[HTML][HTML] Beyond assembly: the increasing flexibility of single-molecule sequencing technology

PW Hook, W Timp - Nature Reviews Genetics, 2023 - nature.com
The maturation of high-throughput short-read sequencing technology over the past two
decades has shaped the way genomes are studied. Recently, single-molecule, long-read …

Spatial-CUT&Tag: spatially resolved chromatin modification profiling at the cellular level

Y Deng, M Bartosovic, P Kukanja, D Zhang, Y Liu, G Su… - Science, 2022 - science.org
Spatial omics emerged as a new frontier of biological and biomedical research. Here, we
present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone …

Transcription factors interact with RNA to regulate genes

O Oksuz, JE Henninger, R Warneford-Thomson… - Molecular cell, 2023 - cell.com
Transcription factors (TFs) orchestrate the gene expression programs that define each cell's
identity. The canonical TF accomplishes this with two domains, one that binds specific DNA …

Prediction of histone post-translational modification patterns based on nascent transcription data

Z Wang, AG Chivu, LA Choate, EJ Rice, DC Miller… - Nature …, 2022 - nature.com
The role of histone modifications in transcription remains incompletely understood. Here, we
examine the relationship between histone modifications and transcription using …

Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin

M Tedesco, F Giannese, D Lazarević, V Giansanti… - Nature …, 2022 - nature.com
Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-
throughput, single-cell assessment of heterochromatin and its underlying genomic …

[PDF][PDF] Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion

E Battistello, KA Hixon, DE Comstock, CK Collings… - Molecular cell, 2023 - cell.com
Highly coordinated changes in gene expression underlie T cell activation and exhaustion.
However, the mechanisms by which such programs are regulated and how these may be …

Tagmentation-based single-cell genomics

AC Adey - Genome Research, 2021 - genome.cshlp.org
It has been just over 10 years since the initial description of transposase-based methods to
prepare high-throughput sequencing libraries, or “tagmentation,” in which a hyperactive …

[HTML][HTML] The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes

S Brahma, S Henikoff - Nature Genetics, 2024 - nature.com
Chromatin accessibility is a hallmark of active transcription and entails ATP-dependent
nucleosome remodeling, which is carried out by complexes such as Brahma-associated …

[HTML][HTML] ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

YC Teng, A Sundaresan, R O'Hara, VU Gant… - Nature …, 2021 - nature.com
ATRX is a tumor suppressor that has been associated with protection from DNA replication
stress, purportedly through resolution of difficult-to-replicate G-quadruplex (G4) DNA …

[HTML][HTML] 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 …