Publications by authors named "G Deikus"
Human endogenous retroviruses (HERVs) occupy a large portion of the human genome. Most HERVs are transcriptionally silent, but they can be reactivated during pathological states such as viral infection and certain cancers. The HERV-K HML-2 clade includes elements that recently integrated have in the human germ line and often contain intact open reading frames that possibly support peptide and protein expression.
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- The study explores the complex process of RNA expression and splicing during early human embryo development, utilizing both long- and short-read RNA sequencing on 73 embryos.
- It identifies over 110,000 new RNA isoforms from known genes and nearly 18,000 isoforms from unannotated genes, revealing a rich landscape of non-coding RNA and associations with transposable elements.
- The findings highlight significant complexity in the human embryo transcriptome, suggesting a need for refined exploration of embryonic development in future research.
Article Synopsis
- Current short-read AIRR-seq methods have limitations in resolving the constant (C) region of antibody transcripts, prompting the development of a new approach called FLAIRR-seq, which achieves 99.99% accuracy in generating human antibody heavy chain transcripts.
- FLAIRR-seq was validated against standard methods, showing comparable results while revealing previously undocumented heavy chain gene features and enabling detailed characterization of antibody gene diversity.
- This new method identified 32 unique IGHC alleles in ten individuals, with 87% being uncharacterized, thus providing the most comprehensive analysis of antibody repertoires to date.
Immunoglobulins (IGs), crucial components of the adaptive immune system, are encoded by three genomic loci. However, the complexity of the IG loci severely limits the effective use of short read sequencing, limiting our knowledge of population diversity in these loci. We leveraged existing long read whole-genome sequencing (WGS) data, fosmid technology, and IG targeted single-molecule, real-time (SMRT) long-read sequencing (IG-Cap) to create haplotype-resolved assemblies of the IG Lambda (IGL) locus from 6 ethnically diverse individuals.
View Article and Find Full Text PDFThe discovery of N-methyldeoxyadenine (6mA) across eukaryotes led to a search for additional epigenetic mechanisms. However, some studies have highlighted confounding factors that challenge the prevalence of 6mA in eukaryotes. We developed a metagenomic method to quantitatively deconvolve 6mA events from a genomic DNA sample into species of interest, genomic regions, and sources of contamination.
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