Biology subjects

Guo, X.

Publications and source records attributed to Guo, X..

At least 217 records · Page 12Linked to original sources

bioRxiv2022

The role and mechanism of NRF2 in endothelial cells and smooth muscle cells of pulmonary artery

Pulmonary hypertension (PH) is a kind of fatal disease. There are no existing drugs that could reverse the diseas. NF-E2-related factor 2 (NRF2) is one of the most important moleculars in the range of cell protection. We examined the expression of NRF2 in PH models and explored the role of NRF2 in regulating abnormal phenotypes in pulmonary artery cells. We determined the expression level of NRF2 in lung tissues of PH model decreased significantly. We found that NRF2 was reduced in rat pulmonary artery endothelial cells (rPAEC) under hypoxia, while it was overexpressed in rat pulmonary artery smooth muscle cells (rPASMC) under hypoxia. Next, the results showed that knockdown NRF2 in rPAEC promoted endothelial-mesenchymal transformation and upregulated reactive oxygen species level. After the rPASMC was treated with siRNA or activator, we found that NRF2 could promote cell proliferation by regulating PDGFR/ERK1/2 and mTOR/P70S6K pathways, and accelerate cell migration by affecting MMP2/3/7. Therefore, the study suggests that the combination of NRF2 activators should be considered to eliminate the promoting effect of NRF2 activators on proliferation and migration of rPASMC. Summary statementHypoxia regulates NRF2 in PAECs and PASMCs differently. We found that NRF2 could promote cell proliferation by regulating PDGFR/ERK1/2 and mTOR/P70S6K pathways, and accelerate cell migration by affecting MMP2/3/7.

cell biology↗

bioRxiv2022

Metabolomic-genomic prediction drastically improves prediction accuracy of breeding values in crop breeding

Metabolomics is intermediate stage between genotype and phenotype, and therefore useful for breeding. Objective was to investigate heritabilities and accuracies of genetic evaluation of malting quality (MQ) traits by integrating both genomic and metabolomic information. In total, 2,430 plots of 562 malting spring barley lines from three years and two locations were included. Five MQ traits were measured in wort produced from each plot. Metabolomic features used were 24,018 Nuclear Magnetic Resonance intensities measured on each wort sample. Methods for statistical analyses were genomic best linear unbiased prediction (GBLUP) and metabolomic-genomic best linear unbiased prediction (MGBLUP). Accuracies of predicted breeding values were compared using two cross-validation strategies: leave-one-year-out (LOYO) and leave-one-line-out (LOLO). Plot heritabilities ranged from 0.060 to 0.279 for GBLUP, and increased to range from 0.123 to 0.283 for MGBLUP. LOLO scheme yielded higher accuracies than LOYO scheme, and MGBLUP yielded higher accuracies than GBLUP regardless of cross-validation scheme. Author SummaryMetabolomics is intermediate stage between genotype and phenotype, and therefore useful for breeding. We carried out a study on 2,430 plots of 562 malting spring barley lines and 24,018 Nuclear Magnetic Resonance intensities measured on each wort sample, to investigate the prediction of breeding values of five malting quality traits by integrating genomic and metabolomic information using a metabolomics-genomic model. Results showed an increase in prediction accuracy for this model compared to a genomic model.

genomics↗

bioRxiv2022

Updating memories of unwanted emotions during human sleep

Post-learning sleep contributes to memory consolidation. Yet, it remains contentious whether sleep affords opportunities to modify or update emotional memories, such as those people would prefer to forget. Here we attempted to update memories during sleep using spoken positive emotional words paired with cues to recent memories for aversive events. Affect updating using positive words during human non-rapid-eye-movement (NREM) sleep, compared with using neutral words instead, reduced negative affect judgments in post-sleep tests, suggesting that the recalled events were perceived as less aversive. EEG analyses showed that emotional words modulated theta and spindle/sigma activity. Specifically, to the extent that theta power was larger for the positive word than for the following memory cue, participants judged the memory cues less negatively. Moreover, to the extent that sigma power was larger for the emotional word than for the following memory cue, participants showed higher forgetting of unwanted memories. Notably, when the onset of individual positive word coincided with the upstate of slow oscillations, a state characterized by increased cortical excitability during NREM sleep, affective updating was more successful. In sum, the affect content of memories was altered via strategic spoken words presentations during sleep, in association with theta power increases and slow-oscillation upstates. These findings offer novel possibilities for modifying unwanted memories during sleep, without requiring conscious confrontations with aversive memories that people would prefer to avoid.

