and Anne C. Ferguson-Smith
Genome Res. March 2018 28: 345-356; Published in Advance January 24, 2018, doi:10.1101/gr.221366.117
...not contribute to a landscape required for the genomic imprinting or transcriptional regulation of adjacent genes across a 1.25-Mb region.DiscussionDense arrays of LINEs accumulate in regions of the where they can be toleratedNearly half of the mammalian is composed of repetitive sequences, yet their influence...
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Method: Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
- John E. McCormack,
- Brant C. Faircloth,
- Nicholas G. Crawford,
- Patricia Adair Gowaty,
- Robb T. Brumfield,
- and Travis C. Glenn
Genome Res. April 2012 22: 746-754; Published in Advance December 29, 2011, doi:10.1101/gr.125864.111
...material, and publication date are at http://www..org/cgi/doi/10.1101/gr.125864.111. 746 Genome Research www..org 22:746–754 2012 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/12; www..org Available evidence indicates that several mammalian divergences occurred extremely rapidly. The basal...
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Research: Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer
- Marcos R.H. Estécio,
- Juan Gallegos,
- Céline Vallot,
- Ryan J. Castoro,
- Woonbok Chung,
- Shinji Maegawa,
- Yasuhiro Oki,
- Yutaka Kondo,
- Jaroslav Jelinek,
- Lanlan Shen,
- Helge Hartung,
- Peter D. Aplan,
- Bogdan A. Czerniak,
- Shoudan Liang,
- and Jean-Pierre J. Issa
Genome Res. October 2010 20: 1369-1382; Published in Advance August 17, 2010, doi:10.1101/gr.107318.110
.... Article and publication date are at http://www..org/cgi/doi/10.1101/gr.107318.110. 20:1369–1382 2010 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/10; www..org Genome Research 1369 www..org DNA sequence in the 4-kb region surrounding the transcription start site (TSS) of a training set composed...
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Research: The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important
- Erika M. Kvikstad and
- Kateryna D. Makova
Genome Res. May 2010 20: 600-613; Published in Advance March 10, 2010, doi:10.1101/gr.099044.109
...chromosomes. Here, using a multiple regression framework, we investigate primate Alu and L1 densities shaped by regional genome features and location on a particular chromosome type. As a result of our analysis, first, we build statistical models explaining up to 79% and 44% of variation in Alu and L1...
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Letter: Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard
- Nicolas Di-Poï,
- Juan I. Montoya-Burgos,
- and Denis Duboule
Genome Res. April 2009 19: 602-610; Published in Advance February 18, 2009, doi:10.1101/gr.087932.108
...in mammalian s . Genome Res. 16 : 164 – 172 . ↵ Simons, C. , Makunin, I.V. , Pheasant, M. , Mattick, J.S. ( 2007 ) Maintenance of transposon-free regions throughout vertebrate evolution . BMC Genomics 8 : 470 , doi: 10.1186/1471-2164-8-470 . ↵ Sinibaldi-Vallebona, P. , Lavia, P. , Garaci, E. , Spadafora, C...
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PERSPECTIVE: Raising the estimate of functional human sequences
- Michael Pheasant and
- John S. Mattick
Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
...Abstract While less than 1.5% of the mammalian genome encodes proteins, it is now evident that the vast majority is transcribed, mainly into non-protein-coding RNAs. This raises the question of what fraction of the genome is functional, i.e., composed of sequences that yield functional products...
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ARTICLE: Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
- Hiroshi Kikuta,
- Mary Laplante,
- Pavla Navratilova,
- Anna Z. Komisarczuk,
- Pär G. Engström,
- David Fredman,
- Altuna Akalin,
- Mario Caccamo,
- Ian Sealy,
- Kerstin Howe,
- Julien Ghislain,
- Guillaume Pezeron,
- Philippe Mourrain,
- Staale Ellingsen,
- Andrew C. Oates,
- Christine Thisse,
- Bernard Thisse,
- Isabelle Foucher,
- Birgit Adolf,
- Andrea Geling,
- Boris Lenhard,
- and Thomas S. Becker
Genome Res. May 2007 17: 545-555; Published in Advance March 26, 2007, doi:10.1101/gr.6086307
..., and the HCNEs will be lost from that segment. Any alternative explanations that would account for the observed disentangling of regulatory and protein-coding elements are highly improbable. Recently, early developmental regulators were found to be associated with transposon-free regions (TFRs) in the human...

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