26 research outputs found
Methodology for Y Chromosome Capture: A complete genome sequence of Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads
This study is a comparison of the efficiency of three technologies used for Y chromosome capture and
the next-generation sequencing (NGS) technologies applied for determining its whole sequence. Our
main findings disclose that streptavidin–biotin magnetic particle-based capture methodology offers
better and a deeper sequence coverage for Y chromosome capture, compared to chromosome sorting
and microdissection procedures. Moreover, this methodology is less time consuming and the most
selective for capturing only Y chromosomal material, in contrast with other methodologies that result
in considerable background material from other, non-targeted chromosomes. NGS results compared
between two platforms, NextSeq 500 and SOLID 5500xl, produce the same coverage results. This is the
first study to explore a methodological comparison of Y chromosome capture and genetic analysis. Our
results indicate an improved strategy for Y chromosome research with applications in several scientific
fields where this chromosome plays an important role, such as forensics, medical sciences, molecular
anthropology and cancer sciences.Spanish Alfonso Martin Escudero Foundation for the financial support to one of the
authors of the present work (MJ Alvarez –Cubero)
Epigenetic engineering shows that a human centromere resists silencing mediated by H3K27me3/K9me3
Centromeres are characterized by the centromere-specific H3 variant CENP-A, which is embedded in chromatin with a pattern characteristic of active transcription that is required for centromere identity. It is unclear how centromeres remain transcriptionally active despite being flanked by repressive pericentric heterochromatin. To further understand centrochromatin’s response to repressive signals, we nucleated a Polycomb-like chromatin state within the centromere of a human artificial chromosome (HAC) by tethering the methyltransferase EZH2. This led to deposition of the H3K27me3 mark and PRC1 repressor binding. Surprisingly, this state did not abolish HAC centromere function or transcription, and this apparent resistance was not observed on a noncentromeric locus, where transcription was silenced. Directly tethering the reader/repressor PRC1 bypassed this resistance, inactivating the centromere. We observed analogous responses when tethering the heterochromatin Editor Suv39h1-methyltransferase domain (centromere resistance) or reader HP1α (centromere inactivation), respectively. Our results reveal that the HAC centromere can resist repressive pathways driven by H3K9me3/H3K27me3 and may help to explain how centromeres are able to resist inactivation by flanking heterochromatin
Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome
Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers
Computational Modeling for Enhancing Soft Tissue Image Guided Surgery: An Application in Neurosurgery
Linear assembly of a human centromere on the Y chromosome
The human genome reference sequence remains incomplete owing to the challenge of assembling long tracts of near-identical tandem repeats in centromeres. We implemented a nanopore sequencing strategy to generate high-quality reads that span hundreds of kilobases of highly repetitive DNA in a human Y chromosome centromere. Combining these data with short-read variant validation, we assembled and characterized the centromeric region of a human Y chromosome