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Resource: Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data
- Fabian A. Buske,
- Denis C. Bauer,
- John S. Mattick,
- and Timothy L. Bailey
Genome Res. July 2012 22: 1372-1381; Published in Advance May 1, 2012, doi:10.1101/gr.130237.111
...Research, Sydney, 2010 NSW, Australia Abstract Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand in its major groove. This sequence-specific process offers a potent mechanism for targeting genomic loci of interest that is of great value...
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Research: Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)
- Sünje J. Pamp,
- Eoghan D. Harrington,
- Stephen R. Quake,
- David A. Relman,
- and Paul C. Blainey
Genome Res. June 2012 22: 1107-1119; Published in Advance March 20, 2012, doi:10.1101/gr.131482.111
...hypothesize that they are involved in modulation of host responses. The presence of polymorphisms among mouse SFB genomes suggests the evolution of distinct SFB lineages. Overall, our results reveal several aspects of SFB adaptation to the mammalian intestinal tract. Footnotes ↵ 7 Corresponding...
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Letter: Genomic mapping of binding regions for the Ecdysone receptor protein complex
- Zareen Gauhar,
- Ling V. Sun,
- Sujun Hua,
- Christopher E. Mason,
- Florian Fuchs,
- Tong-Ruei Li,
- Michael Boutros,
- and Kevin P. White
Genome Res. June 2009 19: 1006-1013; Published in Advance February 23, 2009, doi:10.1101/gr.081349.108
...) that differentiates in response to 20-hydroxyecdysone (20-HE). 20-HE, the natural ligand of this complex, controls major aspects of insect development, including molting, metamorphosis, and reproduction. Direct gene targets of 20-HE signaling were identified by combining this physical binding-site profiling with gene...
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REVIEW: Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
- Victoria P. Belancio,
- Dale J. Hedges,
- and Prescott Deininger
Genome Res. March 2008 18: 343-358; Published in Advance February 6, 2008, doi:10.1101/gr.5558208
...a nick into the plus strand and the structure is resolved to utilize the 3′ end as a primer for the second-strand DNA synthesis (shown in light blue) by an unknown polymerase activity. Finally, the two nicks in the cellular DNA are repaired to complete the L1 integration event. Some aspects of L1...
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Method: Digital transcriptome profiling from attomole-level RNA samples
- Fatih Ozsolak,
- Alon Goren,
- Melissa Gymrek,
- Mitchell Guttman,
- Aviv Regev,
- Bradley E. Bernstein,
- and Patrice M. Milos
Genome Res. April 2010 20: 519-525; Published in Advance February 4, 2010, doi:10.1101/gr.102129.109
...transcriptome surveys from subnanogram RNA quantities in an amplification/ligation-free manner. LQ-RNAseq involves first-strand cDNA synthesis from RNA templates, followed by 3′ polyA tailing of the single-stranded cDNA products and direct single molecule sequencing. We applied LQ-RNAseq to profile S...
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Research: Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells
- Timothy J. Looney,
- Li Zhang,
- Chih-Hsin Chen,
- Jae Hyun Lee,
- Sheila Chari,
- Frank Fuxiang Mao,
- Mattia Pelizzola,
- Lu Zhang,
- Ryan Lister,
- Samuel W. Baker,
- Croydon J. Fernandes,
- Jedidiah Gaetz,
- Kara M. Foshay,
- Kayla L. Clift,
- Zhenyu Zhang,
- Wei-Qiang Li,
- Eric J. Vallender,
- Ulrich Wagner,
- Jane Yuxia Qin,
- Katelyn J. Michelini,
- Branimir Bugarija,
- Donghyun Park,
- Emmanuel Aryee,
- Thomas Stricker,
- Jie Zhou,
- Kevin P. White,
- Bing Ren,
- Gary P. Schroth,
- Joseph R. Ecker,
- Andy Peng Xiang,
- and Bruce T. Lahn
Genome Res. February 2014 24: 267-280; Published in Advance December 5, 2013, doi:10.1101/gr.143891.112
...et al. 2005; Friedman and Kaestner 2006). FAC1 is a component of the nucleosome remodeling factor which catalyzes nucleosome displacement (Wysocka et al. 2006). Robustness of occlusion We examined the correlation of global gene expression profile between 129TF and its fusion partner, and between...
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ARTICLE: Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
- Nathan D. Trinklein,
- Ulaş Karaöz,
- Jiaqian Wu,
- Anason Halees,
- Shelley Force Aldred,
- Patrick J. Collins,
- Deyou Zheng,
- Zhengdong D. Zhang,
- Mark B. Gerstein,
- Michael Snyder,
- Richard M. Myers,
- and Zhiping Weng
Genome Res. June 2007 17: 720-731; doi:10.1101/gr.5716607
...with transient transfection assays and rapid amplification of cDNA ends (5′-RACE) experiments, and demonstrated the power of an analytical approach that integrates the data from many -scale experiments. Extrapolating from these results, we estimate that there are at least 35% more novel promoters than currently...
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