neuroscience↗

bioRxiv2022

Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic ressource for aquaculture

The European flat oyster (Ostrea edulis L.) is the endemic species of the European coasts. Its exploitation has been reduced during the last decades, because of the appearance of two parasites that have led to the collapse of the stocks and the strong decline of the natural oyster beds. O. edulis has been the subject of numerous studies and programs in population genetics and on the presence of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated the effects of these parasites mainly on immunity at the molecular and cellular levels. Several genetic selection programs especially related to resistance to the parasite have been initiated. Within the framework of a European project (PERLE 2) which aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species on the foreshore, obtaining a reference genome has proved to be essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio technology, Illumina, 10X linked and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudo-chromosomes. Annotation of the genome revealed the presence of 35962 protein-coding genes. We analyzed in details the transposable elements (TE) diversity in the flat oyster genome, highlight some specificities in tRNA and miRNA composition and provide first insights in the molecular response of O. edulis to M. refringens. This genome will serve as a reference for genomic studies on O. edulis to better understand its basic physiology or developing genetic markers in breeding projects for aquaculture or natural reef restoration.

genomics↗

bioRxiv2022

Copresent microbiome and short-chain fatty acids profiles of plant biomass utilization in rumen simulation technique system

Rumen contents have considerable utility in converting plant biomass to short- chain fatty acids (SCFAs) when used as inoculum for in vitro fermentation. To better understand the microbial communities and their functions when in vitro ruminal fermentation, the microbiome and SCFAs production were investigated using rumen simulation technique (RUSITEC) system which was inoculated/co- inoculated with rumen contents from goat and cow. This study reconstructed 1677 microbial metagenome-assembled genomes (MAGs) from metagenomic sequencing. The copresent microbiome containing 298 MAGs were found in metagenomic data of these contents and previous ruminal representative samples. These copresent MAGs were overrepresented in decomposing various substrates, especially pectin and xylan. Additionally, the SCFAs productions in RUSITEC were linked with copresent MAGs. Copresent MAGs obtained from this study shows promise to point out the direction for further research on in vitro ruminal fermentation, and enables a better understanding of rumen microbiotal structures and functions under in vitro condition. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/497131v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@310c66org.highwire.dtl.DTLVardef@251334org.highwire.dtl.DTLVardef@fdfecorg.highwire.dtl.DTLVardef@363d8f_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

SARS-CoV-2 S protein antagonizes type I interferon downstream signal pathway through interacting and attenuating phosphorylation of STAT1/STAT2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may keep patients in a clinically asymptomatic state by blocking cellular innate antiviral immunity, but the molecular mechanism remains unclear. Here, we screened the viral proteins of SARS-CoV-2 and found that the spike (S) protein inhibits the activation of interferon-stimulated genes (ISGs) and even reduces the expression of these genes to below background values. Mechanistically, the S protein interacted with STAT1, STAT2, and IRF9 and impedes the phosphorylation of STAT1/STAT2, thus preventing the formation of the interferon-stimulating gene factor 3 (ISGF3) complex and inhibiting the downstream production of Interferon-stimulated genes (ISGs). Remarkably, we also have found that the inhibitory mechanism of the S protein was conservative among SARS-CoV-2 variants and other human coronaviruses, including SARS-CoV, MERS-CoV, HCoV-229E, HCoV-NL63, and HCoV-HKU1. Truncation studies indicated that the most conserved S2 domain played a major inhibitory role. Altogether, our findings unveil a new mechanism by which SARS-CoV-2 S protein attenuated the hosts antiviral immune response and provide new insights into the pathogenic mechanism of coronavirus.

microbiology↗

bioRxiv2022

Community assessment of methods to deconvolve cellular composition from bulk gene expression

