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Genomics & Functional Genomics

  • Prenatal risk assessment of Xp21.1 duplication involving the <em>DMD</em> gene by optical genome mapping
    Open Access
    Prenatal risk assessment of Xp21.1 duplication involving the DMD gene by optical genome mapping

    Yuanyuan Zhang, Qiang Du, Haiming Gao, Yujie Pan, Ningyang Liu, Chuang Qiu, Xiaoliang Liu

    Yuanyuan Zhang ... Xiaoliang Liu

    Published 8 August 2024

    It classifies the Xp21.1 duplications involving 5′-terminal DMD in prenatal case series as likely benign using OGM, which emphasizes the importance of structural evaluation on SVs involving DMD and other large dose-sensitive genes.

  • A scalable approach to topic modelling in single-cell data by approximate pseudobulk projection
    Open Access
    A scalable approach to topic modelling in single-cell data by approximate pseudobulk projection

    Sishir Subedi, Tomokazu S Sumida, Yongjin P Park

    Sishir Subedi ... Yongjin P Park

    Published 6 August 2024

    Random projection of pseudobulk gene expression data improves the scalability and accuracy of single-cell topic modelling.

  • Transient chromatin decompaction at the start of <em>D. melanogaster</em> male embryonic germline development
    Open Access
    Transient chromatin decompaction at the start of D. melanogaster male embryonic germline development

    Yi-Ru Li, Li Bin Ling, Angel Chao, Sebastian D Fugmann, Shu Yuan Yang

    Yi-Ru Li ... Shu Yuan Yang

    Published 11 July 2024

    Our genomics profiling of the earliest fruit fly germline revealed a brief window of major chromatin remodeling in the male germline right after zygotic activation and suggests reprogramming in the early stages of germline to be an evolutionarily conserved phenomenon.

  • Substrate diversity of NSUN enzymes and links of 5-methylcytosine to mRNA translation and turnover
    Open Access
    Substrate diversity of NSUN enzymes and links of 5-methylcytosine to mRNA translation and turnover

    Marco Guarnacci, Pei-Hong Zhang, Madhu Kanchi, Yu-Ting Hung, Hanrong Lin, Nikolay E Shirokikh, Li Yang, Thomas Preiss

    Marco Guarnacci ... Thomas Preiss

    Published 10 July 2024

    This study emphasises the emerging diversity of both, m5C writers and readers, affecting mRNA function and provides multiple new leads for future epitranscriptomic research.

  • Single-housing–induced islet epigenomic changes are related to polymorphisms in diabetic KK mice
    Open Access
    Single-housing–induced islet epigenomic changes are related to polymorphisms in diabetic KK mice

    Takao Nammo, Nobuaki Funahashi, Haruhide Udagawa, Junji Kozawa, Kenta Nakano, Yukiko Shimizu, Tadashi Okamura, Miho Kawaguchi, Takashi Uebanso, Wataru Nishimura, Masaki Hiramoto, Iichiro Shimomura, Kazuki Yasuda

    Takao Nammo ... Kazuki Yasuda

    Published 14 June 2024

    This study demonstrates that non-coding variants in KK mice, a polygenic model of type 2 diabetes, may be involved in the development of diabetes via epigenetic mechanisms during social isolation.

  • Open Access
    Correction: Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing

    Priyanka Mehta, Chinky Shiu Chen Liu, Sristi Sinha, Ramakant Mohite, Smriti Arora, Partha Chattopadhyay, Sandeep Budhiraja, Bansidhar Tarai, Rajesh Pandey

    Priyanka Mehta ... Rajesh Pandey

    Published 14 June 2024

    Transcriptomic analysis of dengue-infected patients reveals altered immune response pathways, transcript diversity, and splicing efficiency, underscoring potential therapeutic targets for treatment.

  • Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing
    Open Access
    Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing

    Priyanka Mehta, Chinky Shiu Chen Liu, Sristi Sinha, Ramakant Mohite, Smriti Arora, Partha Chattopadhyay, Sandeep Budhiraja, Bansidhar Tarai, Rajesh Pandey

    Priyanka Mehta ... Rajesh Pandey

    Published 3 June 2024

    Transcriptomic analysis of dengue-infected patients reveals altered immune response pathways, transcript diversity, and splicing efficiency, underscoring potential therapeutic targets for treatment.

  • The importance of DNA sequence for nucleosome positioning in transcriptional regulation
    Open Access
    The importance of DNA sequence for nucleosome positioning in transcriptional regulation

    Malte Sahrhage, Niels Benjamin Paul, Tim Beißbarth, Martin Haubrock

    Malte Sahrhage ... Martin Haubrock

    Published 3 June 2024

    Machine learning on DNA sequences shows that nucleosomes are positioned by DNA sequence patterns to support the stages of transcription by directing competition between nucleosomes and transcription factors, as well as regulating RNA polymerase II dynamics.

  • Novel variants in <em>TECRL</em> leading to catecholaminergic polymorphic ventricular tachycardia
    Open Access
    Novel variants in TECRL leading to catecholaminergic polymorphic ventricular tachycardia

    Douglas Jones, Jacob Hartung, Elizabeth Lasalle, Alejandro Borquez, Viridiana Murillo, Lucia Guidugli, Kiely N James, Stephen F Kingsmore, Nicole G Coufal

    Douglas Jones ... Nicole G Coufal

    Published 22 May 2024

    We report two novel pathogenic variants in the TECRL gene associated with recessive catecholaminergic polymorphic ventricular tachycardia and extend on the clinical features associated with this rare genetic variant.

  • Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms
    Open Access
    Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms

    Samantha G Fernandez, Lucas Ferguson, Nicholas T Ingolia

    Samantha G Fernandez ... Nicholas T Ingolia

    Published 21 May 2024

    Alternative translation initiation on a single mRNA can generate distinct protein isoforms. This work finds that the ribosome rescue factor, PELOTA, influences start site choice on the developmental transcription factor, C/EBPα.

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