A small proportion of X-linked genes contribute to X chromosome upregulation in early embryos via BRD4-mediated transcriptional activation

Aloe-Emodin Improves Mitophagy in Alzheimer's Disease via Activating the AMPK/PGC-1α/SIRT3 Signaling Pathway

BACKGROUND

Impaired mitophagy results in the accumulation of defective mitochondria that are unable to be cleared effectively in Alzheimer's disease (AD). Aloe-emodin (AE), a key component of the traditional Chinese medicine Rhubarb, exhibits neuroprotective effects against Alzheimer's disease, though the underlying mechanism remains unclear. Studying aloe-emodin's role in enhancing mitophagy is vital for improving cognitive function and reducing neuronal damage in Alzheimer's disease.

METHODS

The APP/PS1 double transgenic mice were adopted as models for AD to assess the effects of aloe-emodin upon cognitive function and its neuroprotective impact on hippocampal neurons. Additionally, we investigated the regulatory mechanisms of proteins within the aforementioned pathway, and the morphological characteristics of mitophagy-related proteins. An AD hippocampal neuron model was developed using Aβ25-35 to evaluate the mitochondrial function, the protein expression of such a pathway and the mitophagy. This approach aims to elucidate the effects and underlying mechanisms of aloe-emodin in relation to AD.

RESULTS

AE activates mitophagy in neurons, improves cognitive dysfunction, reduces hippocampal damage, and alleviates AD symptoms in model mice. AE activates the expression of AMPK, PGC-1α and SIRT3. Increased expression of SIRT3 in mitochondria promotes mitophagy and regulates the function of mitochondrial proteins. When mitochondrial autophagy is enhanced, the expression of Beclin1, LC3, P62, Parkin, and PINK1-related proteins changes. Further in vitro experiments showed that AE can enhance mitochondrial function in Alzheimer's disease cell models. The mitochondrial membrane potential, GSH, ROS and Ca2+ levels gradually recover, alleviating the pathological manifestations of AD. Knocking down SIRT3 leads to increased mitochondrial damage and a reduction in mitophagy in HT22 cells.

CONCLUSION

Experimental results show that AE can activate mitophagy through AMPK/PGC-1α/SIRT3 pathway, alleviate cognitive dysfunction in AD, and reduce damage to hippocampal neurons.

Sperm-borne mRNAs: potential roles in zygote genome activation and epigenetic inheritance

It is well accepted that sperm carry an RNA cargo with functions in early embryo development. However, most research has focused on the role of small RNAs, such as microRNAs, transfer RNAs and long non-coding RNAs, while protein-coding messenger RNAs (mRNAs) received less attention, even though they represent a substantial amount of the sperm RNA pool. Here, we curated mouse transcriptomic data from mature sperm and selected the most abundant mRNAs (above the 0.7 quantile). The obtained gene list was further filtered using two criteria: (i) mRNAs that are statistically higher in the one-cell embryo compared to the MII oocyte transcriptome, indicative of paternal mRNA contribution after fertilization; and (ii) mRNAs that are found bound to ribosomes in the one-cell embryo, indicative of positive translation in the zygote translatome. Our analysis identified 94 genes that form networks functionally involved in epigenetic chromatin organization, gene expression, RNA processing and translation during zygote genome activation. These findings underscore the significant role of sperm-borne mRNAs in early embryonic development and epigenetic inheritance, highlighting the need for further research to fully understand their functions.

Revealing Molecular Connections between Dissolved Organic Matter in Surface Water Sources and Their Cytotoxicity Influenced by Chlorination Disinfection

Dissolved organic matter (DOM) is the primary precursor of disinfection products (DBPs) during chlorination. However, the compositional characteristics of DOM transformation during the chlorination process in different source waters and its relationship to cytotoxicity remain understudied. Here, we used high-resolution mass spectrometry to evaluate chlorination-induced molecular-level changes in DOM derived from different surface water sources. We correlated DOM components with the cytotoxicity profiles of selected DBPs using new alternative methods with predictive toxicological assessments. Our findings indicate a selective chlorination of DOM in natural waters and a tendency for lignin and protein conversion during the manual chlorination process. The reactivity of bioactive compounds decreased in the order of lignin > protein > tannin or ConAC. The cytotoxicity of DOM from source waters is mainly attributed to lignin- and protein-like compounds within the CHO and CHNO groups. Additionally, mitochondrial damage is a highly sensitive indicator of DOM-induced cytotoxicity. The toxicity profiles of DBPs revealed 37 common toxicity-driving components characterized by low mass, medium H/C ratio, low O/C ratio, reduction state, and hydrophobicity. Our findings highlight the need to exploit the health effects of DOM and provide substantial experimental evidence for the necessity to remove potential toxicants.

Lineage-specific dynamics of loss of X upregulation during inactive-X reactivation

In mammals, X chromosome dosage is balanced between sexes through the silencing of one X chromosome in females. Recent single-cell RNA sequencing analysis demonstrated that the inactivation of the X chromosome is accompanied by the upregulation of the active X chromosome (Xa) during mouse embryogenesis. Here, we have investigated if the reactivation of inactive-X (Xi) leads to the loss of Xa upregulation in different cellular or developmental contexts. We find that while Xi reactivation and loss of Xa upregulation are tightly coupled in mouse embryonic epiblast and induced pluripotent stem cells, that is not the case in germ cells. Moreover, we demonstrate that partial reactivation of Xi in mouse extra-embryonic endoderm stem cells and human B cells does not result in the loss of Xa upregulation. Finally, we have established a mathematical model for the transcriptional coordination of two X chromosomes. Together, we conclude that the reactivation of Xi is not always synchronized with the loss of Xa upregulation.

