Understanding 3D genome organization by multidisciplinary methods

I Jerkovic, G Cavalli - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …

[HTML][HTML] CLIP and complementary methods

M Hafner, M Katsantoni, T Köster, J Marks… - Nature Reviews …, 2021 - nature.com
RNA molecules start assembling into ribonucleoprotein (RNP) complexes during
transcription. Dynamic RNP assembly, largely directed by cis-acting elements on the RNA …

Methods for map** 3D chromosome architecture

R Kempfer, A Pombo - Nature Reviews Genetics, 2020 - nature.com
Determining how chromosomes are positioned and folded within the nucleus is critical to
understanding the role of chromatin topology in gene regulation. Several methods are …

Efficient low-cost chromatin profiling with CUT&Tag

HS Kaya-Okur, DH Janssens, JG Henikoff, K Ahmad… - Nature protocols, 2020 - nature.com
Abstract We recently introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an
epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in …

The 4D nucleome project

J Dekker, AS Belmont, M Guttman, VO Leshyk, JT Lis… - Nature, 2017 - nature.com
Abstract The 4D Nucleome Network aims to develop and apply approaches to map the
structure and dynamics of the human and mouse genomes in space and time with the goal …

The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

SB Reiff, AJ Schroeder, K Kırlı, A Cosolo… - Nature …, 2022 - nature.com
Abstract The 4D Nucleome (4DN) Network aims to elucidate the complex structure and
organization of chromosomes in the nucleus and the impact of their disruption in disease …

Transcriptional enhancers: from properties to genome-wide predictions

D Shlyueva, G Stampfel, A Stark - Nature Reviews Genetics, 2014 - nature.com
Cellular development, morphology and function are governed by precise patterns of gene
expression. These are established by the coordinated action of genomic regulatory …

BioID: a screen for protein‐protein interactions

KJ Roux, DI Kim, B Burke… - Current protocols in protein …, 2018 - Wiley Online Library
BioID is a unique method to screen for physiologically relevant protein interactions that
occur in living cells. This technique harnesses a promiscuous biotin ligase to biotinylate …

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

KJ Roux, DI Kim, M Raida, B Burke - Journal of cell biology, 2012 - rupress.org
We have developed a new technique for proximity-dependent labeling of proteins in
eukaryotic cells. Named BioID for proximity-dependent biotin identification, this approach is …

DiMeLo-seq: a long-read, single-molecule method for map** protein–DNA interactions genome wide

N Altemose, A Maslan, OK Smith, K Sundararajan… - Nature …, 2022 - nature.com
Studies of genome regulation routinely use high-throughput DNA sequencing approaches to
determine where specific proteins interact with DNA, and they rely on DNA amplification and …