scholarly journals Exploring the dark matter of the human genome using oligonucleotide-based molecules

2015 ◽  
Vol 7 (13) ◽  
pp. 1627-1630 ◽  
Author(s):  
Concetta Avitabile ◽  
Luca Domenico D'Andrea ◽  
Alessandra Romanelli
Keyword(s):  
Dark Matter ◽  
Human Genome

scholarly journals centroFlye: Assembling Centromeres with Long Error-Prone Reads

2019 ◽  
Author(s):  
Andrey V. Bzikadze ◽  
Pavel A. Pevzner
Keyword(s):  
Dark Matter ◽  
Human Genome ◽  
Short Reads ◽  
Evolutionary Studies ◽  
Centromere Assembly ◽  
Automated Tool ◽  
Reference Human Genome

AbstractAlthough variations in centromeres have been linked to cancer and infertility, centromeres still represent the “dark matter of the human genome” and remain an enigma for both biomedical and evolutionary studies. Since centromeres have withstood all previous attempts to develop an automated tool for their assembly and since their assembly using short reads is viewed as intractable, recent efforts attempted to manually assemble centromeres using long error-prone reads. We describe the centroFlye algorithm for centromere assembly using long error-prone reads, apply it for assembling the human X centromere, and use the constructed assembly to gain insights into centromere evolution. Our analysis reveals putative breakpoints in the previous manual reconstruction of the human X centromere and opens a possibility to automatically close the remaining multi-megabase gaps in the reference human genome.

scholarly journals Probing the dark matter of the human genome with big DNA

2019 ◽  
Vol 41 (3) ◽  
pp. 46-48
Author(s):  
Jon M. Laurent ◽  
Sudarshan Pinglay ◽  
Leslie Mitchell ◽  
Ran Brosh
Keyword(s):  
Dark Matter ◽  
Human Genome ◽  
Human Disease ◽  
Disease Risk ◽  
Regulatory Elements ◽  
Base Pairs ◽  
Protein Coding ◽  
Regulatory Variation ◽  
Expression Of Genes ◽  
Regulatory Dna

Less than 2% of our genome is protein-coding DNA. The vast expanses of non-coding DNA make up the genome's “dark matter”, where introns, repetitive and regulatory elements reside. Variation between individuals in non-coding regulatory DNA is emerging as a major factor in the genetics of numerous diseases and traits, yet very little is known about how such variations contribute to disease risk. Studying the genetics of regulatory variation is technically challenging as regulatory elements can affect genes located tens of thousands of base pairs away, and often, multiple distal regulatory variations, each with a very small effect, combine in an unknown way to significantly modulate the expression of genes. At the Center for Synthetic Regulatory Genomics (SyRGe) we directly tackle these problems in order to systematically elucidate the mechanisms of regulatory variation underlying human disease.

The dark matter of the human genome and its role in human cancers

Gene ◽  
2021 ◽  
pp. 146084
Author(s):  
Ibrahim Bozgeyik
Keyword(s):  
Dark Matter ◽  
Human Genome ◽  
Human Cancers

scholarly journals Extreme Open Science: Companies Sharing Compounds without Restriction

2018 ◽  
Author(s):  
David Drewry ◽  
Carrow Wells ◽  
William J Zuercher ◽  
Timothy Mark Willson
Keyword(s):  
Dark Matter ◽  
Drug Discovery ◽  
Small Molecules ◽  
Human Genome ◽  
Pharmaceutical Company ◽  
Drug Targets ◽  
Kinase Inhibitors ◽  
Open Science ◽  
New Targets ◽  
Shed Light

Although the human genome provides the blueprint for life, most of the proteins it encodes remain poorly studied. We describe how one group of scientists, in seeking new targets for drug discovery, used open science through unrestricted sharing of small molecules to shed light on dark matter of the genome. Starting initially with a single pharmaceutical company before expanding to multiple companies, a precedent was established for sharing published kinase inhibitors as chemical tools. As a result, new drug targets were identified and the science of kinase chemogenomics was established.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

First runs with the ORPHEUS dark matter detector

2002 ◽  
Vol 110 (2) ◽  
pp. 106-108
Author(s):  
G Czapek
Keyword(s):  
Dark Matter

Status of dark matter searches in the Boulby Mine

2002 ◽  
Vol 110 (2) ◽  
pp. 91-93
Author(s):  
S Hart
Keyword(s):  
Dark Matter

Baryonic dark matter

2002 ◽  
Vol 110 (2) ◽  
pp. 16-25 ◽  
Author(s):  
R Rebolo
Keyword(s):  
Dark Matter ◽  
Baryonic Dark Matter
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