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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...Evolutionary expansion of DNA hypomethylation in the mammalian germline Jianghan Qu1, Emily Hodges2, Antoine Molaro3,4, Pascal Gagneux5, Matthew D. Dean1, Gregory J. Hannon3,6,7,8 and Andrew D. Smith1 1Molecular and Computational Biology Section, Division of Biological Sciences, University...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...well-studied human and mouse species. The majority (77%) of newly detected miRNA genes emerged relatively recently in evolution on one of the terminal branches of the phylogeny for the investigated species (Supplemental Table S1), whereas a significantly smaller proportion of previously known mi...
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Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- Michael F. Lin,
- Pouya Kheradpour,
- Stefan Washietl,
- Brian J. Parker,
- Jakob S. Pedersen,
- and Manolis Kellis
Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
...of 29 mammalian s to provide a systematic annotation of individual functional elements embedded within protein-coding regions throughout the human . Since the average codon site in these multiple sequence alignments shows about four synonymous substitutions, we predict that overlapping functional...
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Research: Human long intrinsically disordered protein regions are frequent targets of positive selection
- Arina Afanasyeva,
- Mathias Bockwoldt,
- Christopher R. Cooney,
- Ines Heiland,
- and Toni I. Gossmann
Genome Res. July 2018 28: 975-982; Published in Advance June 1, 2018, doi:10.1101/gr.232645.117
...proteins with intrinsically disordered regions and their ordered counterparts. Our comparative approach with data from more than 90 mammalian s uses a priori knowledge of disordered protein regions, and we show that this increases the power to detect positive selection by an order of magnitude. We can...
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Research: Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
- Antoine Molaro,
- Janet M. Young,
- and Harmit S. Malik
Genome Res. April 2018 28: 460-473; Published in Advance March 16, 2018, doi:10.1101/gr.229799.117
.... Mammalian short H2A repertoires and phylogeny. (A) Maximum-likelihood protein phylogeny of the histone fold domain of canonical H2A and H2A variants from Xenopus, chicken, and representative mammalian species. Bootstrap values are shown at all nodes that have >50% bootstrap support. The tree is rooted using...
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Review: What fraction of the human genome is functional?
- Chris P. Ponting and
- Ross C. Hardison
Genome Res. November 2011 21: 1769-1776; Published in Advance August 29, 2011, doi:10.1101/gr.116814.110
...307: 80–82. PollardKS,HubiszMJ, RosenbloomKR, SiepelA. 2010.Detectionofnonneutral substitution rates on mammalian phylogenies. Genome Res 20: 110–121. PontingCP, Goodstadt L. 2009. Separating derived from ancestral features of mouse and human s. Biochem Soc Trans 37: 734–739. Ponting CP, Nellaker C...
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Research: Frac-seq reveals isoform-specific recruitment to polyribosomes
- Timothy Sterne-Weiler,
- Rocio Teresa Martinez-Nunez,
- Jonathan M. Howard,
- Ivan Cvitovik,
- Sol Katzman,
- Muhammad A. Tariq,
- Nader Pourmand,
- and Jeremy R. Sanford
Genome Res. October 2013 23: 1615-1623; Published in Advance June 19, 2013, doi:10.1101/gr.148585.112
...by highthroughput sequencing. Nat Genet 40: 1413–1415. Pfeiffer BD, Truman JW, Rubin GM. 2012. Using translational enhancers to increase transgene expression in Drosophila. Proc Natl Acad Sci 109: 6626–6631. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2010. Detection of nonneutral substitution rates...
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Research: Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence
- Wouter Meuleman,
- Daan Peric-Hupkes,
- Jop Kind,
- Jean-Bernard Beaudry,
- Ludo Pagie,
- Manolis Kellis,
- Marcel Reinders,
- Lodewyk Wessels,
- and Bas van Steensel
Genome Res. February 2013 23: 270-280; Published in Advance November 2, 2012, doi:10.1101/gr.141028.112
...that during evolution changes in A/T content have driven the relocation of genes to and from the nuclear lamina, in tight association with changes in expression level. Taken together, these results reveal that the spatial organization of mammalian genomes is highly conserved and tightly linked to local...
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Letter: Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
- Tristan Lefébure and
- Michael J. Stanhope
Genome Res. July 2009 19: 1224-1232; Published in Advance March 20, 2009, doi:10.1101/gr.089250.108
...(dN) and synonymous (dS) substitutions, with dN significantly different from dS taken as evidence of non-neutral evolution. Some of these new approaches are designed to detect positive selection at individual sites and lineages and represent a significant advancement over many earlier methods, which...
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LETTER: A comparison of the human and chimpanzee olfactory receptor gene repertoires
- Yoav Gilad,
- Orna Man,
- and Gustavo Glusman
Genome Res. February 2005 15: 224-230; doi:10.1101/gr.2846405
...mammalian gene superfamily, with &gt;1000 members. In humans, but not in mice or dogs, the majority of OR genes have become pseudogenes, suggesting that OR genes in humans evolve under different selection pressures than in other mammals. To explore this further, we compare the OR gene repertoire of human...

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