Allele-specific gene expression, ASE, is an important aspect of gene regulation. We developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq data that aggregates information across multiple single nucleotide variation loci to obtain a gene-level measure of ASE, even when prior phasing information is unavailable. MBASED is capable of one-sample and two-sample analyses and performs well in simulations. We applied MBASED to a panel of cancer cell lines and paired tumor-normal tissue samples, and observed extensive ASE in cancer, but not normal, samples, mainly driven by genomic copy number alterations.
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http://dx.doi.org/10.1186/s13059-014-0405-3 | DOI Listing |
BMC Plant Biol
January 2025
Department of Agricultural, Food and Environmental Sciences, University of Perugia, via Borgo XX giugno 74, Perugia, 06121, Italy.
Whole genome duplication (WGD) is a powerful evolutionary mechanism in plants. Autopolyploids have been comparatively less studied than allopolyploids, with sexual autopolyploidization receiving even less attention. In this work, we studied the transcriptomes of neotetraploids (2n = 4x = 32) obtained by crossing two diploid (2n = 2x = 16) plants of Medicago sativa that produce a significant percentage of either 2n eggs or pollen.
View Article and Find Full Text PDFNat Struct Mol Biol
January 2025
IGMM, University of Montpellier, CNRS, Montpellier, France.
Random X-chromosome inactivation is a hallmark of female mammalian somatic cells. This epigenetic mechanism, mediated by the long noncoding RNA Xist, occurs in the early embryo and is stably maintained throughout life, although inactivation is lost during primordial germ cell (PGC) development. Using a combination of single-cell allele-specific RNA sequencing and low-input chromatin profiling on developing mouse PGCs, we provide a detailed map of X-linked gene reactivation.
View Article and Find Full Text PDFBiochim Biophys Acta Gene Regul Mech
January 2025
School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, P.O. Bhimpur-Padanpur, Jatni, Khurda, Odisha 752050, India; Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai 400094, India. Electronic address:
Pseudoexfoliation (PEX) is an age-related, complex systemic disorder of protein aggregopathy. It is characterized by the extracellular fibril depositions, termed PEX fibrils, initially observed in various organ tissues during pseudoexfoliation syndrome (PEXS) and with significant prominence in the eye during advanced pseudoexfoliation glaucoma (PEXG). The study explores the association between CACNA1A (calcium channel, voltage-dependent, P/Q type, alpha 1 A subunit) variants and PEX in an Indian population.
View Article and Find Full Text PDFHum Mol Genet
January 2025
Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich Research Park, Earlham Road, Norwich NR4 6PN, United Kingdom.
Genomic imprinting is the parent-of-origin dependent monoallelic expression of genes often associated with regions of germline-derived DNA methylation that are maintained as differentially methylated regions (gDMRs) in somatic tissues. This form of epigenetic regulation is highly conserved in mammals and is thought to have co-evolved with placentation. Tissue-specific gDMRs have been identified in human placenta, suggesting that species-specific imprinting dependent on unorthodox epigenetic establishment or maintenance may be more widespread than previously anticipated.
View Article and Find Full Text PDFDev Cell
January 2025
King's College London, Centre for Gene Therapy and Regenerative Medicine, School of Basic & Medical Biosciences, Faculty of Life Sciences and Medicine, London, UK; King's College London, Guy's Hospital Assisted Conception Unit, Department of Women and Children's Health, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, London, UK. Electronic address:
Female primordial germ cells (PGCs) undergo X chromosome reactivation (XCR) during genome-wide reprogramming. XCR kinetics and dynamics are poorly understood at a molecular level. Here, we apply single-cell RNA sequencing and chromatin profiling on germ cells from F mouse embryos, performing a precise appraisal of XCR spanning from migratory-stage PGCs to gonadal germ cells.
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