Replication dynamics identifies the folding principles of the inactive X chromosome.

Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase during X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization for heterochromatin stability and gene regulation.

SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice.

Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher-order chromatin structure of the Xi, the underlying mechanism is largely unknown. Here, we explore the epigenetic state of the Xi in SmcHD1-deficient epiblast stem cells and mouse embryonic fibroblasts in comparison with their wild-type counterparts. The results suggest that SmcHD1 underlies the formation of H3K9me3-enriched blocks on the Xi, which, although the importance of H3K9me3 has been largely overlooked in mice, play a crucial role in the establishment of the stably silenced state. We propose that the H3K9me3 blocks formed on the Xi facilitate robust heterochromatin formation in combination with H3K27me3, and that the substantial loss of H3K9me3 caused by SmcHD1 deficiency leads to aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes.

Passive Exoskeleton-Assisted Gait Shows a Unique Interlimb Coordination Signature Without Restricting Regular Walking.

Exoskeleton assistive devices have been developed as a potential approach to solve gait deficits like paretic propulsion and reduced speed. However, it is unclear how these devices affect inter-limb coordination. The duration and the synchrony of gait coordination was assessed during passive exoskeleton-assisted walking in healthy young individuals. It was hypothesized that inter-limb coordination would be reduced in comparison to normal walking without assistance, thus demonstrating gait with exoskeleton to be more explorative and flexible. Eighteen participants were divided into two groups (EXO: n = 9; NO EXO: n = 9) and performed a 5-min walking trial at a preferred walking speed after a familiarization trial. The duration of inter-limb coordination was examined using cross-recurrence quantification analysis and the synchrony was measured using cross sample entropy. There were no significant differences in spatiotemporal measurements between the two groups. However, in comparison to the no exoskeleton group, there was a reduction in the duration of coordination (mean diagonal length: p < 0.01) and the synchrony of coordination (entropy value: p < 0.05) in the exoskeleton group. These results indicate that exoskeletal-assisted gait is characterized by reduced inter-limb coordination possibly for allowing gait patterns to be more explorative and flexible. This is important in rehabilitation of patients who suffer from coordination deficits.

A passive exoskeleton can assist split-belt adaptation.

An exoskeletal device can assist walking in those with gait deficits. A passive exoskeleton can be a favorable choice for local or home rehabilitation settings because it is affordable, light weight, and less complex to utilize. While there is research that investigates the effects of exoskeleton on gait research examining the effects of such devices on gait adaptation, is rare. This is important because in diseases like stroke, the ability to flexibly adapt is affected, such that functional recovery becomes difficult. The purpose of this study was to characterize gait adaptation patterns that result from exoskeleton usage during a split-belt adaptation task. Healthy young participants were randomly assigned to a unilateral exoskeleton or a no-exoskeleton group. Each participant performed the specific split-belt adaptation tasks on the treadmill, where the speed of each belt could be controlled independently. Symmetry indices of spatiotemporal variables were calculated to quantify gait adaptation. To analyze the adaptation, trials were divided into early and late adaptation. We also analyzed degree of adaptation, and transfer effects. We also measured the symmetry of the positive power generated by the individual legs during the split-belt task to determine if using exoskeleton assistance reduced power in the exoskeleton group versus the no-exoskeleton group. Use of a passive exoskeleton device altered gait adaptation during a split-belt treadmill task in comparison to the control group. Such adaptation was found to be largely restricted to the temporal domain. Changes in the gait coordination patterns consisted of both early and late adaptive changes, especially in intra-limb patterns like stance time rather than inter-limb patterns like step time. Although the symmetry of the positive power generated during the split-belt task was found to be reduced for the exoskeleton-assistance group, it was shown that this was primarily the result of increased positive power generated by the side not receiving exoskeletal assistance. An unpowered assistive device can provide a unique solution for coordinating the lower limbs during different gait tasks. Such a solution could reduce the neural burden of adaptation consequently resulting in a reduction of the mechanical burden of walking during the bilateral gait coordination task. This may be useful for accelerating gait rehabilitation in different patient populations. However, balance control is important to consider during unilateral exoskeletal assistance.

Ectopic Splicing Disturbs the Function of Xist RNA to Establish the Stable Heterochromatin State.

Non-coding Xist RNA plays an essential role in X chromosome inactivation (XCI) in female mammals. It coats the X chromosome in cis and mediates the recruitment of many proteins involved in gene silencing and heterochromatinization. The molecular basis of how Xist RNA initiates chromosomal silencing and what proteins participate in this process has been extensively studied and elucidated. Its involvement in the establishment and maintenance of the X-inactivated state is, however, less understood. The Xist IVS allele we previously reported is peculiar in that it can initiate XCI but fails to establish the inactive state that is stably maintained and, therefore, may provide an opportunity to explore how Xist RNA contributes to establish a robust heterochromatin state. Here we demonstrate that ectopic splicing taking place to produce Xist IVS RNA disturbs its function to properly establish stable XCI state. This finding warrants the potential of Xist IVS RNA to provide further insight into our understanding of how Xist RNA contributes to establish sustainable heterochromatin.

Does XIST safeguard against sex-biased human diseases?

Yu et al. (2021) demonstrate that a subset of X-linked immune genes is repressed on the inactive X chromosome (Xi) in a manner dependent on XIST RNA in B cells, and derepression of these genes upon XIST depletion could bias differentiation of naive B cells and be involved in etiology of female-biased autoimmune diseases.

The Kickstart Walk Assist System for improving balance and walking function in stroke survivors: a feasibility study.

BACKGROUND: Compared with traditional physical therapy for stroke patients, lower extremity exoskeletons can provide patients with greater endurance and more repeatable and controllable training, which can reduce the therapeutic burden of the therapist. However, most exoskeletons are expensive, heavy or require active power to be operated. Therefore, a lighter, easy to wear, easy to operate, low-cost technology for stroke rehabilitation would be a welcome opportunity for stroke survivors, caregivers and clinicians. One such device is the Kickstart Walk Assist system and the purpose of this study was to determine feasibility of using this unpowered exoskeleton device in a sample of stroke survivors. METHODS: Thirty stroke survivors were enrolled in the study and experienced walking with the Kickstart exoskeleton device that provided spring-loaded assistance during gait. After 5 days of wearing the exoskeleton, participants were evaluated in the two states of wearing and not wearing the exoskeleton. Outcome measures included: (a) spatio-temporal gait measures, (b) balance measures and (c) exoskeleton-use feedback questionnaire. RESULTS: In comparison to not wearing the device, when participants wore the Kickstart walking system, weight bearing asymmetry was reduced. The time spent on the 10-m walk test was also reduced, but there was no difference in the timed-up-and-go test (TUGT). Gait analysis data showed reduction in step time and double support time. Stroke survivors were positive about the Kickstart walking system's ability to improve their balance, speed and gait. In addition, their confidence level and willingness to use the device was also positive. CONCLUSIONS: These findings show the feasibility of using the Kickstart walking system for improving walking performance in stroke survivors. Our future goal is to perform a longer duration study with more comprehensive pre- and post-testing in a larger sample of stroke survivors. Trial registration Chinese Clinical Trial Registry, ChiCTR2000032665. Registered 5 May 2020-Retrospectively registered, http://www.chictr.org.cn/showproj.aspx?proj=53288.

Comparison of a portable balance board for measures of persistence in postural sway.

Measuring postural sway is important for determining functional ability or risk of falling. Gathering postural sway measures outside of controlled environments is desirable for reaching populations with limited mobility. Previous studies have confirmed the accuracy of the magnitude of postural sway using the Nintendo Wii Balance Board (WBB). However, it is unclear if the WBB can accurately measure persistence of postural sway, i.e., the pattern of center-of-pressure fluctuations over time. The purpose of this study was to compare measures of persistence of postural sway (through detrended fluctuation analysis) using WBB and a force platform (FP). Seventeen healthy individuals performed three standing conditions: eyes open, eyes closed, and one-leg standing. The WBB (30 Hz) was placed on top on the FP (600 Hz) to collect data simultaneously, then the FP data were downsampled to 100 Hz and 30 Hz. The agreement between WBB and FP for measures of postural sway were influenced by the sampling rate and postural sway direction. Intraclass correlation coefficient was excellent (range: 0.953-0.998) for long-term scaling regions in the anterior-posterior direction, but lower (range: 0.352-0.877) and inconsistent for medial-lateral direction and short-term scaling regions. The three comparison groups (WBB at 30 Hz, FP at 30 Hz, and FP at 100 Hz) showed dissimilar abilities in detecting differences in persistence of postural sway. In summary, the WBB is accurate for quantifying persistence of postural sway measurements in long-term scaling regions in the AP direction, but has limitations for short-term scaling regions and the ML direction.

