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Research: Synchronized replication of genes encoding the same protein complex in fast-proliferating cells
- Ying Chen,
- Ke Li,
- Xiao Chu,
- Lucas B. Carey,
- and Wenfeng Qian
Genome Res. December 2019 29: 1929-1938; Published in Advance October 29, 2019, doi:10.1101/gr.254342.119
...replicated DNA (Stejskal et al. 2015). Consistently, in mouse embryonic stem cells (ESCs), the transcription rates of Pou5f1 and Nanog increased by 28% and 50%, respectively, upon DNA replication (Skinner et al. 2016). A similar phenomenon was also observed in UBC in human primary fibroblasts (Padovan...
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Research: MRC1-dependent scaling of the budding yeast DNA replication timing program
- Amnon Koren,
- Ilya Soifer,
- and Naama Barkai
Genome Res. June 2010 20: 781-790; Published in Advance March 10, 2010, doi:10.1101/gr.102764.109
..., Chang Y, Lyou TM, Townes D, Schu¨beler D, Gilbert DM. 2008. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6: e245. doi: 10.1371/journal.pbio.0060245. Huang M, Zhou Z, Elledge SJ. 1998. The DNA replication and damage checkpoint pathways induce...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...to alter the epigenetic landscape of early embryonic development, their impact on DNA sequence stability is unclear. Here, we leverage the strengths of the laboratory mouse model system to investigate whether a standard ART series (ovarian hyperstimulation, gamete isolation, IVF, embryo culture, and embryo...
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LETTER: Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas
- Neerja Karnani,
- Christopher Taylor,
- Ankit Malhotra,
- and Anindya Dutta
Genome Res. June 2007 17: 865-876; doi:10.1101/gr.5427007
...are boundary elements separating chromosomal domains with different chromatin environments. Although all the DNA in a eukaryotic cell replicates during the S phase of cell cycle, there is a great variability in the actual point in S phase when a given chromosomal segment replicates. Segments are known...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
...(Ameyar-Zazoua et al. 2012; Taliaferro et al. 2013). Lastly, AGO2 facilitates DNA double-strand break repair in Arabidopsis and cultured human cells (Wei et al. 2012). These studies point to critical nuclear roles for AGO2, but the in vivo relevance of these functions, particularly in mammals, remains...
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Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
- Benjamin P. Barré,
- Johan Hallin,
- Jia-Xing Yue,
- Karl Persson,
- Ekaterina Mikhalev,
- Agurtzane Irizar,
- Sylvester Holt,
- Dawn Thompson,
- Mikael Molin,
- Jonas Warringer,
- and Gianni Liti
Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
...) was deleted in NA and WA haploids using homologous recombination with a URA3 cassette. Then, the HPF1 segments to be swapped were PCR-amplified from the desired alleles with Platinum SuperFi (Thermo Fisher Scientific) DNA polymerase and swapped into the orthologous position of the recipient strain using...
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Research: Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis
- Kai Li,
- Jiayue Xu,
- Yanyun Luo,
- Dingfeng Zou,
- Ruiqin Han,
- Shunshun Zhong,
- Qing Zhao,
- Xinyu Mang,
- Mengzhen Li,
- Yanmin Si,
- Yan Lu,
- Pengyu Li,
- Cheng Jin,
- Zhipeng Wang,
- Fang Wang,
- Shiying Miao,
- Bo Wen,
- Linfang Wang,
- Yanni Ma,
- Jia Yu,
- and Wei Song
Genome Res. January 2021 31: 13-26; Published in Advance December 16, 2020, doi:10.1101/gr.264333.120
...%) was in accordance with the RNA-seq data set (Fig. 2C; Supplemental Fig. S3A). We next performed qRT-PCR with cDNA derived from germ cells, Sertoli cells, and Leydig cells to detect the expression pattern of the 20 candidate lncRNAs and observed that six candidate lncRNAs (1700027A15Rik, 1700006J14Rik, 1700052I22Rik...
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Research: Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
- Lisa Barros de Andrade e Sousa,
- Iris Jonkers,
- Laurène Syx,
- Ilona Dunkel,
- Julie Chaumeil,
- Christel Picard,
- Benjamin Foret,
- Chong-Jian Chen,
- John T. Lis,
- Edith Heard,
- Edda G. Schulz,
- and Annalisa Marsico
Genome Res. July 2019 29: 1087-1099; Published in Advance June 7, 2019, doi:10.1101/gr.245027.118
...Napoles et al. 2004). Subsequently, additional chromatin modifications are gained such as the histone variant macroH2A and DNA methylation of gene promoters (Escamilla-Del-Arenal et al. 2011). In recent years, progress has been made in identifying proteins that mediate Xist’s functions as well...
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Research: RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
- Heidi Dvinge,
- Jamie Guenthoer,
- Peggy L. Porter,
- and Robert K. Bradley
Genome Res. October 2019 29: 1591-1604; Published in Advance August 21, 2019, doi:10.1101/gr.246678.118
...-based assay to measure snRNA levels across five biological and three technical replicates, using the MCF-7 and HeLa cell lines. For the calculation of ΔCt, the mean of the 7SK RNA, the signal recognition particle RNA (7SL) and 5S rRNA within each tissue was used as a reference. ΔΔCt was calculated relative...
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RESEARCH: Homologs of the Yeast Longevity Gene LAG1 in Caenorhabditis elegans and Human
- James C. Jiang,
- Paul A. Kirchman,
- Marek Zagulski,
- Jay Hunt,
- and S. Michal Jazwinski
Genome Res. December 1, 1998 8: 1259-1272; doi:10.1101/gr.8.12.1259
...of the high GC content (80%) of this region that resulted in the generation of a stem–loop structure that was not replicated in the PCR. A full-length cDNA was amplified when GC melt was used to eliminate secondary structure in the DNA. The cloning procedure for human TRAM was similar to the cloning of LAG1Hs...

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