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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
...et al. 2014). Nucleosome positioning is highly dynamic, and its regulation is crucial to control chromatin accessibility, recruitment of chromatin modifiers, and transcription factors (Jiang and Pugh 2009; Prendergast and Semple 2011; Bartholomew 2014; Kornberg and Lorch 2020). In most s, genes...
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Research: Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans
- Tess E. Jeffers and
- Jason D. Lieb
Genome Res. January 2017 27: 75-86; Published in Advance November 14, 2016, doi:10.1101/gr.208173.116
...results are consistent with a model in which nucleosome fragility is encoded at the promoters of OPN-type genes, potentiating the high transcriptional plasticity observed at these sites. The presence of these promoter structures in yeast, human, and now C. elegans suggests a well-conserved strategy...
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Resource: Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. July 2019 29: 1198-1210; Published in Advance May 10, 2019, doi:10.1101/gr.245456.118
...or intragenic regions. These consensus clusters were generally of lower abundance, which is consistent with previous studies based on other techniques (Miura et al. 2006; Arribere and Gilbert 2013; Malabat et al. 2015). Given the pervasive nature of transcription in eukaryotes, they could be cryptic promoters...
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Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva,
- Roberta Carloni,
- Tatsiana Auchynnikava,
- Pin Tong,
- Juri Rappsilber,
- A. Arockia Jeyaprakash,
- Keith R. Matthews,
- and Robin C. Allshire
Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
...to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by “writer” and “eraser” enzymes, respectively. Nucleosomal PTMs are recognized by a variety of “reader” proteins...
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Research: An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation
- Andrew M. Lerner,
- Austin J. Hepperla,
- Gregory R. Keele,
- Hashem A. Meriesh,
- Hayretin Yumerefendi,
- David Restrepo,
- Seth Zimmerman,
- James E. Bear,
- Brian Kuhlman,
- Ian J. Davis,
- and Brian D. Strahl
Genome Res. November 2020 30: 1605-1617; Published in Advance October 5, 2020, doi:10.1101/gr.264283.120
...highly transcribed genes results from multiple rounds of transcription, in which each round of transcription mediates a fixed amount of H3K36 methylation per nucleosome across the population of cells. Additionally, the linear rate of H3K36me3 gain across protein-coding genes also suggests that Set2...
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Research: Cell type–specific DNA methylation at intragenic CpG islands in the immune system
- Aimée M. Deaton,
- Shaun Webb,
- Alastair R.W. Kerr,
- Robert S. Illingworth,
- Jacky Guy,
- Robert Andrews,
- and Adrian Bird
Genome Res. July 2011 21: 1074-1086; Published in Advance May 31, 2011, doi:10.1101/gr.118703.110
...RNAmediated histonemodifications (Allo et al. 2009) and the SWI/SNF nucleosome remodelling complex (Batsche et al. 2006) affect splicing in such a manner. It is, therefore, conceivable that differences in intragenic CGI methylation might alter transcript processing in specific cell types. Further studies are now required...
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Method: DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
- Kaifu Chen,
- Yuanxin Xi,
- Xuewen Pan,
- Zhaoyu Li,
- Klaus Kaestner,
- Jessica Tyler,
- Sharon Dent,
- Xiangwei He,
- and Wei Li
Genome Res. February 2013 23: 341-351; Published in Advance November 28, 2012, doi:10.1101/gr.142067.112
...modifications and variant turnover; more importantly, nucleosome physical organization directly regulates the accessibility of DNA to binding proteins such as transcription factors (He et al. 2010). Micrococcal nuclease (MNase) preferably digests chromatin at DNA sites that are not occupied by nucleosomes while...
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Research: Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization
- Alex Tsankov,
- Yoshimi Yanagisawa,
- Nicholas Rhind,
- Aviv Regev,
- and Oliver J. Rando
Genome Res. November 2011 21: 1851-1862; Published in Advance September 13, 2011, doi:10.1101/gr.122267.111
...by Illumina sequencing of mononucleosomal DNA isolated from mid-log cultures. For each species’ chromatin map, we determined the normalized nucleosome occupancy per base pair, correcting for differences in sequencing depth and MNase digestion level (see Methods). In order to investigate the sequence...
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LETTER: A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
- Travis N. Mavrich,
- Ilya P. Ioshikhes,
- Bryan J. Venters,
- Cizhong Jiang,
- Lynn P. Tomsho,
- Ji Qi,
- Stephan C. Schuster,
- Istvan Albert,
- and B. Franklin Pugh
Genome Res. July 2008 18: 1073-1083; Published in Advance June 12, 2008, doi:10.1101/gr.078261.108
...forms a barrier against which nucleosomes are packed, resulting in uniform positioning, which decays at farther distances from the barrier. We present evidence for a novel 3′ NFR that is present at &gt;95% of all genes. 3′ NFRs may be important for transcription termination and anti-sense initiation. We...
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Research: Extensive relationship between antisense transcription and alternative splicing in the human genome
- A. Sorana Morrissy,
- Malachi Griffith,
- and Marco A. Marra
Genome Res. August 2011 21: 1203-1212; Published in Advance June 30, 2011, doi:10.1101/gr.113431.110
...and nucleosome occupancy levels relative to nonoverlapping regions of the same genes. Nucleosome occupancy was highly correlated with Pol II abundance across overlapping regions and with concomitant increases in local alternative exon usage. These results are consistent with an antisense transcription...

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