We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells. Several published methods predict most cell types well, though they either were not trained to evaluate all functional CD8+ T cell states or do so with low accuracy. Several community-contributed methods address this gap, including a deep learning-based approach, whose strong performance establishes the applicability of this paradigm to deconvolution. Despite being developed largely using immune cells from healthy tissues, deconvolution methods predict levels of tumor-derived immune cells well. Our admixed and purified transcriptional profiles will be a valuable resource for developing deconvolution methods, including in response to common challenges we observe across methods, such as sensitive identification of functional CD4+ T cell states.

bioinformatics↗

bioRxiv2022

Population Sequencing Reveals Rht-D1b Contributing the Bigger Seedling Root to Modern Wheat Cultivars

The Green Revolution (GR) has dramatically increased the yield of modern wheat cultivars; however, whether and how GR reshaped the wheat root system remains largely unknown. Here, a large-scale transcriptomic and phenotypical investigation was performed on seedling roots of 406 worldwide bread wheat accessions, showing differential transcriptomes and phenotypes between landrace and modern cultivars, and the GR allele Rht-D1b was the main genetic factor driving this phenotype differential, conferring a significantly larger seedling root to modern cultivars by increasing cell length and root meristem size. In this case, the translational reinitiation of TaRht-D1 underlies Rht-D1bs genetic effects. In contrast, another GR allele, Rht-B1b, has no significant effects on root-related traits, differing from the similar genetic effects of these two GR alleles on reducing plant height. This unexpected effect of Rht-D1b on root systems contributes to a substantially larger root-shoot ratio in modern wheat cultivars. These findings reveal previously overlooked benefits of GR alleles in modern wheat cultivars and provide clues for their future application to form a robust seminal root system.

plant biology↗

bioRxiv2022

Aridity modulates biogeographic distribution and community assembly of cyanobacterial morphotypes in drylands

The patterns of biogeographical distribution and assembly processes of microbiota are of vital importance for understanding ecological adaptation and functioning maintenance that microorganisms provide. Although the assembly of microbial communities was increasingly inspected, the role of their morphological characteristics is still poorly ascertained. Here, by integrating high-throughput sequencing and traditional trait-based classification, we investigated taxonomic and phylogenetic turnovers of different morphotypes of terrestrial cyanobacteria in biocrusts, as a model system, to evaluate the contributions of deterministic and stochastic processes across a large scale in drylands. The results showed that the bundle-forming category dominated in arid ecosystems with high tolerance against environmental fluctuations. Despite strong distance-decay relationships of {beta}-diversity in all categories, both spatial composition and phylogenetic turnover rates of bundle-forming cyanobacteria were significantly lower than unicellular/colonial, heterocystous, and other non-heterocyst filamentous cyanobacteria. Null model analysis of phylogenetic signals and abundance-based neutral model found that stochastic processes prevailed in the assembly, while aridity mediated the balance between determinism and stochasticity and prompted a shifting threshold among morphotypes. Our findings provide a unique perspective to understand the role of microbial morphology, highlighting the differentiation of biogeographic distribution, environmental response, and species preference between morphotypes with consideration of potential functional consequences, and therefore facilitated the prediction of biodiversity loss under climate change.

ecology↗

bioRxiv2022

Membrane-associated shortened Trk receptors promote neuroprotection and robust axon regeneration without ligands

Activation of neurotrophic factor signaling is a promising therapy for neurodegeneration. However, limited availability of both ligands and receptors permits only transient activation. In this study, we conquered this problem by inventing a new system that forces membrane localization of the intracellular domain of neurotrophin receptor TrkB, which results in constitutive activation without ligands. Our new system overcomes the small size limitation of the genome packaging in adeno-associated virus and allows high expression of the transgene. Single gene therapy using the modified form of TrkB enhances neuroprotection in mose models of glaucoma, and stimulates robust axon regeneration after optic nerve injury. Our system may be also applicable to other trophic factor signaling and lead to a significant advance in the field of gene therapy for neurodegenerative disorders.

neuroscience↗

bioRxiv2022

Plant-on-Chip: core morphogenesis processes in the tiny plant Wolffia australiana

A plant can be thought of as a colony comprising numerous growth buds, each developing to its own rhythm. Such lack of synchrony impedes efforts to describe core principles of plant morphogenesis, dissect the underlying mechanisms, and identify regulators. Here, we use the tiniest known angiosperm to overcome this challenge and provide an ideal model system for plant morphogenesis. We present a detailed morphological description of the monocot Wolffia australiana, as well as high-quality genome information. Further, we developed the Plant-on-Chip culture system and demonstrate the application of advanced technologies such as snRNA-seq, protein structure prediction, and gene editing. We provide proof-of-concept examples that illustrate how W. australiana can open a new horizon for deciphering the core regulatory mechanisms of plant morphogenesis. SignificanceWhat is the core morphogenetic process in angiosperms, a plant like a tree indeterminately growing, or a bud sequentially generating limited types of organs? Wolffia australiana, one of the smallest angiosperms in the world may help to make a distinction. Wolffia plantlet constitutes of only three organs that are indispensable to complete life cycle: one leaf, one stamen and one gynoecium. Before the growth tip is induced to flower, it keeps branching from the leaf axil and the branches separate from the main plantlet. Here we present a high-quality genome of W. australiana, detailed morphological description, a Plant-on-Chip cultural system, and some principle-proof experiments, demonstrating that W. australiana is a promising model system for deciphering core developmental program in angiosperms.

plant biology↗

bioRxiv2022

EEG Responses to Auditory Figure-Ground Perception

Speech-in-noise difficulty is commonly reported among hearing-impaired individuals. Recent work has established generic behavioural measures of sound segregation and grouping that are related to speech-in-noise processing but do not require language. In this study, we assessed potential clinical electroencephalographic (EEG) measures of central auditory grouping (stochastic figure-ground test) and speech-in-noise perception (speech-in-babble test) with and without relevant tasks. Auditory targets were presented within background noise (16 talker-babble or randomly generated pure-tones) in 50% of the trials and composed either a figure (pure-tone frequency chords repeating over time) or speech (English names). EEG was recorded while participants were presented with the target stimuli (figure or speech) under different attentional states (relevant task or visual-distractor task). EEG time-domain analysis demonstrated enhanced negative responses during detection of both types of auditory targets within the time window 650-850 ms but only figure detection produced significantly enhanced responses under the distracted condition. Further single-channel analysis showed that simple vertex-to-mastoid acquisition defines a very similar response to more complex arrays based on multiple channels. Evoked-potentials to the generic figure-ground task therefore represent a potential clinical measure of grouping relevant to real-world listening that can be assessed irrespective of language knowledge and expertise even without a relevant task.

neuroscience↗

bioRxiv2022

The Chromosome-level Genome of Dracaena cochinchinesis Provides Insights into its Biological Features and the Mechanism of Dragon's Blood Formation

Dracaena, a remarkably long-lived and slowly maturing species, is famous all over the world for the production of dragons blood, a precious traditional medicine used by different cultures since ancient times. However, lacking a high-quality genome,the molecular mechanisms underlying these traits are largely unknown and that greatly restricts the protection and regeneration of the rare and endangered plant resources. Here, we sequenced and assembled a chromosome-level genome of the Dracaena cochinchinensis, the first to be sequenced of Dracaena Vand. ex L. The D. cochinchinensis genome covering 1.21 Gb with a scaffold N50 of 50.06 Mb, and encodes 31,619 predicted protein-coding genes. We found D. cochinchinensis has undergone two whole genome duplications (WGDs) and two long terminal repeats (LTRs) insertion burst events. The expansion of cis-zeatin O-glucosyltransferase (cZOGT) and small auxin up-regulated RNA (SAUR) genes is account for its longevity and slow growth. In flavonoids biosynthesis pathway, transcription factors bHLH and MYB were predicted as the core regulators, and ROS as the specific signal molecule during the process of injury-induced dragons blood formation. Our study not only provides high-quality genomic knowledge of D. cochinchinensis, but also deciphered the mystery of its longevity, and preliminarily elucidated the molecular mechanism of dragons blood formation, which will facilitate the resource protection and sustainable utilization of Dracaena. SHORT SUMMARYThis study reports a chromosome-level genome assembly for D. cochinchinensis, the first genome of Dracaena Vand. ex L. It 29 provides valuable genetic resources and creates a large scope for studying Dracaena. We found the significant expansion of genes associated with its longevity and slow growth, and genes in flavonoids biosynthesis were first completely identified. Moreover, transcription factors bHLH and MYB as the core regulator of flavonoids biosynthesis, and ROS as the specific signal molecule during the process of injury-induced dragons blood formation were also identified. These results not only deciphered the mystery of its longevity, but also elucidated the molecular mechanism of dragon[s blood formation preliminarily, which will facilitate the resource protection and sustainable utilization of Dracaena.

genomics↗

bioRxiv2022

Molecular mechanics underlying flat-to-round membrane budding in live secretory cells

Membrane budding entails forces to transform flat membrane into vesicles essential for cell survival. Accumulated studies have identified coat-proteins (e.g., clathrin) as potential budding factors. However, forces mediating many non-coated membrane buddings remain unclear. By visualizing proteins in mediating endocytic budding in live neuroendocrine cells, performing in vitro protein reconstitution and physical modelling, we discovered how non-coated-membrane budding is mediated: actin filaments and dynamin generate a pulling force transforming flat membrane into {Lambda}-shape; subsequently, dynamin helices surround and constrict {Lambda}-profiles base, transforming {Lambda}- to {Omega}-profile, and then constrict {Omega}-profiles pore, converting {Omega}-profiles to vesicles. These mechanisms control budding speed, vesicle size and number, generating diverse endocytic modes differing in these parameters. Their impact is widespread beyond secretory cells, as the unexpectedly powerful functions of dynamin and actin, previously thought to mediate fission and overcome tension, respectively, may contribute to many dynamin/actin-dependent non- coated-membrane buddings, coated-membrane buddings, and other membrane remodelling processes.

cell biology↗

bioRxiv2022

A novel fully-spliced accessory gene in equine lentivirus with distinct Rev-responsive element

All lentiviruses encode an accessory protein Rev, whose main biological function is to mediate the nuclear export of unspliced and incompletely spliced viral transcripts by binding to a viral cis-acting element (termed the Rev-responsive element, RRE) that is located within env-encoding region. Equine infectious anemia virus (EIAV) is a member of the Lentivirus genus in the Retroviridae family, and is considered an important model for the study of lentivirus pathogenesis. Here, we identified a novel transcript from the EIAV genome that encodes a viral protein, named Mat, with unknown function. The transcript mat is fully spliced and comprises parts of the coding regions of MA and TM. Interestingly, the expression of Mat depends on Rev and the CRM1 pathway. Rev could specifically bind to Mat mRNA to promote its nuclear export. We further identified that the first exon of Mat mRNA, which is located within the Gag-encoding region, acts as an unreported RRE. Altogether, we identified a novel fully spliced transcript mat with an unusual RRE, which interacts with Rev for nuclear export through the CRM1 pathway. Our findings may help to expend the understanding of gene transcription and expression of lentivirus. Author summaryIn lentiviruses, the nuclear export of viral transcripts is an important step in controlling viral gene expression. Generally, the unspliced and incompletely spliced (that is, intron-containing) transcripts are exported via the CRM1-dependent export pathway in a process mediated by the viral Rev protein by binding to the Rev-responsive element (RRE) located within the Env-coding region. However, the completely spliced (intronless) transcripts are exported via an endogenous cellular pathway which is Rev independent. Here we identified a novel intronless transcript from EIAV and demonstrated that it encodes a viral protein, termed Mat. Interestingly, we have determined that the expression of Mat depends on Rev, and identified that the first exon of Mat mRNA could specifically bind to Rev and be exported to the cytoplasm, which suggests that first exon of Mat mRNA is a second RRE of EIAV. These findings update the EIAV genome structure and highlight the diversification of post-transcriptional regulation patterns in EIAV, and provides important insights into the Rev-dependent nuclear export of completely spliced transcripts in lentiviruses.

molecular biology↗

bioRxiv2022

Study on gene knockout mice and human mutant individual reveals absence of CEP78 causes photoreceptor and sperm flagella impairments

