Publications tagged "Basic Genome"
RNA LEVER mediates long-range regulation of ε-globin by keeping PRC2 in check
Polycomb Repressive Complex 2 (PRC2) is an epigenetic regulator required for gene silencing during embryonic development. Previous studies have reported that PRC2 interacts with RNA in a promiscuous...
The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the “library hypothesis”
Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenoty...
Generating high quality assemblies for genomic analysis of transposable elements
The advent of long-read sequencing holds great promise for research on transposable elements (TEs). Long reads may finally allow us to obtain reliable assemblies of repetitive regions, and thus shed...
Enhancer hijacking determines intra- and extrachromosomal circular MYCN amplicon architecture in neuroblastoma
MYCN amplification drives one in six cases of neuroblastoma. The supernumerary gene copies are commonly found on highly rearranged, extrachromosomal circular DNA. The exact amplicon structure has no...
HyPo: Super fast and accurate polisher for long read genome assemblies
Efforts towards making population-scale long read genome assemblies (especially human genomes) viable have intensified recently with the emergence of many fast assemblers. The reliance of these fast...
A diploid assembly-based benchmark for variants in the Major Histocompatibility Complex
We develop the first human benchmark derived from a diploid assembly for the openly-consented Genome in a Bottle/Personal Genome Project Ashkenazi son (HG002). As a proof-of-principle, we focus on a...
Persistent chromatin states, pervasive transcription, and shared cis-regulatory sequences have shaped the C. elegans genome
Despite highly conserved chromatin states and cis-regulatory elements, studies of metazoan genomes reveal that gene organization and the strategies to control mRNA expression can vary widely among a...
Combinatorial analysis of Saccharomyces cerevisiae regulatory elements
Gene expression in Saccharomyces cerevisiae is regulated at multiple levels. Genomic and epigenomic mapping of transcription factors and chromatin components has led to the definition and delineatio...
The shufflon of IncI1 plasmids is rearranged constantly during different growth conditions
Nanopore long-read sequencing was used to measure recombination of the IncI1 shufflon at different bacterial growth stages and in different host cells. The entire shufflon region was amplified and t...
Single-molecule long-read sequencing reveals the chromatin basis of gene expression
Genome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remains poorly studied at the single-cell level. Here we present a ...
Ancestral admixture and structural mutation define global biodiversity in fission yeast
Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizo...
Xdrop: targeted sequencing of long DNA molecules from low input samples using droplet sorting
Long-read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore such technologies are ideal for genome-gap closure, solving structural rearrangements and s...
Utilization of Hybrid Assembly Approach to Determine the Genome of an Opportunistic Pathogenic Fungus, Candida albicans TIMM 1768
Candida albicans TIMM1768 is a highly virulent strain utilized as a model organism for the study of gastrointestinal and oral candidiasis. Despite being a model strain, identification of its genetic...
Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
The Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members ...
Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing
Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-...
Finding Nemo: Hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the Clownfish (Amphiprion ocellaris) genome assembly
Background Some of the most widely recognised coral-reef fishes are clownfish or anemonefishes, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species d...
De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read
One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ∼1.8 metres in length and live to age ≥48 years. The Murray cod...
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...