Quiescence in stem cells is traditionally considered as a state of inactive dormancy or with poised potential. Naive mouse embryonic stem cells (ESCs) can enter quiescence spontaneously or upon inhibition of MYC or fatty acid oxidation, mimicking embryonic diapause in vivo. The molecular underpinning and developmental potential of quiescent ESCs (qESCs) are relatively unexplored. Here we show that qESCs possess an expanded or unrestricted cell fate, capable of generating both embryonic and extraembryonic cell types (e.g., trophoblast stem cells). These cells have a divergent metabolic landscape comparing to the cycling ESCs, with a notable decrease of the one-carbon metabolite S -adenosylmethionine. The metabolic changes are accompanied by a global reduction of H3K27me3, an increase of chromatin accessibility, as well as the de-repression of endogenous retrovirus MERVL and trophoblast master regulators. Depletion of methionine adenosyltransferase Mat2a or deletion of Eed in the polycomb repressive complex 2 results in removal of the developmental constraints towards the extraembryonic lineages. Our findings suggest that quiescent ESCs are not dormant but rather undergo an active transition towards an unrestricted cell fate.

X chromosome inactivation triggers a dramatic reprogramming of transcription and chromosome architecture. However, how the chromatin organization of inactive X chromosome is established de novo in vivo remains elusive. Here, we identified an Xist-separated megadomain structure (X-megadomains) on the inactive X chromosome in mouse extraembryonic lineages and extraembryonic endoderm (XEN) cell lines, and transiently in the embryonic lineages, before Dxz4-delineated megadomain formation at later stages in a strain-specific manner. X-megadomain boundary coincides with strong enhancer activities and cohesin binding in an Xist regulatory region required for proper Xist activation in early embryos. Xist regulatory region disruption or cohesin degradation impaired X-megadomains in extraembryonic endoderm cells and caused ectopic activation of regulatory elements and genes near Xist, indicating that cohesin loading at regulatory elements promotes X-megadomains and confines local gene activities. These data reveal stepwise X chromosome folding and transcriptional regulation to achieve both essential gene activation and global silencing during the early stages of X chromosome inactivation. Hi-C analysis identifies Xist-separated megadomains (X-megadomains) on the inactive X chromosome in mouse early embryos. Cohesin loading at Xist regulatory elements promotes X-megadomain formation and restricts nearby gene activity.

DNA repair dysregulation is a key driver of cancer development. Understanding the molecular mechanisms underlying DNA repair dysregulation in cancer cells is crucial for cancer development and therapies. Here, we report that enhancer of zeste homolog 2 (EZH2) directly methylates poly(adenosine diphosphate-ribose) polymerase-1 (PARP-1), an essential enzyme involved in DNA repair, and regulates its activity. Functionally, EZH2-catalyzed methylation represses PARP1 catalytic activity, down-regulates the recruitment of x-ray repair cross-complementing group-1 to DNA lesions and its associated DNA damage repair; on the other hand, it protects the cells from nicotinamide adenine dinucleotide overconsumption upon DNA damage formation. Meanwhile, EZH2-mediated methylation regulates PARP1 transcriptional and oncogenic activity, at least in part, through impairing PARP1-E2F1 interaction and E2F1 transcription factor activity. EZH2 and PARP1 inhibitors synergistically suppress prostate cancer growth. Collectively, our findings uncover an insight of EZH2 functions in fine-tuning PARP1 activity during DNA damage repair and cancer progression, which provides a rationale for combinational targeting EZH2 and PARP1 in cancer.

PDF file - 2219K, CO enhances DNA damage of PCa cells.

XX female and XY male therian mammals equalize X-linked gene expression through the mitotically-stable transcriptional inactivation of one of the two X chromosomes in female somatic cells. Here, we describe an essential function of the X-linked homolog of an ancestral X-Y gene pair, Kdm5c - Kdm5d , in the expression of Xist lncRNA, which is required for stable X-inactivation. Ablation of Kdm5c function in females results in a significant reduction in Xist RNA expression. Kdm5c encodes a demethylase that enhances Xist expression by converting histone H3K4me2/3 modifications into H3K4me1. Ectopic expression of mouse and human KDM5C , but not the Y-linked homolog KDM5D , induces Xist in male mouse embryonic stem cells (mESCs). Similarly, marsupial (opossum) Kdm5c but not Kdm5d also upregulates Xist in male mESCs, despite marsupials lacking Xist , suggesting that the KDM5C function that activates Xist in eutherians is strongly conserved and predates the divergence of eutherian and metatherian mammals. In support, prototherian (platypus) Kdm5c also induces Xist in male mESCs. Together, our data suggest that eutherian mammals co-opted the ancestral demethylase KDM5C during sex chromosome evolution to upregulate Xist for the female-specific induction of X-inactivation.