BackgroundCone-rod dystrophy (CRD) is a genetically inherited retinal disease characterized by photoreceptor degeneration. In some rare cases, CRD and hearing loss can be associated with male fertility, while the underlying mechanism is not well known. MethodsUsing CRISPR/Cas9 system, we generated Cep78-/- mice. And electroretinogram (ERG), immunofluorescence staining and transmission electron microscopy (TEM) were used to analyze visual function and photoreceptor ciliary structure changes in Cep78-/- mouse. HE/PAS staining, scanning-electron microscopy (SEM) were conducted to Cep78-/- mice and human CRD patient with CEP78 protein loss to illustrate male infertility and multiple morphological abnormalities of the sperm flagella (MMAF) caused by CEP78 deficiency. TEM and immunofluorescence staining were performed to characterize morphological and molecular changes of sperm flagella microtubule arrangement, centriole development and spermatid head shaping in Cep78-/- mice. Mass-spectrometry analyses were conducted to identify protein abnormalities after Cep78 deletion and Cep78 interacting proteins in spermiogenesis. Co-immunoprecipitation was used to show the Cep78-Ift20-Ttc21a trimer. The role of Cep78-Ift20-Ttc21a trimer in cilliogenesis and centriole elongation was assessed by cilia induction assay. ResultsCep78 knockout mice exhibited impaired function and morphology of photoreceptors, typified by reduced electroretinogram amplitudes, disrupted translocation of cone arrestin, attenuated and disorganized photoreceptor outer segments (OS) disks and widen OS bases, as well as interrupted cilia elongations and structures. Cep78 deletion also caused male infertility and MMAF, with disordered "9 + 2" structure and triplet microtubules in sperm flagella. CEP78 forms a trimer with intraflagellar transport (IFT) proteins IFT20 and TTC21A essential for sperm flagella formation, is essential for their interaction and stability, and recruits IFT20 to centrosome. Insufficiency of any component in the trimer causes centriole elongation and cilia shortening. Additionally, absence of CEP78 protein in human leaded to similar phenotypes in vision and MMAF as Cep78-/- mice. ConclusionsWe found CEP78 as the causative gene of CRD with MMAF in human and mouse. Cep78 forms a trimer with Ift20 and Ttc21a, and regulate the interaction, stability and localization of the trimer proteins, which regulate cilliogenesis, centriole length, and sperm flagella formation. FundingThis work was supported by the National Key R&D Program (2021YFC2700200 to X.G); National Natural Science Foundation of China (82020108006, 81730025 to C.Z, 81971439, 81771641 to X.G, 82070974 to X.C, 82060183 to X.S); Shanghai Outstanding Academic Leaders (2017BR013 to C.Z); and Six Talent Peaks Project in Jiangsu Province (YY-019 to X.G). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

developmental biology↗

bioRxiv2022

Collateral cleavage of 28s rRNA by RfxCas13d causes death of mice

The CRISPR-Cas13 system is an RNA-guided RNA-targeting system, and has been widely used in transcriptome engineering with potentially important clinical applications. However, it is still controversial whether Cas13 exhibits collateral activity in mammalian cells. Here, we found that knocking down gene expression using RfxCas13d in the adult brain neurons caused death of mice, which was not resulted from the loss of target gene function or off-target effects. Mechanistically, we showed that RfxCas13d exhibited collateral activity in mammalian cells, which is positively correlated with the abundance of target RNA. The collateral activity of RfxCas13d could cleave 28s rRNA into two fragments, leading to translation attenuation and activation of the ZAK-JNK/p38-immediate early gene (IEG) pathway. These results provide new mechanistic insights into the collateral activity of RfxCas13d and warn that the biosafety of CRISPR-Cas13 system needs further evaluation before applying it to clinical treatments.

bioengineering↗

bioRxiv2021

Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF

Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B(1-5). Here, we show that the acidic domain of DNA repair factor APLF (APLFAD) can assemble the histone octamer in a single step, and deposit it on DNA to form nucleosomes. The crystal structure of the APLFAD-histone octamer complex shows that APLFAD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLFAD affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted. one sentence summaryHistone chaperone APLF assembles histones H2A-H2B/H3-H4 into histone octamers to deposit them onto DNA and form nucleosomes.

biochemistry↗