The spatial organization of transcriptional control

A Hafner, A Boettiger - Nature Reviews Genetics, 2023 - nature.com
In animals, the sequences for controlling gene expression do not concentrate just at the
transcription start site of genes, but are frequently thousands to millions of base pairs distal …

The nexus of cfDNA and nuclease biology

DSC Han, YMD Lo - Trends in Genetics, 2021 - cell.com
Cell-free DNA (cfDNA) is a widely used noninvasive biomarker for diagnosis and prognosis
of multiple disease states. Emerging evidence suggests that cfDNA might not just be passive …

CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells

DH Janssens, DJ Otto, MP Meers, M Setty, K Ahmad… - Genome biology, 2022 - Springer
Abstract Cleavage Under Targets and Tagmentation (CUT&Tag) is an antibody-directed
transposase tethering strategy for in situ chromatin profiling in small samples and single …

Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation

S Henikoff, JG Henikoff, HS Kaya-Okur, K Ahmad - Elife, 2020 - elifesciences.org
Chromatin accessibility mapping is a powerful approach to identify potential regulatory
elements. A popular example is ATAC-seq, whereby Tn5 transposase inserts sequencing …

Epigenetic regulators as the gatekeepers of hematopoiesis

CP Rodrigues, M Shvedunova, A Akhtar - Trends in Genetics, 2021 - cell.com
Hematopoiesis is the process by which both fetal and adult organisms derive the full
repertoire of blood cells from a single multipotent progenitor cell type, the hematopoietic …

LanceOtron: a deep learning peak caller for genome sequencing experiments

LD Hentges, MJ Sergeant, CB Cole, DJ Downes… - …, 2022 - academic.oup.com
Motivation Genome sequencing experiments have revolutionized molecular biology by
allowing researchers to identify important DNA-encoded elements genome wide. Regions …

Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?

AE Yaschenko, M Fenech, S Mazzoni-Putman… - Current opinion in plant …, 2022 - Elsevier
Gene expression differences between distinct cell types are orchestrated by specific sets of
transcription factors and epigenetic regulators acting upon the genome. In plants, the …

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 …

Tracing the origin of cell-Free DNA molecules through tissue-Specific epigenetic signatures

A Oberhofer, AJ Bronkhorst, C Uhlig, V Ungerer… - Diagnostics, 2022 - mdpi.com
All cell and tissue types constantly release DNA fragments into human body fluids by various
mechanisms including programmed cell death, accidental cell degradation and active …

[PDF][PDF] Simultaneous profiling of multiple chromatin proteins in the same cells

S Gopalan, Y Wang, NW Harper, M Garber, TG Fazzio - Molecular cell, 2021 - cell.com
Methods derived from CUT&RUN and CUT&Tag enable genome-wide mapping of the
localization of proteins on chromatin from as few as one cell. These and other mapping …