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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...levels from the two methods were significantly correlated (Supplemental Fig. 2A) (Spearman's correlations [rho], 0.792–0.816 across replicates). Moreover, gene-level allele-specific RNA expression was moderately concordant between the two approaches (Supplemental Fig. 2B) (weighted rho = 0.61, Methods...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
...imbalances that can have functional consequences on phenotypes. Environmental signals also impact allele-specific expression, but how they contribute to this cross talk remains understudied. Here, we explored how genotype, parent-of-origin, tissue, sex, and dietary fat simultaneously influence ASE biases...
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Research: Limited allele-specific gene expression in highly polyploid sugarcane
- Gabriel Rodrigues Alves Margarido,
- Fernando Henrique Correr,
- Agnelo Furtado,
- Frederik C. Botha,
- and Robert James Henry
Genome Res. February 2022 32: 297-308; Published in Advance December 23, 2021, doi:10.1101/gr.275904.121
...availability of high-throughput RNA sequencing (RNA-seq) assays and methods for quantitative genotyping of single-nucleotide variants (SNVs) has allowed ASE to be studied in sugarcane (Vilela et al. 2017; Sforça et al. 2019; Cai et al. 2020; Correr et al. 2021). However, these previous investigations focused...
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Research: Allele-specific alternative splicing and its functional genetic variants in human tissues
- Kofi Amoah,
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Yiwei Sun,
- Christina Burghard,
- Boon Xin Tan,
- Ei-Wen Yang,
- and Xinshu Xiao
Genome Res. March 2021 31: 359-371; Published in Advance January 15, 2021, doi:10.1101/gr.265637.120
...modulated alternative splicing (GMAS) via identification of allele-specific splicing events. We demonstrate that GMAS events are shared across tissues and individuals more often than expected by chance, consistent with their genetically driven nature. Moreover, although the allelic bias of GMAS exons varies...
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Method: High-throughput characterization of genetic effects on DNA–protein binding and gene transcription
- Cynthia A. Kalita,
- Christopher D. Brown,
- Andrew Freiman,
- Jenna Isherwood,
- Xiaoquan Wen,
- Roger Pique-Regi,
- and Francesca Luca
Genome Res. November 2018 28: 1701-1708; Published in Advance September 25, 2018, doi:10.1101/gr.237354.118
...traits are in noncoding regions and contribute to phenotypes by disrupting regulatory sequences. To characterize these variants, we developed a streamlined protocol for a high-throughput reporter assay, Biallelic Targeted STARR-seq (BiT-STARR-seq), that identifies allele-specific expression (ASE) while...
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Research: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
- Amanda J. Lea,
- Julie Peng,
- and Julien F. Ayroles
Genome Res. October 2022 32: 1826-1839; Published in Advance October 13, 2022, doi:10.1101/gr.276430.121
...to their progenitor B cells, and the transformation process is known to induce certain artifacts (Redon et al. 2006; Akey et al. 2007). Thus, although we believe LCLs represent a powerful model for high-throughput and large-scale G×E mapping, future work in primary tissues or induced pluripotent stem cells...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...Variation in histone configurations correlates with gene expression1 across nine inbred strains of mice2 Anna L. Tyler1,∗, Catrina Spruce1,∗, Romy Kursawe2, Annat Haber2, Robyn L. Ball1, Wendy4 A. Pitman1, Alexander D. Fine1, Narayanan Raghupathy1, Michael Walker1, Vivek M. Philip1,5 Christopher L...
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Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
- Kaixuan Luo,
- Jianling Zhong,
- Alexias Safi,
- Linda K. Hong,
- Alok K. Tewari,
- Lingyun Song,
- Timothy E. Reddy,
- Li Ma,
- Gregory E. Crawford,
- and Alexander J. Hartemink
Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
...by high-throughput sequencing (ChIP-seq), provided that a selective antibody exists for the TF. Although The ENCODE Project Consortium has generated such data for hundreds of human TFs, the data are typically from only a small number of cell types because of a major limitation of ChIP-seq: A separate...
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Methods: SNP-specific array-based allele-specific expression analysis
- Hans T. Bjornsson,
- Thomas J. Albert,
- Christine M. Ladd-Acosta,
- Roland D. Green,
- Michael A. Rongione,
- Christina M. Middle,
- Rafael A. Irizarry,
- Karl W. Broman,
- and Andrew P. Feinberg
Genome Res. May 2008 18: 771-779; Published in Advance March 27, 2008, doi:10.1101/gr.073254.107
...variation, and a fifth gene that falls into one of those classes, which could not be determined with the tissue samples currently at hand, as well as five genotyping errors in HapMap. Discussion In summary, we have developed an array hybridization-based approach to high-throughput allele-specific gene...
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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
...).Taken together, these features show both the quality and richness of the data and their usefulness to further annotate the regulatory landscape of the Drosophila at these important stages of embryogenesis.Allele-specific variation is common across genotypes and regulatory layersTo quantify the impact of cis...
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