Single-Cell DNA Methylation Analysis of Chicken Lampbrush Chromosomes

DNA methylation is an essential epigenetic regulation mechanism implicated in transcription and replication control, developmental reprogramming, retroelements silencing and other genomic processes. During mammalian development, a specific DNA methylation pattern should be established in germ cells to allow embryonic development. Less is known about germ cell DNA methylation in other species. To close this gap, we performed a single-cell methylome analysis of chicken diplotene oocytes. We comprehensively characterized methylation patterns in these cells, obtained methylation-based chicken genome segmentation and identified oocyte-specific methylated gene promoters. Our data show that despite the formation of specific transcriptionally hyperactive genome architecture in chicken diplotene oocytes, methylation patterns in these cells closely resemble genomic distribution observed in somatic tissues

A HGF Mutation in the Familial Case of Primary Lymphedema: A Report

Lymphedema is a disorder that leads to excessive swelling due to lymphatic insufficiency, resulting in the accumulation of protein-rich interstitial fluid. Primary lymphedema predominantly impacts the lower extremities and is frequently linked to hereditary factors. This condition is known to be associated with variants in several genes, such as FOXC2, FLT4, and SOX18. However, many cases remain unexplained, suggesting undiscovered gene associations. This study describes a novel mutation in the hepatocyte growth factor (HGF) gene, a previously hypothesized candidate for lymphedema pathogenesis. This mutation was identified in affected members of a multigenerational family presenting with primary leg lymphedema, consistent with an autosomal dominant inheritance pattern

Time origin and structural analysis of the induced CRISPR/cas9 megabase-sized deletions and duplications involving the Cntn6 gene in mice

AbstractIn a previous study using one-step CRISPR/Cas9 genome editing in mouse zygotes, we created five founders carrying a 1,137 kb deletion and two founders carrying the same deletion, plus a 2,274 kb duplication involving the Cntn6 gene (encoding contactin-6). Using these mice, the present study had the following aims: (i) to establish stage of origin of these rearrangements; (ii) to determine the fate of the deleted DNA fragments; and (iii) to estimate the scale of unpredicted DNA changes accompanying the rearrangements. The present study demonstrated that all targeted deletions and duplications occurred at the one-cell stage and more often in one pronucleus only. FISH analysis revealed that there were no traces of the deleted DNA fragments either within chromosome 6 or on other chromosomes. These data were consistent with the Southern blot analysis showing that chromosomes with deletion often had close to expected sizes of removed DNA fragments. High-throughput DNA sequencing of two homozygotes for duplication demonstrated that there were no unexpected significant or scale DNA changes either at the gRNA and joint sites or other genome sites. Thus, our data suggested that CRISPR/Cas9 technology could generate megabase-sized deletions and duplications in mouse gametes at a reasonably specific level.</jats:p

Molecular Plasmonic Silver Forests for the Photocatalytic-Driven Sensing Platforms

Structural electronics, as well as flexible and wearable devices are applications that are possible by merging polymers with metal nanoparticles. However, using conventional technologies, it is challenging to fabricate plasmonic structures that remain flexible. We developed three-dimensional (3D) plasmonic nanostructures/polymer sensors via single-step laser processing and further functionalization with 4-nitrobenzenethiol (4-NBT) as a molecular probe. These sensors allow ultrasensitive detection with surface-enhanced Raman spectroscopy (SERS). We tracked the 4-NBT plasmonic enhancement and changes in its vibrational spectrum under the chemical environment perturbations. As a model system, we investigated the sensor’s performance when exposed to prostate cancer cells’ media over 7 days showing the possibility of identifying the cell death reflected in the environment through the effects on the 4-NBT probe. Thus, the fabricated sensor could have an impact on the monitoring of the cancer treatment process. Moreover, the laser-driven nanoparticles/polymer intermixing resulted in a free-form electrically conductive composite that withstands over 1000 bending cycles without losing electrical properties. Our results bridge the gap between plasmonic sensing with SERS and flexible electronics in a scalable, energy-efficient, inexpensive, and environmentally friendly way.</jats:p

Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants

Abstract Background Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type—whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). Methods We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Results Applied to 66 human samples Exo-C achieved 100% recall and 73% precision in detecting chromosomal translocations and SNVs. We further benchmarked its performance for inversions and CNVs and demonstrated its utility in detecting mosaic SVs and resolving diagnostically challenging cases. Conclusions Through several case studies, we demonstrate how Exo-C’s multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders