Tagmentation Buffer (2x)

Cyclin-dependent kinase inhibitor 1A mediates mouse line- and fate-dependent cellular responses in Cx3cr1-Cre genetic tools
Yamasaki, Ayato et al.
Microglia, the resident macrophages in the central nervous system (CNS), have been intensively studied using rodent genetic models, including the Cre-loxP system. Among them are tamoxifen (TAM)-inducible CX3C chemokine receptor 1 (Cx3cr1)-Cre mouse lines (Cx3cr1CreERT2), which have enabled in-depth analyses of the...

Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding
Whiting, F.J.H., Mossner, M., Gabbutt, C. et al.
Cancer treatment frequently fails due to the evolution of drug-resistant cell phenotypes driven by genetic or non-genetic changes. The origin, timing, and rate of spread of these adaptations are critical for understanding drug resistance mechanisms but remain challenging to observe directly. We present a mathe...

CRISPR screen decodes SWI/SNF chromatin remodeling complex assembly
Schwaemmle, Hanna et al.
The SWI/SNF (or BAF) complex is an essential chromatin remodeler, which is frequently mutated in cancer and neurodevelopmental disorders. These are often heterozygous loss-of-function mutations, indicating a dosage-sensitive role for SWI/SNF subunits. However, the molecular mechanisms regulating SWI/SNF subunit dosa...

Eosinophil innate immune memory after bacterial skin infection promotes allergic lung inflammation
Radhouani, Mariem et al.
Microbial exposure at barrier interfaces drives development and balance of the immune system, but the consequences of local infections for systemic immunity and secondary inflammation are unclear. Here, we show that skin exposure to the bacterium Staphylococcus aureus persistently shapes the immune sys...

Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq
Haikuo Li et al.
The epigenome of a cell is tightly correlated with gene transcription, which controls cell identity and diverse biological activities. Recent advances in spatial technologies have improved our understanding of tissue heterogeneity by analyzing transcriptomics or epigenomics with spatial information preserved, but ha...

Recurrent patterns of widespread neuronal genomic damage shared by major neurodegenerative disorders
Zinan Zhou et al.
Amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease (AD) are common neurodegenerative disorders for which the mechanisms driving neuronal death remain unclear. Single-cell whole-genome sequencing of 429 neurons from three C9ORF72 ALS, six C9ORF72 FTD, seven AD, and twenty-thre...

Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy
Guanlan Dong et al.
Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease that is linked to exposure to repetitive head impacts (RHI), yet little is known about its pathogenesis. Applying two single-cell whole-genome sequencing methods to hundreds of neurons from prefrontal cortex of 15 individuals with CTE, and 4 with ...

Combinatorial mapping of E3 ubiquitin ligases to their target substrates
Chase C. Suiter et al.
Highlights Developed a combinatorial assay to test E3-substrate interactions at scale Identified known and unknown E3-substrate relationships across three screens Assessment of in silico models points to scalable computational substrate discovery Computed models of E3-...

Minimization of gene editing off-target effects by tissue restriction of expression
Nam-Gyun Kim et al.
Therapeutic in vivo gene editing with highly specific nucleases has the potential to revolutionize treatment for a wide range of human diseases, including genetic disorders and latent viral infections like herpes simplex virus (HSV). However, challenges regarding specificity, efficiency, delivery, and safe...

HIRA protects telomeres against R-loop-induced instability in ALT cancer cells
Michelle Lee Lynskey et al.
Highlights HIRA establishes greater telomeric chromatin accessibility after ATRX-DAXX loss Deposition of new H3.3 by HIRA-UBN restricts telomeric ssDNA and TERRA R-loops Unresolved TERRA R-loops block new H3.3 deposition by HIRA-UBN CHK1 phosphorylation of H3.3 is critical to pr...

Enhancing single-cell ATAC sequencing with formaldehyde fixation, cryopreservation, and multiplexing for flexible analysis
Tobias Hohl et al.
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) revolutionized the field of epigenetics since its emergence by providing a means to uncover chromatin dynamics and other factors affecting gene expression. The development of single-cell (sc) applications in recent years led to an even deeper...

On the identification of differentially-active transcription factors from ATAC-seq data
Felix Ezequiel Gerbaldo et al.
ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approa...

HNF1β bookmarking involves Topoisomerase 1 activation and DNA topology relaxation in mitotic chromatin
Alessia Bagattin et al.
Highlights HNF1β mitotic site binding is preserved with a specific methanol/formaldehyde ChIP BTBD2, an HNF1β partner, mediates mitosis-specific interaction with TOP1 HNF1β recruits TOP1 and induces DNA relaxation around bookmarked HNF1β sites An HNF1β m...

Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo
Jack Kucinski et al.
Fusion-positive rhabdomyosarcoma is an aggressive pediatric cancer molecularly characterized by arrested myogenesis. The defining genetic driver, PAX3::FOXO1, functions as a chimeric gain-of-function transcription factor. An incomplete understanding of PAX3::FOXO1’s in vivo epigenetic mechanisms has hindered t...

CRISPR screen decodes SWI/SNF chromatin remodeling complex assembly
Hanna Schwaemmle et al.
The SWI/SNF (or BAF) complex is an essential chromatin remodeler that regulates DNA accessibility at developmental genes and enhancers. SWI/SNF subunits are among the most frequently mutated genes in cancer and neurodevelopmental disorders. These mutations are often heterozygous loss-of-function alleles, indicating ...

Clock-dependent chromatin accessibility rhythms regulate circadian transcription
Ye Yuan et al.
Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly ...

PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites
Andrew Dimond et al.
PBK/TOPK is a mitotic kinase implicated in haematological and non-haematological cancers. Here we show that the key haemopoietic regulators Ikaros and Aiolos require PBK-mediated phosphorylation to dissociate from chromosomes in mitosis. Eviction of Ikaros is rapidly reversed by addition of the PBK-inhibitor OTS514,...

Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements
Benjamin J. Patty et al.
Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding...

High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method
Cobb L. et all.
Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, whi...

On the identification of differentially-active transcription factors from ATAC-seq data
Gerbaldo F. et al.
ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approa...

Improved metagenome assemblies through selective enrichment of bacterial genomic DNA from eukaryotic host genomic DNA using ATAC-seq
Lindsey J Cantin et al.
Genomics can be used to study the complex relationships between hosts and their microbiota. Many bacteria cannot be cultured in the laboratory, making it difficult to obtain adequate amounts of bacterial DNA and to limit host DNA contamination for the construction of metagenome-assembled genomes (MAGs). For example,...

A fast and inexpensive plate-based NGS library preparation method for insect genomics
Lauren Cobb et al.
Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, whi...

Therapeutic targeting of EP300/CBP by bromodomain inhibition in hematologic malignancies
Luciano Nicosia et al.
CCS1477 (inobrodib) is a potent, selective EP300/CBP bromodomain inhibitor which induces cell-cycle arrest and differentiation in hematologic malignancy model systems. In myeloid leukemia cells, it promotes rapid eviction of EP300/CBP from an enhancer subset marked by strong MYB occupancy and high H3K27 acetylation,...

ARID1A governs the silencing of sex-linked transcription during male meiosis in the mouse
Menon D.U. et al.
We present evidence implicating the BAF (BRG1/BRM Associated Factor) chromatin remodeler in meiotic sex chromosome inactivation (MSCI). By immunofluorescence (IF), the putative BAF DNA binding subunit, ARID1A (AT-rich Interaction Domain 1a), appeared enriched on the male sex chromosomes during diplonema of meiosis I...

CXCR4 signaling strength regulates hematopoietic multipotent progenitor fate through extrinsic and intrinsic mechanisms
Vincent Rondeau et al.
How cell-extrinsic niche-related and cell-intrinsic cues drive lineage specification of hematopoietic multipotent progenitors (MPPs) in the bone marrow (BM) is partly understood. We show that CXCR4 signaling strength regulates localization and fate of MPPs. In mice phenocopying the BM myeloid skewing of patients wit...

YAP/BRD4-controlled ROR1 promotes tumor-initiating cells andhyperproliferation in pancreatic cancer.
Yamazaki M. et al.
Tumor-initiating cells are major drivers of chemoresistance and attractive targets for cancer therapy, however, their identity in human pancreatic ductal adenocarcinoma (PDAC) and the key molecules underlying their traits remain poorly understood. Here, we show that a cellular subpopulation with partial epithelial-m...

A neurodevelopmental epigenetic programme mediated bySMARCD3-DAB1-Reelin signalling is hijacked to promote medulloblastomametastasis.
Zou Han et al.
How abnormal neurodevelopment relates to the tumour aggressiveness of medulloblastoma (MB), the most common type of embryonal tumour, remains elusive. Here we uncover a neurodevelopmental epigenomic programme that is hijacked to induce MB metastatic dissemination. Unsupervised analyses of integrated publicly availab...

EBF1 is continuously required for stabilizing local chromatinaccessibility in pro-B cells.
Zolotarev Nikolay et al.
The establishment of de novo chromatin accessibility in lymphoid progenitors requires the "pioneering" function of transcription factor (TF) early B cell factor 1 (EBF1), which binds to naïve chromatin and induces accessibility by recruiting the BRG1 chromatin remodeler subunit. However, it remains unclear whet...