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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...for each autosome and the X Chromosome revealed that supercoils on X propagate over a larger distance than those on autosomes, and the difference corresponds to the difference in extent of the GC-rich region (Fig. 2B). However, because X-linked genes undergo a dosage compensation process in which...
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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
.... Conserved nucleosome positioning defines replication origins. Genes Dev 24: 748–753. Ercan S, Lubling Y, Segal E, Lieb JD. 2011. High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Genome Res 21: 237–244. Gerstein MB, Rozowsky J, Yan K-K, Wang D, Cheng C, Brown JB, Davis CA...
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Research: Extreme HOT regions are CpG-dense promoters in C. elegans and humans
- Ron A.-J. Chen,
- Przemyslaw Stempor,
- Thomas A. Down,
- Eva Zeiser,
- Sky K. Feuer,
- and Julie Ahringer
Genome Res. July 2014 24: 1138-1146; Published in Advance March 20, 2014, doi:10.1101/gr.161992.113
...(Fenouil et al. 2012; Vavouri and Lehner 2012). We therefore investigated the relationship between CpG density and chromatin accessibility at C. elegans promoters. We first separated promoters of highly expressed genes into those with high and low CpG density and compared their nucleosome distribution...
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Resource: The time-resolved transcriptome of C. elegans
- Max E. Boeck,
- Chau Huynh,
- Lou Gevirtzman,
- Owen A. Thompson,
- Guilin Wang,
- Dionna M. Kasper,
- Valerie Reinke,
- LaDeana W. Hillier,
- and Robert H. Waterston
Genome Res. October 2016 26: 1441-1450; Published in Advance August 16, 2016, doi:10.1101/gr.202663.115
...reveal many more. Operons About 70% of C. elegans transcripts are trans-spliced, with the SL1 splice leader used for genes with independent promoters and the Figure 2. The relative abundance of novel versus known junctions in alternatively spliced pairs within WormBase gene models. For each splice...
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Research: Broad chromosomal domains of histone modification patterns in C. elegans
- Tao Liu,
- Andreas Rechtsteiner,
- Thea A. Egelhofer,
- Anne Vielle,
- Isabel Latorre,
- Ming-Sin Cheung,
- Sevinc Ercan,
- Kohta Ikegami,
- Morten Jensen,
- Paulina Kolasinska-Zwierz,
- Heidi Rosenbaum,
- Hyunjin Shin,
- Scott Taing,
- Teruaki Takasaki,
- A. Leonardo Iniguez,
- Arshad Desai,
- Abby F. Dernburg,
- Hiroshi Kimura,
- Jason D. Lieb,
- Julie Ahringer,
- Susan Strome,
- and X. Shirley Liu
Genome Res. February 2011 21: 227-236; Published in Advance December 22, 2010, doi:10.1101/gr.115519.110
...chromosome and is most concentrated upstream of active X-linked genes. Since then, a limited number of histone modifications or variants have been mapped in C. elegans. These studies showed that the organization of C. elegans genic chromatin has properties similar to those of other organisms and additionally...
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Research: Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
- Swann Floc'hlay,
- Emily S. Wong,
- Bingqing Zhao,
- Rebecca R. Viales,
- Morgane Thomas-Chollier,
- Denis Thieffry,
- David A. Garfield,
- and Eileen E.M. Furlong
Genome Res. February 2021 31: 211-224; Published in Advance December 11, 2020, doi:10.1101/gr.266338.120
...embryonic development. We collected Drosophila F1 hybrid embryos from eight crosses and quantified allele-specific changes in TF occupancy (using open chromatin [ATAC-seq] as a proxy), enhancer and promoter activity (using H3K27ac or H3K4me3 and H3K27ac ChIP-seq as proxies, respectively), and gene...
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Research: Critical roles of long noncoding RNAs in Drosophila spermatogenesis
- Kejia Wen,
- Lijuan Yang,
- Tuanlin Xiong,
- Chao Di,
- Danhui Ma,
- Menghua Wu,
- Zhaoyu Xue,
- Xuedi Zhang,
- Li Long,
- Weimin Zhang,
- Jiaying Zhang,
- Xiaolin Bi,
- Junbiao Dai,
- Qiangfeng Zhang,
- Zhi John Lu,
- and Guanjun Gao
Genome Res. September 2016 26: 1233-1244; Published in Advance August 11, 2016, doi:10.1101/gr.199547.115
...-PCR, respectively. RpL32 was used as an internal control. Values represent means ± SEM for three biological replicates. Mst35Ba was used as a testis-specific control. X8C (a Chromosome X-linked intergenic region that has been determined to be silent for transcription) was used as a negative control to rule out...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...that the interplay of chromatin organization with other epigenetic features extends beyond normal neurodevelopment into neurodevelopmental disorders.Rett syndromeDue to variants in the X-linked gene MeCP2, Rett syndrome is a neurodevelopmental condition characterized by a brief period of typical neurodevelopment...
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