43rd International Asilomar Chromatin, Chromosomes, and Epigenetics Conference

Article Biochemistry & Molecular Biology

Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline

Pravrutha Raman et al.

Summary: Histones and their posttranslational modifications play diverse chromatin functions in eukaryotes. This study reveals the presence of five H2B variants widely present in mammalian genomes, with two new variants identified. These variants are broadly retained in mammals and expressed in germline cells. The findings suggest that H2B variants likely have important roles in mammalian germline cells through unconventional chromatin packaging or nonchromatin functions.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns

A. Rasim Barutcu et al.

Summary: The nucleus contains distinct classes of membraneless domains, including nuclear speckles and the lamina. These structures are associated with specific types of retained introns, with speckles being linked to short GC-rich introns involved in RNA processing, translation, and the cell cycle. Retained introns associated with speckles show differential regulation across diverse cellular contexts, including the cell cycle, highlighting their role in gene regulation and cell cycle progression.

MOLECULAR CELL (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Principles of nucleosome recognition by chromatin factors and enzymes

Robert K. McGinty et al.

Summary: The recent cryoelectron microscopy structures of chromatin complexes show that many chromatin proteins interact with their nucleosome substrate by using similar arginine anchor and variant arginine interactions. These proteins target specific histone structures on the nucleosome surface and can also interact with and distort nucleosomal DNA for complementary binding.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2021)

Add to Collection

Article Biochemistry & Molecular Biology

The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation

Tapan Sharma et al.

Summary: Skeletal muscle regeneration is mediated by myoblasts that undergo epigenomic changes to establish the gene expression program of differentiated myofibers. mSWI/SNF chromatin remodeling enzymes coordinate with lineage-determining transcription factors to establish the epigenome of differentiated myofibers. Bromodomains bind to acetylated lysines on histone N-terminal tails and other proteins. The mutually exclusive ATPases of mSWI/SNF complexes, BRG1 and BRM, contain bromodomains with undefined functional importance in skeletal muscle differentiation. Pharmacological inhibition of mSWI/SNF bromodomain function using the small molecule PFI-3 reduced differentiation in cell culture and in vivo through decreased myogenic gene expression, while increasing cell cycle-related gene expression and the number of cells remaining in the cell cycle. Comparative gene expression analysis with data from myoblasts depleted of BRG1 or BRM showed that bromodomain function was required for a subset of BRG1- and BRM-dependent gene expression. Reduced binding of BRG1 and BRM after PFI-3 treatment showed that the bromodomain is required for stable chromatin binding at target gene promoters to alter gene expression. Our findings demonstrate that mSWI/SNF ATPase bromodomains permit stable binding of the mSWI/SNF ATPases to promoters required for cell cycle exit and establishment of muscle-specific gene expression.

NUCLEIC ACIDS RESEARCH (2021)

Add to Collection

Article Multidisciplinary Sciences

The Penn State Protein Ladder system for inexpensive protein molecular weight markers

Ryan T. Santilli et al.

Summary: The Penn State Protein Ladder system produces protein molecular weight markers through plasmid expression in E. coli, allowing for easy migration, purification, and detection on SDS-PAGE gels. Additionally, polycistronic expression vectors have been designed for more efficient production and as positive controls for recombinant protein expression and purification in research laboratories.

SCIENTIFIC REPORTS (2021)

Add to Collection

Article Multidisciplinary Sciences

Activation of gene expression by detergent-like protein domains

Bradley K. Broyles et al.

Summary: Machine learning analysis revealed several functionality rules of transcriptional activation domains (tADs), including distribution patterns of specific amino acid residues. These rules are not absolute, but contribute to understanding the mechanism of gene expression activation.

ISCIENCE (2021)

Add to Collection

Article Cell Biology