Incomplete transcriptional dosage compensation of chicken and platypus sex chromosomes is balanced by post-transcriptional compensation

Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between sexes and with autosomes. A need for dosage compensation has long been thought to be critical in vertebrates. However, this was questioned by findings of unequal mRNA abundance measurements in monotreme mammals and birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females and a correlation with differential loading of histone modifications. We also observed unbalanced transcripts of Z genes in chicken. Surprisingly, however, we found that protein abundance ratios were 1:1 between the sexes in both species, indicating a post-transcriptional layer of dosage compensation. We conclude that sex chromosome output is maintained in chicken and platypus (and perhaps many other non therian vertebrates) via a combination of transcriptional and post-transcriptional control, consistent with a critical importance of sex chromosome dosage compensation.

Compensation of gene dosage on the mammalian X

Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show 'natural' differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.

Sex chromosome-encoded protein homologs: current progress and open questions

The complexity of biological sex differences is markedly evident in human physiology and pathology. Although many of these differences can be ascribed to the expression of sex hormones, another contributor to sex differences lies in the sex chromosomes beyond their role in sex determination. Although largely nonhomologous, the human sex chromosomes express seventeen pairs of homologous genes, referred to as the 'X-Y pairs.' The X chromosome-encoded homologs of these Y-encoded proteins are crucial players in several cellular processes, and their dysregulation frequently results in disease development. Many diseases related to these X-encoded homologs present with sex-biased incidence or severity. By contrast, comparatively little is known about the differential functions of the Y-linked homologs. Here, we summarize and discuss the current understanding of five of these X-Y paired proteins, with recent evidence of differential functions and of having a potential link to sex biases in disease, highlighting how amino acid-level sequence differences may differentiate their functions and contribute to sex biases in human disease.

Computational protocol for the identification of X-linked genes contributing to X chromosome upregulation from RNA-sequencing datasets

The X chromosome/autosome ratio has been widely used to profile XCU at the chromosomal level. However, this approach overlooks features of inside genes. Here, we present a computational protocol for the identification of X-linked genes contributing to X chromosome upregulation from RNA-sequencing datasets. We describe steps for selecting data, preparing software, processing data, and data analysis. This protocol quantifies the contribution value and contribution increment of each X-linked gene to XCU. For complete details on the use and execution of this protocol, please refer to Lyu et al. (2022).1.

Establishing the Link between X-Chromosome Aberrations and TP53 Status, with Breast Cancer Patient Outcomes

Ubiquitous to normal female human somatic cells, X-chromosome inactivation (XCI) tightly regulates the transcriptional silencing of a single X chromosome from each pair. Some genes escape XCI, including crucial tumour suppressors. Cancer susceptibility can be influenced by the variability in the genes that escape XCI. The mechanisms of XCI dysregulation remain poorly understood in complex diseases, including cancer. Using publicly available breast cancer next-generation sequencing data, we show that the status of the major tumour suppressor TP53 from Chromosome 17 is highly associated with the genomic integrity of the inactive X (Xi) and the active X (Xa) chromosomes. Our quantification of XCI and XCI escape demonstrates that aberrant XCI is linked to poor survival. We derived prognostic gene expression signatures associated with either large deletions of Xi; large amplifications of Xa; or abnormal X-methylation. Our findings expose a novel insight into female cancer risks, beyond those associated with the standard molecular subtypes.

Limitations of X:autosome ratio as a measurement of X-chromosome upregulation

Lentini and Reinius address issues in interpreting non-allelic gene expression measurements of dosage compensation during murine embryonic development.

Response to Lentini and Reinius

Lyu et al. respond to the letter from Lentini and Reinius.

The compleX balancing act of controlling X-chromosome dosage and how it impacts mammalian germline development

In female mammals, the two X chromosomes are subject to epigenetic gene regulation in order to balance X-linked gene dosage with autosomes and in relation to males, which have one X and one Y chromosome. This is achieved by an intricate interplay of several processes; X-chromosome inactivation and reactivation elicit global epigenetic regulation of expression from one X chromosome in a stage-specific manner, whilst the process of X-chromosome upregulation responds to this by fine-tuning transcription levels of the second X. The germline is unique in its function of transmitting both the genetic and epigenetic information from one generation to the next, and remodelling of the X chromosome is one of the key steps in setting the stage for successful development. Here, we provide an overview of the complex dynamics of X-chromosome dosage control during embryonic and germ cell development, and aim to decipher its potential role for normal germline competency.

Dosage compensation: A new player in X chromosome upregulation

Dosage balance between sex chromosomes and autosomes can be achieved through diverse mechanisms across vertebrates and invertebrates. A new study discovers a key player that contributes to X chromosome upregulation (XCU) during early mouse development and associates the dysregulation of XCU with human bile duct cancer pathogenesis.