Clonal hematopoiesis: mechanisms driving dominance of stem cell clones

GA Challen, MA Goodell - Blood, The Journal of the American …, 2020 - ashpublications.org
The discovery of clonal hematopoiesis (CH) in older individuals has changed the way
hematologists and stem cell biologists view aging. Somatic mutations accumulate in stem …

Three-dimensional genome organization in immune cell fate and function

S Cuartero, G Stik, R Stadhouders - Nature Reviews Immunology, 2023 - nature.com
Immune cell development and activation demand the precise and coordinated control of
transcriptional programmes. Three-dimensional (3D) organization of the genome has …

Subtype-specific 3D genome alteration in acute myeloid leukaemia

J Xu, F Song, H Lyu, M Kobayashi, B Zhang, Z Zhao… - Nature, 2022 - nature.com
Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies,
and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases …

DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation

Y An, X Zhao, Z Zhang, Z Xia, M Yang, L Ma… - Nature …, 2023 - nature.com
Plasma cell-free DNA (cfDNA) are small molecules generated through a non-random
fragmentation procedure. Despite commendable translational values in cancer liquid biopsy …

Pharmacological restriction of genomic binding sites redirects PU. 1 pioneer transcription factor activity

SJ Taylor, J Stauber, O Bohorquez, G Tatsumi… - Nature Genetics, 2024 - nature.com
Transcription factor (TF) DNA-binding dynamics govern cell fate and identity. However, our
ability to pharmacologically control TF localization is limited. Here we leverage chemically …

Hi-C analyses with GENOVA: a case study with cohesin variants

RH van der Weide, T van den Brand… - NAR genomics and …, 2021 - academic.oup.com
Conformation capture-approaches like Hi-C can elucidate chromosome structure at a
genome-wide scale. Hi-C datasets are large and require specialised software. Here, we …

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

G Wutz, R Ladurner, BG St Hilaire, RR Stocsits… - Elife, 2020 - elifesciences.org
Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin
complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is …

STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma

D Surdez, S Zaidi, S Grossetête, K Laud-Duval… - Cancer cell, 2021 - cell.com
STAG2, a cohesin family gene, is among the most recurrently mutated genes in cancer.
STAG2 loss of function (LOF) is associated with aggressive behavior in Ewing sarcoma, a …

Cohesin subunit RAD21: From biology to disease

H Cheng, N Zhang, D Pati - Gene, 2020 - Elsevier
RAD21 (also known as KIAA0078, NXP1, HR21, Mcd1, Scc1, and hereafter called RAD21),
an essential gene, encodes a DNA double-strand break (DSB) repair protein that is …

STAG2 mutations reshape the cohesin-structured spatial chromatin architecture to drive gene regulation in acute myeloid leukemia

A Fischer, B Hernández-Rodríguez, R Mulet-Lazaro… - Cell Reports, 2024 - cell.com
Cohesin shapes the chromatin architecture, including enhancer-promoter interactions. Its
components, especially STAG2, but not its paralog STAG1, are frequently mutated in …