Characterization of genetic-origin-dependent monoallelic expression in mouse embryonic stem cells.

Monoallelic gene expression occurs in various mammalian cells and can be regulated genetically, epigenetically and/or stochastically. We identified 145 monoallelically expressed genes (MoEGs), including seven known imprinted genes, in mouse embryonic stem cells (ESCs) derived from reciprocal F1 hybrid blastocysts and cultured in 2i/LIF. As all MoEGs except for the imprinted genes were expressed in a genetic-origin-dependent manner, we focused on this class of MoEGs for mechanistic studies. We showed that a majority of the genetic-origin-dependent MoEGs identified in 2i/LIF ESCs remain monoallelically expressed in serum/LIF ESCs, but become more relaxed or even biallelically expressed upon differentiation. These MoEGs and their regulatory regions were highly enriched for single nucleotide polymorphisms. In addition, some MoEGs were associated with retrotransposon insertions/deletions, consistent with the fact that certain retrotransposons act as regulatory elements in pluripotent stem cells. Interestingly, most MoEGs showed allelic differences in enrichment of histone H3K27me and H3K4me marks, linking allelic epigenetic differences and monoallelic expression. In contrast, there was little or no allelic difference in CpG methylation or H3K9me. Taken together, our study highlights the impact of genetic variation including single nucleotide polymorphisms and retrotransposon insertions/deletions on monoallelic epigenetic marks and expression in ESCs.

Publisher Correction: Female mice lacking Ftx lncRNA exhibit impaired X-chromosome inactivation and a microphthalmia-like phenotype.

In the original HTML version of this Article, the affiliation details for Hirosuke Shiura, Hidetoshi Hasuwa and Takashi Kohda were incorrect, as detailed in the associated Publisher Correction. These errors have been corrected in both the HTML version of the Article.

RNA-FISH and Immunofluorescence of Mouse Preimplantation and Postimplantation Embryos.

There are two modes of X chromosome inactivation (XCI) in the mouse. One mode is imprinted XCI: it is initiated at around the four-cell stage in favor of the paternal X chromosome, and is maintained in the extraembryonic tissues. The other mode is random XCI, which takes place in the epiblast lineage at the periimplantation stage. X-linked noncoding Xist RNA, which becomes upregulated on the X chromosome to be inactivated at the onset of XCI and plays a critical role in both imprinted and random XCI, and its accumulation in the nucleus have been referred to as one of the hallmarks of the presence of the inactivated X chromosome. RNA-FISH has therefore been an invaluable method for the study of XCI. As XCI status changes dynamically during periimplantation development in the mouse, analysis using samples from these developmental stages is absolutely necessary for elucidation of the molecular basis of XCI mechanisms. However, dissection of the embryos at around the periimplantation stages is not easy, and this impedes in vivo analysis of the kinetics of XCI. Here, we describe our methods for dissecting the periimplantation stage embryo and subsequent procedures for RNA-FISH and immunostaining.

Female mice lacking Ftx lncRNA exhibit impaired X-chromosome inactivation and a microphthalmia-like phenotype.

X-chromosome inactivation (XCI) is an essential epigenetic process in female mammalian development. Although cell-based studies suggest the potential importance of the Ftx long non-protein-coding RNA (lncRNA) in XCI, its physiological roles in vivo remain unclear. Here we show that targeted deletion of X-linked mouse Ftx lncRNA causes eye abnormalities resembling human microphthalmia in a subset of females but rarely in males. This inheritance pattern cannot be explained by X-linked dominant or recessive inheritance, where males typically show a more severe phenotype than females. In Ftx-deficient mice, some X-linked genes remain active on the inactive X, suggesting that defects in random XCI in somatic cells cause a substantially female-specific phenotype. The expression level of Xist, a master regulator of XCI, is diminished in females homozygous or heterozygous for Ftx deficiency. We propose that loss-of-Ftx lncRNA abolishes gene silencing on the inactive X chromosome, leading to a female microphthalmia-like phenotype.

Role of SmcHD1 in establishment of epigenetic states required for the maintenance of the X-inactivated state in mice.

