Elastic dosage compensation by X-chromosome upregulation

The pivotal role of the X-chromosome in the genetic architecture of the human brain

Genes on the X-chromosome are extensively expressed in the human brain. However, little is known for the X-chromosome's impact on the brain anatomy, microstructure, and functional network. We examined 1,045 complex brain imaging traits from 38,529 participants in the UK Biobank. We unveiled potential autosome-X-chromosome interactions, while proposing an atlas outlining dosage compensation (DC) for brain imaging traits. Through extensive association studies, we identified 72 genome-wide significant trait-locus pairs (including 29 new associations) that share genetic architectures with brain-related disorders, notably schizophrenia. Furthermore, we discovered unique sex-specific associations and assessed variations in genetic effects between sexes. Our research offers critical insights into the X-chromosome's role in the human brain, underscoring its contribution to the differences observed in brain structure and functionality between sexes.

Imprinted X chromosome inactivation at the gamete-to-embryo transition

In mammals, dosage compensation involves two parallel processes: (1) X inactivation, which equalizes X chromosome dosage between males and females, and (2) X hyperactivation, which upregulates the active X for X-autosome balance. The field currently favors models whereby dosage compensation initiates "de novo" during mouse development. Here, we develop "So-Smart-seq" to revisit the question and interrogate a comprehensive transcriptome including noncoding genes and repeats in mice. Intriguingly, de novo silencing pertains only to a subset of Xp genes. Evolutionarily older genes and repetitive elements demonstrate constitutive Xp silencing, adopt distinct signatures, and do not require Xist to initiate silencing. We trace Xp silencing backward in developmental time to meiotic sex chromosome inactivation in the male germ line and observe that Xm hyperactivation is timed to Xp silencing on a gene-by-gene basis. Thus, during the gamete-to-embryo transition, older Xp genes are transmitted in a "pre-inactivated" state. These findings have implications for the evolution of imprinting.

Appropriate glycemic management protects the germline but not the uterine environment in hyperglycemia

Emerging evidence indicates that parental diseases can impact the health of subsequent generations through epigenetic inheritance. Recently, it was shown that maternal diabetes alters the metaphase II oocyte transcriptome, causing metabolic dysfunction in offspring. However, type 1 diabetes (T1D) mouse models frequently utilized in previous studies may be subject to several confounding factors due to severe hyperglycemia. This limits clinical translatability given improvements in glycemic control for T1D subjects. Here, we optimize a T1D mouse model to investigate the effects of appropriately managed maternal glycemic levels on oocytes and intrauterine development. We show that diabetic mice with appropriate glycemic control exhibit better long-term health, including maintenance of the oocyte transcriptome and chromatin accessibility. We further show that human oocytes undergoing in vitro maturation challenged with mildly increased levels of glucose, reflecting appropriate glycemic management, also retain their transcriptome. However, fetal growth and placental function are affected in mice despite appropriate glycemic control, suggesting the uterine environment rather than the germline as a pathological factor in developmental programming in appropriately managed diabetes.

Out of the Silence: Insights into How Genes Escape X-Chromosome Inactivation

The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes to continue to be expressed from the otherwise inactive X chromosome-in some cases constitutively, while other genes are variable between individuals, tissues or cells. In this review we discuss the advantages and disadvantages of the approaches that have been used to identify escapees. The identity of escapees provides important clues to mechanisms underlying escape from XCI, an arena of study now moving from correlation to functional studies. As most escapees show greater expression in females, the not-so-inactive X chromosome is a substantial contributor to sex differences in humans, and we highlight some examples of such impact.

Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation

Sex chromosome dosage compensation is a model to understand the coordinated evolution of transcription; however, the advanced age of the sex chromosomes in model systems makes it difficult to study how the complex regulatory mechanisms underlying chromosome-wide dosage compensation can evolve. The sex chromosomes of Poecilia picta have undergone recent and rapid divergence, resulting in widespread gene loss on the male Y, coupled with complete X Chromosome dosage compensation, the first case reported in a fish. The recent de novo origin of dosage compensation presents a unique opportunity to understand the genetic and evolutionary basis of coordinated chromosomal gene regulation. By combining a new chromosome-level assembly of P. picta with whole-genome bisulfite sequencing and RNA-seq data, we determine that the YY1 transcription factor (YY1) DNA binding motif is associated with male-specific hypomethylated regions on the X, but not the autosomes. These YY1 motifs are the result of a recent and rapid repetitive element expansion on the P. picta X Chromosome, which is absent in closely related species that lack dosage compensation. Taken together, our results present compelling support that a disruptive wave of repetitive element insertions carrying YY1 motifs resulted in the remodeling of the X Chromosome epigenomic landscape and the rapid de novo origin of a dosage compensation system.

