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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...skeletal muscle from which we observed an increase in chimeric mtRNA associated with aging (PRJNA793055). When we compared each samples’ sum total of chimeric mtRNA transcripts for all rat samples to the global transcriptome, we identified 6104 differentially expressed genes associated with the chimeric mt...
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Research: Allele-specific control of replication timing and genome organization during development
- Juan Carlos Rivera-Mulia,
- Andrew Dimond,
- Daniel Vera,
- Claudia Trevilla-Garcia,
- Takayo Sasaki,
- Jared Zimmerman,
- Catherine Dupont,
- Joost Gribnau,
- Peter Fraser,
- and David M. Gilbert
Genome Res. June 2018 28: 800-811; Published in Advance May 7, 2018, doi:10.1101/gr.232561.117
...for most asynchronous regions (see text for details).Next, we analyzed the global chromatin properties of the genomic regions in which the two alleles replicate synchronously in hybrid mouse ESCs, comparing chromosomal segments that replicate early vs. late during S-phase. Consistent with previous studies...
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Research: The chromatin environment shapes DNA replication origin organization and defines origin classes
- Christelle Cayrou,
- Benoit Ballester,
- Isabelle Peiffer,
- Romain Fenouil,
- Philippe Coulombe,
- Jean-Christophe Andrau,
- Jacques van Helden,
- and Marcel Méchali
Genome Res. December 2015 25: 1873-1885; Published in Advance November 11, 2015, doi:10.1101/gr.192799.115
..., compared to 97 reads/peak for all IS), suggesting that replication initiation is favored in proximity of the transcriptionmachinery. The superposition of the “paused” form of RNA Pol II (inhibition of RNA Pol II initiation by flavopiridol) with global RNA Pol II at origins (Supplemental Fig. S6) suggests...
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Research: Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery
- Xiuli Bi,
- Ying-Juan Cheng,
- Bo Hu,
- Xiaoli Ma,
- Rui Wu,
- Jia-Wei Wang,
- and Chang Liu
Genome Res. July 2017 27: 1162-1173; Published in Advance April 6, 2017, doi:10.1101/gr.215186.116
...with experiments showing global rearrangement of chromatin triggered by various environmental and developmental factors, such as light (Barneche et al. 2014; Bourbousse et al. 2015), microbial infection (Pavet et al. 2006), and cell differentiation (Tessadori et al. 2007), all these studies highlight a close...
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Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
...replication. We therefore aimed to investigate the role of H3.3 in DNA replication and origin firing and to adapt tools to study these processes to the C. elegans model system.ResultsGenome-wide replication timing in C. elegans embryosWe first determined whether loss of H3.3 causes global changes...
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Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
- Jing Liu,
- Zongji Wang,
- Jing Li,
- Luohao Xu,
- Jiaqi Liu,
- Shaohong Feng,
- Chunxue Guo,
- Shengchan Chen,
- Zhanjun Ren,
- Jinpeng Rao,
- Kai Wei,
- Yuezhou Chen,
- Erich D. Jarvis,
- Guojie Zhang,
- and Qi Zhou
Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
...-linked region exhibited half the female read coverage relative to autosomes (Fig. 1E). The two evolutionary strata constituted the SDR of emu sex chromosomes and showed a generally male-biased gene expression pattern of Z-linked genes because of the lack of global dosage compensation (Fig. 1E; Supplemental...
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Research: Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
- Christelle Cayrou,
- Philippe Coulombe,
- Alice Vigneron,
- Slavica Stanojcic,
- Olivier Ganier,
- Isabelle Peiffer,
- Eric Rivals,
- Aurore Puy,
- Sabine Laurent-Chabalier,
- Romain Desprat,
- and Marcel Méchali
Genome Res. September 2011 21: 1438-1449; Published in Advance July 12, 2011, doi:10.1101/gr.121830.111
...’Informatique, de Robotique et deMicroelectronique de Montpellier, UM2-CNRS, 34095 Montpellier, France In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle. Their genomic organization and their genetic nature remain elusive. Here, we characterized Oris by nascent strand (NS...
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Research: Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
- Gilad D. Evrony,
- Dwight R. Cordero,
- Jun Shen,
- Jennifer N. Partlow,
- Timothy W. Yu,
- Rachel E. Rodin,
- R. Sean Hill,
- Michael E. Coulter,
- Anh-Thu N. Lam,
- Divya Jayaraman,
- Dianne Gerrelli,
- Diana G. Diaz,
- Chloe Santos,
- Victoria Morrison,
- Antonella Galli,
- Ulrich Tschulena,
- Stefan Wiemann,
- M. Jocelyne Martel,
- Betty Spooner,
- Steven C. Ryu,
- Princess C. Elhosary,
- Jillian M. Richardson,
- Danielle Tierney,
- Christopher A. Robinson,
- Rajni Chibbar,
- Dana Diudea,
- Rebecca Folkerth,
- Sheldon Wiebe,
- A. James Barkovich,
- Ganeshwaran H. Mochida,
- James Irvine,
- Edmond G. Lemire,
- Patricia Blakley,
- and Christopher A. Walsh
Genome Res. August 2017 27: 1323-1335; Published in Advance June 19, 2017, doi:10.1101/gr.219899.116
...samples by RNA-seq and RT-PCR is not due to overall splicing inefficiency in the assayed samples or global capture of unspliced transcripts during RNA-seq sample preparation, but rather a specific feature of intron 6. The baseline decreased efficiency of intron 6 splicing compared to other intronsmight...
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Research: Dynamic effects of interacting genes underlying rice flowering-time phenotypic plasticity and global adaptation
- Tingting Guo,
- Qi Mu,
- Jinyu Wang,
- Adam E. Vanous,
- Akio Onogi,
- Hiroyoshi Iwata,
- Xianran Li,
- and Jianming Yu
Genome Res. May 2020 30: 673-683; Published in Advance April 16, 2020, doi:10.1101/gr.255703.119
...conditions requires a concerted effort from both public and private sectors. Although advances in genomics, breeding, and precision agriculture have been recognized as solution components for global food security (McCouch et al. 2013; Huang et al. 2015; Zeng et al. 2017; Wang et al. 2018), enriched knowledge...
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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...with Tigmint using synteny with the H. melpomene v2.5 .Pan- alignmentIn comparison to using a single as a reference, a pan- represents a composite of different s and serves as a global reference with which to make comparisons between s (e.g., conservation and unique sequences) or features (e.g., gene and TE...

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