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Genome compaction
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Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial intermediate presequence protease MIP/Oct1, which carries out precursor processing, has not yet been established to have a role in human disease.
13p
vioraclene
31-03-2024
2
2
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The clinical utility of molecular profiling of tumor tissue to guide treatment of patients with advanced solid tumors is unknown. Our objectives were to evaluate the frequency of genomic alterations, clinical “actionability” of somatic variants, enrollment in mutation-targeted or other clinical trials, and outcome of molecular profiling for advanced solid tumor patients at the Princess Margaret Cancer Centre (PM).
12p
vioraclene
31-03-2024
5
2
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The circadian clock and the daily rhythms it produces are crucial for human health, but are often disrupted by the modern environment. At the same time, circadian rhythms may influence the efficacy and toxicity of therapeutics and the metabolic response to food intake.
11p
vioraclene
31-03-2024
6
1
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The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation. In addition, many agricultural and horticultural species are derived from interspecific hybridization.
16p
vialfrednobel
29-01-2022
13
0
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Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure.
15p
viaristotle
29-01-2022
9
0
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A recent super-resolution imaging study by Boettiger et al. elegantly demonstrates that three epigenetically defined, and functionally disparate, chromatin states have distinct folding characteristics in Drosophila nuclei.
3p
viaristotle
29-01-2022
8
1
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Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism.
26p
viarchimedes
26-01-2022
10
0
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Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes.
25p
viarchimedes
26-01-2022
5
0
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Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation. For the example of assemblies of model organisms and two bacterial pan-genomes, we compare simplitigs to unitigs, the best existing representation, and demonstrate that simplitigs provide a substantial improvement in the cumulative sequence length and their number.
24p
viarchimedes
26-01-2022
7
0
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Four-stranded G-quadruplexes (G4s) are DNA secondary structures in the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship between the folding of promoter G4s, transcription and chromatin state.
14p
viarchimedes
26-01-2022
10
0
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Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel way to understand the core principles of life.
18p
viarchimedes
26-01-2022
8
0
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The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. Here, we present a chromosome-scale assembly of ectophytic Peltaster fructicola, a surface-dwelling extremophile, based on long-read DNA sequencing technology, to assess possible mechanisms associated with genome compaction.
13p
vijeeni2711
24-07-2021
3
0
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Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberellin biosynthesis in sugarcane.
15p
vilichoo2711
25-06-2021
11
1
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Processing of reads from high throughput sequencing is often done in terms of edges in the de Bruijn graph representing all k-mers from the reads. The memory requirements for storing all k-mers in a lookup table can be demanding, even after removal of read errors, but can be alleviated by using a memory efficient data structure.
19p
viwyoming2711
16-12-2020
15
0
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Modern biological science generates a vast amount of data, the analysis of which presents a major challenge to researchers. Data are commonly represented in tables stored as plain text files and require line-by-line parsing for analysis, which is time consuming and error prone.
5p
viwyoming2711
16-12-2020
11
0
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Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level.
7p
vikentucky2711
26-11-2020
8
0
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A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. “Shotgun” metagenome is an analytically challenging type of genomic data - containing sequences of all genes from the totality of a complex microbial community.
11p
vioklahoma2711
19-11-2020
15
2
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The spatial configuration of chromosomes is essential to various cellular processes, notably gene regulation, while architecture related alterations, such as translocations and gene fusions, are often cancer drivers. Thus, eliciting chromatin conformation is important, yet challenging due to compaction, dynamics and scale.
15p
vicolorado2711
22-10-2020
11
0
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CRISPR/Cas9 genome editing strategy has been applied to a variety of species and the tRNA-processing system has been used to compact multiple gRNAs into one synthetic gene for manipulating multiple genes in rice.
8p
viuchiha2711
21-04-2020
10
0
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Panicum hallii Vasey (Hall’s panicgrass) is a compact, perennial C4 grass in the family Poaceae, which has potential to enable bioenergy research for switchgrass (Panicum virgatum L.). Unlike P. hallii, switchgrass has a large genome.
12p
vihamax2711
21-04-2020
14
2
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