Searching journal content for articles similar to Rivera-Mulia et al. 28 (6): 800.

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  1. 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
    ...,000 transcripts (Fig. 1C; Methods). Of the detected transcripts, 8657 transcripts had at least 10 reads in both replicates. In allele-specific analyses, a common challenge is reference allele bias which is the tendency for reads that match the reference to align with a higher probability than reads containing...
  2. Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
    • Rita Tam,
    • Mareike Möller,
    • Runpeng Luo,
    • Zhenyan Luo,
    • Ashley Jones,
    • Sambasivam Periyannan,
    • John P. Rathjen,
    • and Benjamin Schwessinger
    Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
    ...upregulated during infection time points (4, 6, or 8 dpi) to shortlist Avr candidates. Heterozygous biallelic genes were used for allele-specific expression (ASE) analysis.Next, we assessed the impact of inter-haplotype variation on genes by analyzing their sequence conservation and synteny (Fig. 5D). We...
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  3. Method: Allele-specific RNA N6-methyladenosine modifications reveal functional genetic variants in human tissues
    • Shuo Cao,
    • Haoran Zhu,
    • Jinru Cui,
    • Sun Liu,
    • Yuhe Li,
    • Junfang Shi,
    • Junyuan Mo,
    • Zihan Wang,
    • Hailan Wang,
    • Jiaxin Hu,
    • Lizhi Chen,
    • Yuan Li,
    • Laixin Xia,
    • and Shan Xiao
    Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
    .... To address this gap, we developed a method to accurately and sensitively detect transcriptome-wide allele-specific m6A (ASm6A) from MeRIP-seq data and applied it to uncover 12,056 high-confidence ASm6A modifications from 25 human tissues. We also identified 1184 putative functional variants for ASm6A...
  4. 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
    ...) and autopolyploids (Yant and Bomblies 2015). It is usually accompanied by a so-called genomic shock and an increase in allelic diversity, which can consequently cause changes to gene expression profiles (Chen and Ni 2006; Feldman and Levy 2009; Baduel et al. 2018). Such alterations include allele-specific expression...
  5. 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
    ...at a time. In general, it remains a great challenge, both computationally and experimentally, to identify causal genetic variants specific to each tissue type.In this study, we carried out global analyses of allele-specific alternative splicing using RNA-seq data from a large panel of human tissues...
  6. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ...the entire X Chromosome with long reads measuring the level of methylation and genomic variants to gain allele-specific information (Fig. 2E; Lee et al. 2020). This provides a far more quantitative and comprehensive view than targeting a few genes (Johansson et al. 2023), enabling investigation of severely...
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  7. Research: Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
    • Juan Carlos Rivera-Mulia,
    • Sebo Kim,
    • Haitham Gabr,
    • Abhijit Chakraborty,
    • Ferhat Ay,
    • Tamer Kahveci,
    • and David M. Gilbert
    Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
    ...as the replication timing (RT) program and is regulated during development, coordinated with 3D organization and transcriptional activity. However, transcription and RT are not sufficiently coordinated to predict each other, suggesting an indirect relationship. Here, we exploit -wide RT profiles from 15 human cell...
  8. Research: Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans
    • Dale Muzzey,
    • Gavin Sherlock,
    • and Jonathan S. Weissman
    Genome Res. June 2014 24: 963-973; Published in Advance April 14, 2014, doi:10.1101/gr.166322.113
    ...Sherlock, G J Weissman Weissman, J Gavin, Sherlock JS Weissman Sherlock 1088-9051 genome;gr.166322.113 10.1101/gr.166322.113 Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans Research Extensive and coordinated control of allele-specific...
  9. Method: TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes
    • Liguo Zhang,
    • Yang Zhang,
    • Yu Chen,
    • Omid Gholamalamdari,
    • Yuchuan Wang,
    • Jian Ma,
    • and Andrew S. Belmont
    Genome Res. February 2021 31: 251-264; Published in Advance December 18, 2020, doi:10.1101/gr.266239.120
    ...lamina to speckle axis correlating with a gradient in gene expression levels and DNA replication timing. Hi-C A1 and A2 active subcompartment regions formed the apexes of chromatin loops protruding into the nuclear interior from the nuclear periphery, with A1 apexes localizing closer to nuclear speckles...
  10. Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
    • João L. Reis-Cunha,
    • Samuel A. Pimenta-Carvalho,
    • Laila V. Almeida,
    • Anderson Coqueiro-dos-Santos,
    • Catarina A. Marques,
    • Jennifer A. Black,
    • Jeziel Damasceno,
    • Richard McCulloch,
    • Daniella C. Bartholomeu,
    • and Daniel C. Jeffares
    Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
    ...parasite clades suggests that not only the environment but specific genomic modifications in this group may explain why chromosomal duplications are more restricted. Some of these modifications are: megabase-sized chromosomes, minichromosomes, and differences in DNA replication regulation. T. brucei...
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