Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis

2023-03-07

Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis

Transposable elements (TEs) are abundant in metazoan genomes and have multifaceted effects on host fitness. However, the mechanisms underlying the functions of TEs are still not fully understood. Here, we combine Hi-C, ATAC-seq, and ChIP-seq assays to report the existence of multimegabase supersized loop (SSL) clusters in the Xenopus tropicalis sperm.

Linking chromatin acylation mark-defined proteome and genome in living cells

2023-03-07

Linking chromatin acylation mark-defined proteome and genome in living cells

A generalizable strategy with programmable site specificity for in situ profiling of histone modifications on unperturbed chromatin remains highly desirable but challenging. We herein developed a single-site-resolved multi-omics (SiTomics) strategy for systematic mapping of dynamic modifications and subsequent profiling of chromatinized proteome and genome defined by specific chromatin acylations in living cells. By leveraging the genetic code expansion strategy, our SiTomics toolkit revealed distinct crotonylation (e.g., H3K56cr) and β-hydroxybutyrylation (e.g., H3K56bhb) upon short chain fatty acids stimulation and established linkages for chromatin acylation mark-defined proteome, genome, and functions.

Menin “reads” H3K79me2 mark in a nucleosomal context

2023-02-25

Menin “reads” H3K79me2 mark in a nucleosomal context

A cryo–electron microscopy structure of menin bound to an H3K79me2 nucleosome revealed that menin engages with the nucleosome using its fingers and palm domains and recognizes the methylation mark through a π-cation interaction. In cells, menin is selectively associated with H3K79me2 on chromatin, particularly in gene bodies.

Ir-Catalyzed Regioselective Dihydroboration of Thioalkynes toward Gem-Diboryl Thioethers

2023-02-08

Ir-Catalyzed Regioselective Dihydroboration of Thioalkynes toward Gem-Diboryl Thioethers

While 1,1-diboryl (gem-diboryl) compounds are valuable synthetic building blocks, currently, related studies have mainly focused on those 1,1-diboryl alkanes without a hetero functional group in the α-position.

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

2023-02-01

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

Our work sheds light on the molecular basis of cfDNA fragmentation towards broader applications in cancer liquid biopsy.

Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells

2023-01-13

Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells

The induced BAs can not only enhance the imaging signals at target genomic loci using a single sgRNA, either at repetitive or non-repetitive sequences, but also recruit epigenetic modulators such as histone methyltransferase SUV39H1 to locally repress transcription. As such, SIMBA can be applied to simultaneously visualize and manipulate, in principle, any genomic locus with controllable timing in living cells.