Cross-species imputation and comparison of single-cell transcriptomic profiles

Cross-species comparison and prediction of gene expression profiles are important to understand regulatory changes during evolution and to transfer knowledge learned from model organisms to humans. Single-cell RNA-seq (scRNA-seq) profiles enable us to capture gene expression profiles with respect to variations among individual cells; however, cross-species comparison of scRNA-seq profiles is challenging because of data sparsity, batch effects, and the lack of one-to-one cell matching across species. Moreover, single-cell profiles are challenging to obtain in certain biological contexts, limiting the scope of hypothesis generation. Here we developed Icebear, a neural network framework that decomposes single-cell measurements into factors representing cell identity, species, and batch factors. Icebear enables accurate prediction of single-cell gene expression profiles across species, thereby providing high-resolution cell type and disease profiles in under-characterized contexts. Icebear also facilitates direct cross-species comparison of single-cell expression profiles for conserved genes that are located on the X chromosome in eutherian mammals but on autosomes in chicken. This comparison, for the first time, revealed evolutionary and diverse adaptations of X-chromosome upregulation in mammals.

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.

RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mammals

In mammals, X-chromosomal genes are expressed from a single copy since males (XY) possess a single X chromosome, while females (XX) undergo X inactivation. To compensate for this reduction in dosage compared with two active copies of autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation. However, the existence and mechanisms of X-to-autosome dosage compensation are still under debate. Here we show that X-chromosomal transcripts have fewer m6A modifications and are more stable than their autosomal counterparts. Acute depletion of m6A selectively stabilizes autosomal transcripts, resulting in perturbed dosage compensation in mouse embryonic stem cells. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation is partly regulated by epitranscriptomic RNA modifications.

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.

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

Females have two X chromosomes and males have only one in most mammals. X chromosome inactivation (XCI) occurs in females to equalize X-dosage between sexes. Besides, mammals also balance the dosage between X chromosomes and autosomes via X chromosome upregulation (XCU) to fine-tune X-linked expression and thus maintain genomic homeostasis. Despite some studies highlighting the importance of XCU in somatic cells, little is known about how XCU is achieved and its developmental role during early embryogenesis. Herein, using mouse preimplantation embryos as the model, we reported that XCU initially occurs upon major zygotic genome activation and co-regulates X-linked expression in cooperation with imprinted XCI during preimplantation development. An in-depth analysis further indicated, unexpectedly, only a small proportion of, but not X chromosome-wide, X-linked genes contribute greatly to XCU. Furthermore, we identified that bromodomain containing 4 (BRD4) plays a key role in the transcription activation of XCU during preimplantation development. BRD4 deficiency or inhibition caused an impaired XCU, thus leading to reduced developmental potential and mitochondrial dysfunctions of blastocysts. Our finding was also supported by the tight association of BRD4 dysregulation and XCU disruption in the pathology of cholangiocarcinoma. Thus, our results not only advanced the current knowledge of X-dosage compensation and provided a mechanism for understanding XCU initiation but also presented an important clue for understanding the developmental and pathological role of XCU.

A lifelong duty: how Xist maintains the inactive X chromosome

Female eutherians transcriptionally silence one X chromosome to balance gene dosage between the sexes. X-chromosome inactivation (XCI) is initiated by the lncRNA Xist, which assembles many proteins within the inactive X chromosome (Xi) to trigger gene silencing and heterochromatin formation. It is well established that gene silencing on the Xi is maintained through repressive epigenetic processes, including histone deacetylation and DNA methylation. Recent studies revealed a new mechanism where RNA-binding proteins that interact directly with the RNA contribute to the maintenance of Xist localization and gene silencing. In addition, a surprising plasticity of the Xi was uncovered with many genes becoming upregulated upon experimental deletion of Xist. Intriguingly, immune cells normally lose Xist from the Xi, suggesting that thisXist dependence is utilized in vivo to dynamically regulate gene expression from the Xi. These new studies expose fundamental regulatory mechanisms for the chromatin association of RNAs, highlight the need for studying the maintenance of XCI and Xist localization in a gene- and cell-type-specific manner, and are likely to have clinical impact.

Controlled X-chromosome dynamics defines meiotic potential of female mouse in vitro germ cells

The mammalian germline is characterized by extensive epigenetic reprogramming during its development into functional eggs and sperm. Specifically, the epigenome requires resetting before parental marks can be established and transmitted to the next generation. In the female germline, X‐chromosome inactivation and reactivation are among the most prominent epigenetic reprogramming events, yet very little is known about their kinetics and biological function. Here, we investigate X‐inactivation and reactivation dynamics using a tailor‐made in vitro system of primordial germ cell‐like cell (PGCLC) differentiation from mouse embryonic stem cells. We find that X‐inactivation in PGCLCs in vitro and in germ cell‐competent epiblast cells in vivo is moderate compared to somatic cells, and frequently characterized by escaping genes. X‐inactivation is followed by step‐wise X‐reactivation, which is mostly completed during meiotic prophase I. Furthermore, we find that PGCLCs which fail to undergo X‐inactivation or reactivate too rapidly display impaired meiotic potential. Thus, our data reveal fine‐tuned X‐chromosome remodelling as a critical feature of female germ cell development towards meiosis and oogenesis.