X inactivation in mammals is regulated by epigenetic modifications. Functional deficiency of SmcHD1 has been shown to cause de-repression of X-inactivated genes in post-implantation female mouse embryos, suggesting a role of SmcHD1 in the maintenance of X inactivation. Here, we show that de-repression of X-inactivated genes accompanied a local reduction in the enrichment of H3K27me3 in mouse embryonic fibroblasts deficient for SmcHD1. Furthermore, many of these genes overlapped with those having a significantly lower enrichment of H3K27me3 at the blastocyst stage in wild type. Intriguingly, however, depletion of SmcHD1 did not compromise the X-inactivated state in immortalized female mouse embryonic fibroblasts, in which X inactivation had been established and maintained. Taking all these findings together, we suggest that SmcHD1 facilitates the incorporation of H3K27me3 and perhaps other epigenetic modifications at gene loci that are silenced even with the lower enrichment of H3K27me3 at the early stage of X inactivation. The epigenetic state at these loci would, however, remain as it is at the blastocyst stage in the absence of SmcHD1 after implantation, which would eventually compromise the maintenance of the X-inactivated state at later stages.

What makes the maternal X chromosome resistant to undergoing imprinted X inactivation?

In the mouse, while either X chromosome is chosen for inactivation in a random fashion in the embryonic tissue, the paternally derived X chromosome is preferentially inactivated in the extraembryonic tissues. It has been shown that the maternal X chromosome is imprinted so as not to undergo inactivation in the extraembryonic tissues. X-linked noncoding Xist RNA becomes upregulated on the X chromosome that is to be inactivated. An antisense noncoding RNA, Tsix, which occurs at the Xist locus and has been shown to negatively regulate Xist expression in cis, is imprinted to be expressed from the maternal X in the extraembryonic tissues. Although Tsix appears to be responsible for the imprint laid on the maternal X, those who disagree with this idea would point out the fact that Tsix has not yet been expressed from the maternal X when Xist becomes upregulated on the paternal but not the maternal X at the onset of imprinted X-inactivation in preimplantation embryos. Recent studies have demonstrated, however, that there is a prominent difference in the chromatin structure at the Xist locus depending on the parental origin, which I suggest might account for the repression of maternal Xist in the absence of maternal Tsix at the preimplantation stages.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.

The 5' region of Xist RNA has the potential to associate with chromatin through the A-repeat.

X inactive-specific transcript (Xist) is a long noncoding RNA that plays an essential role in X chromosome inactivation. Although Xist RNA, like common protein-coding mRNAs, is transcribed by RNA polymerase II, spliced and polyadenylated, it is retained in the nucleus and associates with the X chromosome it originates from. It has been assumed that Xist RNA recruits proteins involved in epigenetic modifications and chromatin compaction to the X chromosome. One of the major proteins constituting the nuclear matrix, hnRNP U, has been shown to be required for the association of Xist RNA with the inactive X chromosome (Xi). In this study, we found that the first 950-nt sequence of Xist RNA had the potential to associate with chromatin in a manner independent of hnRNP U. Furthermore, its chromatin association is apparently dependent on the presence of an intact A-repeat sequence, which is one of the repeats in Xist/XIST RNA conserved among many mammalian species, and has been shown to be important for Xist RNA-mediated silencing. Taking this unexpected finding and a previous study demonstrating the effect of Xist RNA lacking the A-repeat on the formation of the silent heterochromatin domain together, we suggest that the A-repeat captures chromatin near the initial loading site of Xist RNA and relocates it into the core of the heterochromatin domain.

Defects in dosage compensation impact global gene regulation in the mouse trophoblast.

Xist RNA, which is responsible for X inactivation, is a key epigenetic player in the embryogenesis of female mammals. Of the several repeats conserved in Xist RNA, the A-repeat has been shown to be essential for its silencing function in differentiating embryonic stem cells. Here, we introduced a new Xist allele into mouse that produces mutated Xist RNA lacking the A-repeat (XistCAGΔ5' ). XistCAGΔ5' RNA expressed in the embryo coated the X chromosome but failed to silence it. Although imprinted X inactivation was substantially compromised upon paternal transmission, allele-specific RNA-seq in the trophoblast revealed that XistCAGΔ5' RNA still retained some silencing ability. Furthermore, the failure of imprinted X inactivation had more significant impacts than expected on genome-wide gene expression. It is likely that dosage compensation is required not only for equalizing X-linked gene expression between the sexes but also for proper global gene regulation in differentiated female somatic cells.

