Structural insights into the recognition of native nucleosomes by pioneer transcription factors.

Pioneer transcription factors possess the unique ability to bind to nucleosomal DNA and locally open closed chromatin, enabling the binding of additional chromatin-associated factors. These factors are pivotal in determining cell fate. Structural studies of pioneer transcription factors interacting with nucleosomes have predominantly relied on model systems incorporating canonical DNA motifs within synthetic, strongly positioned DNA.

WP-MOD: a multi-omics and taxonomy database for woody plants.

Woody plants, including trees, shrubs, and woody vines, are vital components of terrestrial ecosystems, playing a critical role in maintaining biodiversity, regulating climate, and supporting human livelihoods. Over the past decade, the accumulation of high-throughput sequencing, multi-omics data, and taxonomic information on woody plants has increased significantly, highlighting the need for an integrative woody plant database. Here, we present the Woody Plant Multi-Omics Database (WP-MOD, https://www.

Revealing potential mechanisms of native and non-native snail coexistence through fecal microbiomes and dietary compositions.

Understanding how animals coexist within an ecosystem is essential for the conservation of biodiversity. In China, large populations of a non-native snail Rumina decollata (a highly invasive species reported by various other countries) coexist with two native snail species (Acusta ravida and Euphaedusa aculus). However, the potential mechanisms that facilitate this non-native and native snail coexistence remain uncertain.

ANAgdb: a multi-omics and taxonomy database for ANA-grade.

Background: The ANA-grade, encompassing early-diverging angiosperm lineages, Amborellales, Nymphaeales, and Austrobaileyales, represents a fundamental phase in the evolutionary history of flowering plants. Since the completion of key assembly of the Amborella genome, the continuous influx of omics data from the lineage underscores the need for a specialized database.

Results: Here, we introduce the ANA-grade Genome Database (ANAgdb, https://anagenome.

Preoperative risk prediction models for acute kidney injury after noncardiac surgery: an independent external validation cohort study.

Background: Numerous models have been developed to predict acute kidney injury (AKI) after noncardiac surgery, yet there is a lack of independent validation and comparison among them.

Methods: We conducted a systematic literature search to review published risk prediction models for AKI after noncardiac surgery. An independent external validation was performed using a retrospective surgical cohort at a large Chinese hospital from January 2019 to October 2022.

The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity.

Centromeric chromatin plays a crucial role in kinetochore assembly and chromosome segregation. Centromeres are specified through the loading of the histone H3 variant CENP-A by the conserved chaperone Scm3/HJURP. The N-terminus of Scm3/HJURP interacts with CENP-A, while the C-terminus facilitates centromere localization by interacting with the Mis18 holocomplex via a small domain, called the Mis16-binding domain (Mis16-BD) in fission yeast.

Bibliometric and visual analysis of intraoperative hypotension from 2004 to 2022.

Background: Intraoperative hypotension (IOH) is a common complication occurring in surgical practice. This study aims to comprehensively review the collaboration and impact of countries, institutions, authors, journals, keywords, and critical papers on intraoperative hypotension from the perspective of bibliometric, and to evaluate the evolution of knowledge structure clustering and identify research hotspots and emerging topics.

Methods: Articles and reviews related to IOH published from 2004 to 2022 were retrieved from the Web of Science Core Collection.

The human LIN28B nucleosome is inherently pre-positioned for efficient binding of multiple OCT4s without H3 K27 acetylation.

Pioneer transcription factors possess the unique ability to access DNA within tightly packed chromatin structures, playing pivotal roles in cell differentiation and reprogramming. However, their precise mechanism for recognizing nucleosomes has remained mystery. Recent structural and biochemical investigations into the binding interactions between the human pioneer factor OCT4 and the LIN28B nucleosome by Sinha et al.

Structural mechanism of synergistic targeting of the nucleosome by PU.1 and C/EBPα.

Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation.

Structural mechanism of LIN28B nucleosome targeting by OCT4.

Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown.

Clinical outcomes of implantation of posterior chamber phakic intraocular lens for pathologic and non-pathologic myopia.

Background: To compare the clinical outcomes of posterior chamber phakic intraocular lens (pIOL) implantation for non-pathological myopia and pathological myopia.

Methods: This retrospective case series study which were conducted in Beijing Tongren Eye Center between July 2017 and Oct 2021 comprised 192 eyes of 100 consecutive patients undergoing pIOL implantation. Eyes were divided into two groups based on having pathological myopia or not.

Structural mechanism of nucleosome targeting by OCT4 for pluripotency.

Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the nucleosomal DNA targets is unknown.

Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae).

The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C.

Identification and validation of glomerulotubular crosstalk genes mediating IgA nephropathy by integrated bioinformatics.

Background: IgA nephropathy (IgAN), which has been reported as the most prevalent glomerulonephritis globally, is the major contributor to end-stage renal diseases. This bioinformatics study aimed to explore glomerulotubular crosstalk genes and dysregulated pathways relating to the pathogenesis of IgAN.

Methods: The microarray datasets from the Gene Expression Omnibus (GEO) database were searched.

Preparation of scFv stabilized chromatosomes for single-particle cryo-EM structure determination.

The chromatosome, a nucleosome bound to a histone H1, is the structural unit of metazoan chromatin. Determination of the high-resolution structure of the chromatosome is challenging due to the dynamic nature of H1 binding. Here, we present a protocol for purifying an optimized single-chain antibody variable fragment (scFv) that can be used to stabilize the chromatosome for single-particle cryo-EM studies.

Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation.

Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA.

Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms.

The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively.

Structures of Native-like Nucleosomes: One Step Closer toward Understanding the Structure and Function of Chromatin.

Genomic DNA in eukaryotes is organized into chromatin through association with core histone proteins to form nucleosomes. To understand the structure and function of chromatin, we must determine the structures of nucleosomes containing native DNA sequences. However, to date, our knowledge of nucleosome structures is mainly based on the crystallographic studies of the nucleosomes containing non-native DNA sequences.

Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome.

ATP-dependent chromatin remodeling factors of SWI/SNF2 family including ISWI, SNF2, CHD1 and INO80 subfamilies share a conserved but functionally non-interchangeable ATPase domain. Here we report cryo-electron microscopy (cryo-EM) structures of the nucleosome bound to an ISWI fragment with deletion of the AutoN and HSS regions in nucleotide-free conditions and the free nucleosome at ∼ 4 Å resolution. In the bound conformation, the ATPase domain interacts with the super helical location 2 (SHL 2) of the nucleosomal DNA, with the N-terminal tail of H4 and with the α1 helix of H3.