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Resource: Improved definition of the mouse transcriptome via targeted RNA sequencing
- Giovanni Bussotti,
- Tommaso Leonardi,
- Michael B. Clark,
- Tim R. Mercer,
- Joanna Crawford,
- Lorenzo Malquori,
- Cedric Notredame,
- Marcel E. Dinger,
- John S. Mattick,
- and Anton J. Enright
Genome Res. May 2016 26: 705-716; doi:10.1101/gr.199760.115
...start (Methods). To independently validate alternative transcription start sites, we analyzed Mouse ENCODE ChIP-seq profiles and DNase I hypersensitivity (DHS) data on tissue samples matching those considered in this work. A total of nine RNA polymerase II and EP300 ChIP-seq data sets (Fig. 4A) along...
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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...not allow comparison of the accumulation levels of modifications between samples caused by the lack of normalization of samples (Bonhoure et al. 2014), that is, among different developmental stages (Li et al. 2014). We thus performed quantitative ChIP-seq or “spike-in” ChIP-seq (Bonhoure et al. 2014; Li et...
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Research: CTCF looping is established during gastrulation in medaka embryos
- Ryohei Nakamura,
- Yuichi Motai,
- Masahiko Kumagai,
- Candice L. Wike,
- Haruyo Nishiyama,
- Yoichiro Nakatani,
- Neva C. Durand,
- Kaori Kondo,
- Takashi Kondo,
- Tatsuya Tsukahara,
- Atsuko Shimada,
- Bradley R. Cairns,
- Erez Lieberman Aiden,
- Shinichi Morishita,
- and Hiroyuki Takeda
Genome Res. June 2021 31: 968-980; Published in Advance May 18, 2021, doi:10.1101/gr.269951.120
...polymorphic medaka strains, d-rR and Hamochi, were used as experimental and spike-in chromatin, respectively. The spike-in normalized CTCF ChIP-seq signals of 6 and 30 hpf showed comparable levels (Supplemental Fig. S2A,B), suggesting that the CTCF is indeed binding to chromatin from the early stages...
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Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...TSA treatment in mESCs. Samples were derived from three biological replicate experiments. (C) Representative snapshot of genomic region showing H3ac ChIP-seq read coverage calibrated to the spike-in galGal4 . (D) Metaplot showing the average calibrated H3ac ChIP-seq signal from DMSO- or TSA...
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Research: Promoter-specific dynamics of TATA-binding protein association with the human genome
- Yuko Hasegawa and
- Kevin Struhl
Genome Res. December 2019 29: 1939-1950; Published in Advance November 15, 2019, doi:10.1101/gr.254466.119
...al. 2014. Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Res 24: 1157–1168. doi:10.1101/gr.168260.113 ↵Chen WY, Zhang J, Geng H, Du Z, Nakadai T, Roeder RG. 2013. A TAF4 coactivator function for E proteins that involves enhanced...
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Research: Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest
- Andrea Orioli,
- Viviane Praz,
- Philippe Lhôte,
- and Nouria Hernandez
Genome Res. May 2016 26: 624-635; Published in Advance March 3, 2016, doi:10.1101/gr.201400.115
...-specific ChIP-qPCR (Supplemental Fig. S1A), we performed Pol III ChIP-seq in IMR90hTert cells. From a set of 110–170 million aligned reads per condition (Supplemental Table S1, column I), we generated Pol III enrichment profiles at a compilation of 622 tRNA genes (Chan and Lowe 2009), as well as other...
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Research: Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock
- François Mange,
- Viviane Praz,
- Eugenia Migliavacca,
- Ian M. Willis,
- Frédéric Schütz,
- Nouria Hernandez,
- and the CycliX Consortium
Genome Res. June 2017 27: 973-984; Published in Advance March 24, 2017, doi:10.1101/gr.217521.116
...spiked with a small, constant amount of human chromatin for sample-to-sample normalization (Bonhoure et al. 2014). We analyzed a set of loci either annotated as Pol III genes in the assembly or found significantly occupied by Pol III in one of our previousChIP-seq analyses (Canella 2012; Bonhoure et al...
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