Maintenance of Xist Imprinting Depends on Chromatin Condensation State and Rnf12 Dosage in Mice.

In female mammals, activation of Xist (X-inactive specific transcript) is essential for establishment of X chromosome inactivation. During early embryonic development in mice, paternal Xist is preferentially expressed whereas maternal Xist (Xm-Xist) is silenced. Unlike autosomal imprinted genes, Xist imprinting for Xm-Xist silencing was erased in cloned or parthenogenetic but not fertilized embryos. However, the molecular mechanism underlying the variable nature of Xm-Xist imprinting is poorly understood. Here, we revealed that Xm-Xist silencing depends on chromatin condensation states at the Xist/Tsix genomic region and on Rnf12 expression levels. In early preimplantation, chromatin decondensation via H3K9me3 loss and histone acetylation gain caused Xm-Xist derepression irrespective of embryo type. Although the presence of the paternal genome during pronuclear formation impeded Xm-Xist derepression, Xm-Xist was robustly derepressed when the maternal genome was decondensed before fertilization. Once Xm-Xist was derepressed by chromatin alterations, the derepression was stably maintained and rescued XmXpΔ lethality, indicating that loss of Xm-Xist imprinting was irreversible. In late preimplantation, Oct4 served as a chromatin opener to create transcriptional permissive states at Xm-Xist/Tsix genomic loci. In parthenogenetic embryos, Rnf12 overdose caused Xm-Xist derepression via Xm-Tsix repression; physiological Rnf12 levels were essential for Xm-Xist silencing maintenance in fertilized embryos. Thus, chromatin condensation and fine-tuning of Rnf12 dosage were crucial for Xist imprint maintenance by silencing Xm-Xist.

An Xist-activating antisense RNA required for X-chromosome inactivation.

The transcriptional imbalance due to the difference in the number of X chromosomes between male and female mammals is remedied through X-chromosome inactivation, the epigenetic transcriptional silencing of one of the two X chromosomes in females. The X-linked Xist long non-coding RNA functions as an X inactivation master regulator; Xist is selectively upregulated from the prospective inactive X chromosome and is required in cis for X inactivation. Here we discover an Xist antisense long non-coding RNA, XistAR (Xist Activating RNA), which is encoded within exon 1 of the mouse Xist gene and is transcribed only from the inactive X chromosome. Selective truncation of XistAR, while sparing the overlapping Xist RNA, leads to a deficiency in Xist RNA expression in cis during the initiation of X inactivation. Thus, the Xist gene carries within its coding sequence an antisense RNA that drives Xist expression.

A new Xist allele driven by a constitutively active promoter is dominated by Xist locus environment and exhibits the parent-of-origin effects.

The dosage difference of X-linked genes between the sexes in mammals is compensated for by genetic inactivation of one of the X chromosomes in XX females. A noncoding RNA transcribed from the Xist gene at the onset of X chromosome inactivation coats the X chromosome in cis and induces chromosome-wide heterochromatinization. Here, we report a new Xist allele (Xist(CAG)) driven by a CAG promoter, which is known to be constitutively active in many types of cells. The paternal transmission of Xist(CAG) resulted in the preferential inactivation of the targeted paternal X (Xp) not only in the extra-embryonic but also the embryonic lineage, whereas maternal transmission ended with embryonic lethality at the early postimplantation stage with a phenotype that resembled mutant embryos carrying a maternal deficiency in Tsix, an antisense negative regulator of Xist, in both sexes. Interestingly, we found that the upregulation of Xist(CAG) in preimplantation embryos temporally differed depending on its parental origin: its expression started at the 4- to 8-cell stages when paternally inherited, and Xist(CAG) was upregulated at the blastocyst stage when maternally inherited. This might indicate that the Xist locus on Xp is permissive to transcription, but the Xist locus on the maternal X (Xm) is not. We extrapolated from these findings that the maternal Xist allele might manifest a chromatin structure inaccessible by transcription factors relative to the paternal allele. This might underlie the mechanism for the maternal repression of Xist at the early cleavage stage when Tsix expression has not yet occurred on Xm.