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Research: Genomic analyses provide insights into peach local adaptation and responses to climate change
- Yong Li,
- Ke Cao,
- Nan Li,
- Gengrui Zhu,
- Weichao Fang,
- Changwen Chen,
- Xinwei Wang,
- Jian Guo,
- Qi Wang,
- Tiyu Ding,
- Jiao Wang,
- Liping Guan,
- Junxiu Wang,
- Kuozhan Liu,
- Wenwu Guo,
- Pere Arús,
- Sanwen Huang,
- Zhangjun Fei,
- and Lirong Wang
Genome Res. April 2021 31: 592-606; Published in Advance March 9, 2021, doi:10.1101/gr.261032.120
...temperature 18°C, annual average air humidity >70%, annual precipitation >1400 mm) (Supplemental Table S3).Genome-wide environmental association studies of 51 environmental variablesAlthough we obtained candidate genes underlying adaptation by identifying selective sweeps, many adaptive events in natural...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...of electrophoretic mobility shift assays (EMSA) (Hellman and Fried 2007). In an EMSA, labeled probes corresponding to the DNA of interest are synthesized or isolated and are consequently incubated with a purified protein of interest or with a mixture of proteins (e.g., a nuclear extract). To determine if direct...
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METHODS: Whole Genome Analysis of Genetic Alterations in Small DNA Samples Using Hyperbranched Strand Displacement Amplification and Array–CGH
- José M. Lage,
- John H. Leamon,
- Tanja Pejovic,
- Stefan Hamann,
- Michelle Lacey,
- Deborah Dillon,
- Richard Segraves,
- Bettina Vossbrinck,
- Antonio González,
- Daniel Pinkel,
- Donna G. Albertson,
- Jose Costa,
- and Paul M. Lizardi
Genome Res. February 1, 2003 13: 294-307; doi:10.1101/gr.377203
...the spot, resulting in unreliable ratios. Remarkably, in an experiment in which two different yeast s were amplified by Bst DNA polymerase, and compared by array–CGH (Fig. 3 , panel in lower right), the Cy3/Cy5 ratios were found to be very close to 1:1, indicating that the over-representation and under...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...(Hartmann et al. 2017; Yang et al. 2019; Fouché et al. 2023). SVs can influence gene expression, for example by the insertion or deletion of regulatory elements upstream of a gene (Butelli et al. 2012). Deleterious SVs are typically eliminated from populations by strong purifying selection (Elyashiv et al...
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Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...that for pleiotropic CREs, there is no simple relationship between sequence and functional conservation between species.View larger version: In this window In a new window Figure 5. CRE sequence conservation patterns per tissue. (A) Weak negative selection inferred from human polymorphisms, separated by the tissue...
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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...). Complementary approaches such as optical mapping of single >150-kb molecules via nanochannel arrays (Lam et al. 2012) or chromatin interaction mapping (Lieberman-Aiden et al. 2009) likewise facilitate assemblies of ever-increasing contiguity and completeness. Apart from intensely studied model organisms, e...
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Research: RNA structure replaces the need for U2AF2 in splicing
- Chien-Ling Lin,
- Allison J. Taggart,
- Kian Huat Lim,
- Kamil J. Cygan,
- Luciana Ferraris,
- Robbert Creton,
- Yen-Tsung Huang,
- and William G. Fairbrother
Genome Res. January 2016 26: 12-23; Published in Advance November 13, 2015, doi:10.1101/gr.181008.114
...and 5′ ss into close proximity (Fig. 3C). While the selected example contains a striking amount of intron bridging structure, it was not clear whether shorter runs of AC and GT repeats could also create bridging interactions. To determine the minimal number of repeats that are required to drive intron...
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Perspective: What does our genome encode?
- John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
...be exercised in selecting cell and tissue types, ideally with close input from the disease communities. Second, selection of transcription factors should be well-matched to known aspects of disease physiology or that of pathogenic cell types. Finally, continuously updated maps of connections between distal...
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Research: Massive turnover of functional sequence in human and other mammalian genomes
- Stephen Meader,
- Chris P. Ponting,
- and Gerton Lunter
Genome Res. October 2010 20: 1335-1343; Published in Advance August 6, 2010, doi:10.1101/gr.108795.110
...subject to selective constraint and thus may be considered functional. In addition, we define g as the full extent of the euchromatic sequence of a , and gsel = g 3 asel as the amount of sequence that has been subject to purifying selection.) This estimate of asel was obtained by contrasting nucleotide...
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Method: mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain
- Paul Hammer,
- Michaela S. Banck,
- Ronny Amberg,
- Cheng Wang,
- Gabriele Petznick,
- Shujun Luo,
- Irina Khrebtukova,
- Gary P. Schroth,
- Peter Beyerlein,
- and Andreas S. Beutler
Genome Res. June 2010 20: 847-860; Published in Advance May 7, 2010, doi:10.1101/gr.101204.109
.... Eight sequencing libraries were constructed using cDNA from independent animals (two SNL and two control for each time point, 2 wk and 2 mo) and sequenced on an Illumina Genome Analyzer II (GAII) as described (Bentley et al. 2008). Genome-wide read mapping Of 260millionhigh-qualitymRNA-seq reads...
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