Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale

J Jeffet, S Margalit, Y Michaeli… - Essays in …, 2021 - portlandpress.com
The human genome contains multiple layers of information that extend beyond the genetic
sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident …

Recruitment of the m6A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48

S Nabeel-Shah, S Pu, GL Burke, N Ahmed… - Genome Biology, 2024 - Springer
Abstract Background N6-methyladenosine (m6A), the most abundant internal modification
on eukaryotic mRNA, and N6, 2′-O-dimethyladenosine (m6Am), are epitranscriptomic …

Single-molecule telomere length characterization by optical mapping in nano-channel array: perspective and review on telomere length measurement

L Uppuluri, D Varapula, E Young, H Riethman… - Environmental …, 2021 - Elsevier
In humans, the telomere consists of tandem 5′ TTAGGG3′ DNA repeats on both ends of
all 46 chromosomes. Telomere shortening has been linked to aging and age-related …

Elucidation of the molecular mechanism of the breakage-fusion-bridge (BFB) cycle using a CRISPR-dCas9 cellular model<? mode longmeta?>

M Singh, K Raseley, AM Perez… - Nucleic Acids …, 2024 - academic.oup.com
Chromosome instability (CIN) is frequently observed in many tumors. The breakage-fusion-
bridge (BFB) cycle has been proposed to be one of the main drivers of CIN during …

ATRX modulates the escape from a telomere crisis

HEB Geiller, A Harvey, RE Jones, JW Grimstead… - PLoS …, 2022 - journals.plos.org
Telomerase activity is the principal telomere maintenance mechanism in human cancers,
however 15% of cancers utilise a recombination-based mechanism referred to as alternative …

Dam assisted fluorescent tagging of chromatin accessibility (dafca) for optical genome mapping in nanochannel arrays

G Nifker, A Grunwald, S Margalit, Z Tulpova… - ACS …, 2023 - ACS Publications
Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in
order to perform genomic tasks such as gene activation and transcription. Hence, chromatin …

Customized optical mapping by CRISPR–Cas9 mediated DNA labeling with multiple sgRNAs

HZ Abid, E Young, J McCaffrey, K Raseley… - Nucleic Acids …, 2021 - academic.oup.com
Whole-genome mapping technologies have been developed as a complementary tool to
provide scaffolds for genome assembly and structural variation analysis (,). We recently …

Multicolor whole-genome mapping in nanochannels for genetic analysis

L Uppuluri, T Jadhav, Y Wang, M Xiao - Analytical chemistry, 2021 - ACS Publications
Analysis of structural variations (SVs) is important to understand mutations underlying
genetic disorders and pathogenic conditions. However, characterizing SVs using short-read …

Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM) Can Potentially Define the ALT Positivity of Cancer

K Raseley, Z Jinwala, D Zhang, M Xiao - Genes, 2023 - mdpi.com
Telomeres play an essential role in protecting the ends of linear chromosomes and
maintaining the integrity of the human genome. One of the key hallmarks of cancers is their …

NPGREAT: assembly of human subtelomere regions with the use of ultralong nanopore reads and linked-reads

E Adam, D Ranjan, H Riethman - BMC bioinformatics, 2022 - Springer
Background Human subtelomeric DNA regulates the length and stability of adjacent
telomeres that are critical for cellular function, and contains many gene/pseudogene …