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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...at single-base resolution from the annotated transcription start site (TSS) to transcription end site (TES), normalized to yeast spike-ins and the control sample (see Methods). (C) Smoothed splines of the read density profiles for gene CEMIP2 shown in panel B (see Methods). (D) Cumulative sums...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...is feasible for the yeast species investigated in the study but is less common in bacteria.It is notable that many of the problems facing the inference that a gene emerged de novo apply equally to discerning whether these genes arose through rapid divergence from functional genes that retain no similarity...
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Review: A systematic review on the biochemical threshold of mitochondrial genetic variants
- Karan K. Smith,
- Jesse D. Moreira,
- Callum R. Wilson,
- June O. Padera,
- Ashlee N. Lamason,
- Liying Xue,
- Deepa M. Gopal,
- David B. Flynn,
- and Jessica L. Fetterman
Genome Res. March 2024 34: 341-365; Published in Advance April 16, 2024, doi:10.1101/gr.278200.123
..., complexes, and tissues is unclear. We performed a systematic review of the literature to identify the biochemical threshold of specific pathogenic mtDNA variants based on the protein-encoding gene affected, tissue type, and degree of heteroplasmy (VAF). Our findings suggest that few studies have evaluated...
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Research: Widespread and precise reprogramming of yeast protein–genome interactions in response to heat shock
- Vinesh Vinayachandran,
- Rohit Reja,
- Matthew J. Rossi,
- Bongsoo Park,
- Lila Rieber,
- Chitvan Mittal,
- Shaun Mahony,
- and B. Franklin Pugh
Genome Res. March 2018 28: 357-366; Published in Advance February 14, 2018, doi:10.1101/gr.226761.117
...Widespread and precise reprogramming of yeast protein– interactions in response to heat shock Vinesh Vinayachandran1,2, Rohit Reja1,3, Matthew J. Rossi1, Bongsoo Park1,2, Lila Rieber1, Chitvan Mittal1, Shaun Mahony1 and B. Franklin Pugh1 1Center for Eukaryotic Gene Regulation, Department...
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Method: Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus
- Bharat Panwar,
- Benjamin J. Schmiedel,
- Shu Liang,
- Brandie White,
- Enrique Rodriguez,
- Kenneth Kalunian,
- Andrew J. McKnight,
- Rachel Soloff,
- Gregory Seumois,
- Pandurangan Vijayanand,
- and Ferhat Ay
Genome Res. April 2021 31: 659-676; Published in Advance March 5, 2021, doi:10.1101/gr.265249.120
...of different cell types, we here analyze six major circulating immune cell types from SLE patient blood. Our results show that presence of an interferon response signature stratifies patients into two distinct groups (IFNneg vs. IFNpos). Comparing these two groups using differential gene expression...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...and continuous growth also resulted in the loss of light-specific gated growth.Wolffia is like the yeast of flowering plants with a core set of angiosperm genes, small size, rapid unrestricted growth, and growing in direct contact with its environment. Before Arabidopsis, duckweed was widely used as a model...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...with autism and related disorders and to gene-level statistics of the protected data sets characterizing the genes’ roles in autism. However, GPF is versatile and can manage genotypic data from other small or large family collections. Here, we highlight the primary features of GPF within the context of GPF...
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Research: A quantitative framework for characterizing the evolutionary history of mammalian gene expression
- Jenny Chen,
- Ross Swofford,
- Jeremy Johnson,
- Beryl B. Cummings,
- Noga Rogel,
- Kerstin Lindblad-Toh,
- Wilfried Haerty,
- Federica di Palma,
- and Aviv Regev
Genome Res. January 2019 29: 53-63; Published in Advance December 14, 2018, doi:10.1101/gr.237636.118
...et al. 2008; Areal et al. 2011; Yue et al. 2014) and reproduction-related genes (Swanson et al. 2001; Torgerson et al. 2002), respectively.DiscussionHere, we combined a large data set of comparative gene expression profiles across mammals with systematic analysis and showed that the divergence...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...al. 2024). Limited phylogenetic analyses of SET domain proteins across 20 representative fungal species suggested extensive gene duplications, losses, and domain rearrangements, implying unique HMT regulatory mechanisms in fungi (Ding et al. 2022). However, comprehensive, systematic analysis of SET...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
...simplification or node scaling was applied in VRPG for this visualization. All other options were left with defaults.The DOG2 deletionThe yeast paralog gene pairs DOG1 and DOG2 encode 2-deoxyglucose-6-phosphate phosphatase involved in glucose metabolism. They are homologous to the human PUDP (previously known...
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