Beyond assembly: the increasing flexibility of single-molecule sequencing technology
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 …
decades has shaped the way genomes are studied. Recently, single-molecule, long-read …
[HTML][HTML] The era of 3D and spatial genomics
BAM Bouwman, N Crosetto, M Bienko - Trends in genetics, 2022 - cell.com
Over a decade ago the advent of high-throughput chromosome conformation capture (Hi-C)
sparked a new era of 3D genomics. Since then the number of methods for mapping the 3D …
sparked a new era of 3D genomics. Since then the number of methods for mapping the 3D …
SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding
A fundamental question in gene regulation is how cell-type-specific gene expression is
influenced by the packaging of DNA within the nucleus of each cell. We recently developed …
influenced by the packaging of DNA within the nucleus of each cell. We recently developed …
Modification mapping by nanopore sequencing
LK White, JR Hesselberth - Frontiers in Genetics, 2022 - frontiersin.org
Next generation sequencing (NGS) has provided biologists with an unprecedented view into
biological processes and their regulation over the past 2 decades, fueling a wave of …
biological processes and their regulation over the past 2 decades, fueling a wave of …
[HTML][HTML] Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression
To understand how chromatin domains coordinate gene expression, we dissected select
genetic elements organizing topology and transcription around the Prdm14 super enhancer …
genetic elements organizing topology and transcription around the Prdm14 super enhancer …
Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture
Chromosome conformation capture (3C) methods measure the spatial proximity between
DNA elements in the cell nucleus. Many methods have been developed to sample 3C …
DNA elements in the cell nucleus. Many methods have been developed to sample 3C …
Extracting multi-way chromatin contacts from Hi-C data
There is a growing realization that multi-way chromatin contacts formed in chromosome
structures are fundamental units of gene regulation. However, due to the paucity and …
structures are fundamental units of gene regulation. However, due to the paucity and …
Long-read sequencing to understand genome biology and cell function
Determining the sequence of DNA and RNA molecules has a huge impact on the
understanding of cell biology and function. Recent advancements in next-generation short …
understanding of cell biology and function. Recent advancements in next-generation short …
[HTML][HTML] Exploring 3D chromatin contacts in gene regulation: the evolution of approaches for the identification of functional enhancer-promoter interaction
Mechanisms underlying gene regulation are key to understand how multicellular organisms
with various cell types develop from the same genetic blueprint. Dynamic interactions …
with various cell types develop from the same genetic blueprint. Dynamic interactions …
Functional genomic assays to annotate enhancer–promoter interactions genome wide
Enhancers are pivotal for regulating gene transcription that occurs at promoters.
Identification of the interacting enhancer–promoter pairs and understanding the …
Identification of the interacting enhancer–promoter pairs and understanding the …