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Research: Genome-wide analysis of long noncoding RNA stability
- Michael B. Clark,
- Rebecca L. Johnston,
- Mario Inostroza-Ponta,
- Archa H. Fox,
- Ellen Fortini,
- Pablo Moscato,
- Marcel E. Dinger,
- and John S. Mattick
Genome Res. May 2012 22: 885-898; Published in Advance March 9, 2012, doi:10.1101/gr.131037.111
...-transcriptional regulation of lncRNAs and their half-lives. Although many are easily detectable by a variety of techniques, it has been assumed that lncRNAs are generally unstable, but this has not been examined genome-wide. Utilizing a custom noncoding RNA array, we determined the half-lives of ∼800 lncRNAs and ∼12,000 mRNAs...
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Research: PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX
- Erwan Delbarre,
- Kristina Ivanauskiene,
- Jane Spirkoski,
- Akshay Shah,
- Kristin Vekterud,
- Jan Øivind Moskaug,
- Stig Ove Bøe,
- Lee H. Wong,
- Thomas Küntziger,
- and Philippe Collas
Genome Res. June 2017 27: 913-921; Published in Advance March 24, 2017, doi:10.1101/gr.215830.116
...oligonucleotides were from Invitrogen (MSS212902 (Atrx siRNA), MSS273927 (Daxx siRNA), and MSS205135 (Hira siRNA). H3.3-SNAP labeling and immunofluorescence MEFswere transfectedwithH3.3-SNAP and treated 24 h later as described in Supplemental Figure 3 (Ray-Gallet et al. 2011). After treatment, cells were processed...
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Research: H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2
- Carol C.L. Chen,
- Preeti Goyal,
- Mohammad M. Karimi,
- Marie H. Abildgaard,
- Hiroshi Kimura,
- and Matthew C. Lorincz
Genome Res. January 2018 28: 37-51; Published in Advance December 11, 2017, doi:10.1101/gr.224717.117
...10ph at TTRs in H3K9me2-depleted ESCs is associated with changes in transcription, we conducted strand-specific mRNA-seq in Ehmt1−/− and Ehmt2−/− ESCs as well as the control WT parent line. In Ehmt2−/− and Ehmt1−/− ESCs , 950 and 791 genes were up-regulated (|z| > 0.8), respectively. Up-regulated...
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Research: H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress
- Anna Sawicka,
- Dominik Hartl,
- Malgorzata Goiser,
- Oliver Pusch,
- Roman R. Stocsits,
- Ido M. Tamir,
- Karl Mechtler,
- and Christian Seiser
Genome Res. November 2014 24: 1808-1820; Published in Advance August 18, 2014, doi:10.1101/gr.176255.114
...to phosphorylated H3S10 initiates a cascade of events leading to the release of RNA Polymerase II (RNAPII) from the promoter–proximal paused state (Zippo et al. 2009). In contrast to H3S10ph, the impact of H3S28 phosphorylation on stimulus-induced transcriptional regulation is much less studied (Sawicka and Seiser...
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Research: Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division
- Alexej Abyzov,
- Rebecca Iskow,
- Omer Gokcumen,
- David W. Radke,
- Suganthi Balasubramanian,
- Baikang Pei,
- Lukas Habegger,
- The 1000 Genomes Project Consortium,
- Charles Lee,
- and Mark Gerstein
Genome Res. December 2013 23: 2042-2052; Published in Advance September 11, 2013, doi:10.1101/gr.154625.113
...processed pseudogenes (Goncxalves et al. 2000; Zhang et al. 2003, 2004) yet avoid regulation by miRNAs 2013 Abyzov et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http...
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