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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...Chromosome contains two classes of genomic sequence with distinct evolutionary histories (Mueller et al. 2013). Most human X-Chromosome sequence is ancestral, containing genes retained from the ancestral autosome from which the mammalian sex chromosomes evolved some 200–300 million years ago (Ohno 1967; Lahn...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...incompatibility factors on the X Chromosomes within the sim-complex (Tao and Hartl 2003; Masly and Presgraves 2007). The sim-complex s also contain a duplication of mh, whose protein product interacts with the X-linked heterochromatic satellite called 359-bp—a member of the 1.688 gm/cm3 satellites, to maintain...
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Letter: Does the human X contain a third evolutionary block? Origin of genes on human Xp11 and Xq28
- Margaret L. Delbridge,
- Hardip R. Patel,
- Paul D. Waters,
- Daniel A. McMillan,
- and Jennifer A. Marshall Graves
Genome Res. August 2009 19: 1350-1360; Published in Advance May 13, 2009, doi:10.1101/gr.088625.108
...from the Xp11 and Xq28 regions of the human X chromosome? The region around Xp11 on the short arm, and Xq28 on the long arm of the human X chromosome contains several large inverted repeats, which contain concentrations of the expanded gene families (e.g., MAGE, SSX) with testis-specific expression...
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Resource: The pig X and Y Chromosomes: structure, sequence, and evolution
- Benjamin M. Skinner,
- Carole A. Sargent,
- Carol Churcher,
- Toby Hunt,
- Javier Herrero,
- Jane E. Loveland,
- Matt Dunn,
- Sandra Louzada,
- Beiyuan Fu,
- William Chow,
- James Gilbert,
- Siobhan Austin-Guest,
- Kathryn Beal,
- Denise Carvalho-Silva,
- William Cheng,
- Daria Gordon,
- Darren Grafham,
- Matt Hardy,
- Jo Harley,
- Heidi Hauser,
- Philip Howden,
- Kerstin Howe,
- Kim Lachani,
- Peter J.I. Ellis,
- Daniel Kelly,
- Giselle Kerry,
- James Kerwin,
- Bee Ling Ng,
- Glen Threadgold,
- Thomas Wileman,
- Jonathan M.D. Wood,
- Fengtang Yang,
- Jen Harrow,
- Nabeel A. Affara,
- and Chris Tyler-Smith
Genome Res. January 2016 26: 130-139; Published in Advance November 11, 2015, doi:10.1101/gr.188839.114
...the species (Mueller et al. 2013). Human X Chromosomes contain multiple inverted repeats with high sequence identity, enriched for testis-expressed genes (Warburton et al. 2004). Mice have a greater number of X-ampliconic genes thanhumans, apparently driven by a genomic conflict between X and Y sequences...
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Research: Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs
- Adrian A. Valli,
- Bruno A.C.M. Santos,
- Silvia Hnatova,
- Andrew R. Bassett,
- Attila Molnar,
- Betty Y. Chung,
- and David C. Baulcombe
Genome Res. April 2016 26: 519-529; Published in Advance March 11, 2016, doi:10.1101/gr.199703.115
...with the indicated plasmids in solidmedia containing either paromomycin (test for plasmid integration), spectinomycin (test for splicing events), or 5-Fl (test for amiRNA production). Valli et al. 524 Genome Research www..org The miRNA genes of C. reinhardtii, like the DCL3 protein, also have nonplant...
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ARTICLE: Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27
- Natalay Kouprina,
- Adam Pavlicek,
- Vladimir N. Noskov,
- Greg Solomon,
- John Otstot,
- William Isaacs,
- John D. Carpten,
- Jeffrey M. Trent,
- Joanna Schleutker,
- J. Carl Barrett,
- Jerzy Jurka,
- and Vladimir Larionov
Genome Res. November 2005 15: 1477-1486; doi:10.1101/gr.4212705
...and African Great Ape SPANX-B genes contain only two copies of the 9-bp repeat, the human SPANX-B gene exhibits two additional copies of the repeat. Asterisks mark deviations from the repeat consensus. We also checked for the occurrence of genomic rearrangements in the SPANX-C locus in X-linked prostate...
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Research: Assessment of palindromes as platforms for DNA amplification in breast cancer
- Jamie Guenthoer,
- Scott J. Diede,
- Hisashi Tanaka,
- Xiaoyu Chai,
- Li Hsu,
- Stephen J. Tapscott,
- and Peggy L. Porter
Genome Res. February 2012 22: 232-245; Published in Advance July 13, 2011, doi:10.1101/gr.117226.110
...graph) and MDA231 (upper graph) containing a normally occurring inverted repeat (Warburton et al. 2004). Graphs display P-values (−10log10) of GAPF analyses comparing cell lines with normal PBL reference. The solid bars under the graphs mark GAPF-positive regions (P-value [−10log10] > 30, run > 50 bp...
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Research: Human postmeiotic sex chromatin and its impact on sex chromosome evolution
- Ho-Su Sin,
- Yosuke Ichijima,
- Eitetsu Koh,
- Mikio Namiki,
- and Satoshi H. Namekawa
Genome Res. May 2012 22: 827-836; Published in Advance February 28, 2012, doi:10.1101/gr.135046.111
...T, Dean MD, Nachman MW. 2010. Widespread overexpression of the X chromosome in sterile F1 hybrid mice. PLoS Genet 6: e1001148. doi: 10.1371/journal.pgen.1001148. Greaves IK, Rangasamy D, Devoy M, Marshall Graves JA, Tremethick DJ. 2006. The X and Y chromosomes assemble into H2A.Z-containing...
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Research: Localized hypermutation and associated gene losses in legume chloroplast genomes
- Alan M. Magee,
- Sue Aspinall,
- Danny W. Rice,
- Brian P. Cusack,
- Marie Sémon,
- Antoinette S. Perry,
- Saša Stefanović,
- Dan Milbourne,
- Susanne Barth,
- Jeffrey D. Palmer,
- John C. Gray,
- Tony A. Kavanagh,
- and Kenneth H. Wolfe
Genome Res. December 2010 20: 1700-1710; Published in Advance October 26, 2010, doi:10.1101/gr.111955.110
.... 1991a; Smith et al. 1991), and shown by a dot-matrix plot in Supplemental Figure S2A, P. sativum accD contains several in-frame internal repeats of up to 37 codons long. L. sativus accD has a similarly repetitive structure, but the sections of the gene that are repeated are different in the two species...
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REVIEW: Recombination Hot Spots and Human Disease
- Smita M. Purandare and
- Pragna I. Patel
Genome Res. August 1, 1997 7: 773-786; doi:10.1101/gr.7.8.773
...(CYP–REP), containing an Alu element and a tandem 10-bp direct repeat flanks the active CYP2D6 gene in the wild-type allele. It is thought that the CYP2D6 deletion and duplication alleles are reciprocal products, generated by homologous recombination between nonallelic CYP–REP elements. Large...

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