Long non-coding RNAs (lncRNAs) have been postulated to function in a number of DNA-based processes, most notably transcription. The detection of lncRNAs in situ can offer insights into their function. Fluorescence in situ hybridization (FISH) enables the detection of specific nucleic acid sequences, including lncRNAs, within individual cells. Current RNA FISH techniques can inform both the localization and expression level of RNA transcripts. Together with advances in microscopy, these in situ techniques now allow for visualization and quantification of even lowly expressed or unstable lncRNAs. When combined with detection of associated proteins and chromatin modifications by immunofluorescence, RNA FISH can lend essential insights into lncRNA function. Here, we describe an integrated set of protocols to detect, individually or in combination, specific RNAs, DNAs, proteins, and histone modifications in single cells at high sensitivity using conventional fluorescence microscopy.

BACKGROUND:Benefits of laparoscopic surgery are well recognised but uptake in rural settings of low- and middle-income countries is limited due to implementation barriers. Gasless laparoscopy has been proposed as an alternative but requires a trained rural surgical workforce to upscale. This study evaluates a feasibility of implementing a structured laparoscopic training programme for rural surgeons of North-East India. METHODS:A 3-day training programme was held at Kolkata Medical College in March 2019. Laparoscopic knowledge and Fundamentals of Laparoscopic Skills (FLS) were assessed pre and post simulation training using multiple choice questions and the McGill Inanimate System for Training and Evaluation of Laparoscopic Skills (MISTELS), respectively. Competency with an abdominal lift device was assessed using the Objective Structured Assessment of Technical Skills (OSATS) and live operating performance via the Global Operative Assessment of Laparoscopic Skills (GOALS) scores during live surgery. Costs of the training programme and qualitative feedback were evaluated. RESULTS:Seven rural surgeons participated. There was an improvement in knowledge acquisition (mean difference in MCQ score 5.57 (SD = 4.47)). The overall normalised mean MISTELS score for the FLS tasks improved from 386.02 (SD 110.52) pre-to 524.40 (SD 94.98) post-training (p = 0.09). Mean OSATS score was 22.4 out of 35 (SD 3.31) indicating competency with the abdominal lift device whilst a mean GOALS score of 16.42 out of 25 (SD 2.07) indicates proficiency in performing diagnostic laparoscopy using the gasless technique during live operating. Costs of the course were estimated at 354 USD for trainees and 461 USD for trainers. CONCLUSION:Structured training programme in gasless laparoscopy improves overall knowledge and skills acquisition in laparoscopic surgery for rural surgeons of North-East India. It is feasible to deliver a training programme in gasless laparoscopy for rural surgeons. Larger studies are needed to assess the benefits for wider adoption in a similar context.

India is located at a critical geographic crossroads for understanding the dispersal of Homo sapiens out of Africa and into Asia and Oceania. Here we report evidence for long-term human occupation, spanning the last ~80 thousand years, at the site of Dhaba in the Middle Son River Valley of Central India. An unchanging stone tool industry is found at Dhaba spanning the Toba eruption of ~74 ka (i.e., the Youngest Toba Tuff, YTT) bracketed between ages of 79.6 ± 3.2 and 65.2 ± 3.1 ka, with the introduction of microlithic technology ~48 ka. The lithic industry from Dhaba strongly resembles stone tool assemblages from the African Middle Stone Age (MSA) and Arabia, and the earliest artefacts from Australia, suggesting that it is likely the product of Homo sapiens as they dispersed eastward out of Africa.

Archaeological records documenting the timing and use of northern Great Barrier Reef offshore islands by Aboriginal and Torres Strait Islander peoples throughout the Holocene are limited when compared to the central and southern extents of the region. Excavations on Lizard Island, located 33 km from Cape Flattery on the mainland, provide high resolution evidence for periodic, yet sustained offshore island use over the past 4000 years, with focused exploitation of diverse marine resources and manufacture of quartz artefacts. An increase in island use occurs from around 2250 years ago, at a time when a hiatus or reduction in offshore island occupation has been documented for other Great Barrier Reef islands, but concurrent with demographic expansion across Torres Strait to the north. Archaeological evidence from Lizard Island provides a previously undocumented occupation pattern associated with Great Barrier Reef late Holocene island use. We suggest this trajectory of Lizard Island occupation was underwritten by its place within the Coral Sea Cultural Interaction Sphere, which may highlight its significance both locally and regionally across this vast seascape.

Imprinted X-inactivation silences genes exclusively on the paternally-inherited X-chromosome and is a paradigm of transgenerational epigenetic inheritance in mammals. Here, we test the role of maternal vs. zygotic Polycomb repressive complex 2 (PRC2) protein EED in orchestrating imprinted X-inactivation in mouse embryos. In maternal-null (Eedm-/-) but not zygotic-null (Eed-/-) early embryos, the maternal X-chromosome ectopically induced Xist and underwent inactivation. Eedm-/- females subsequently stochastically silenced Xist from one of the two X-chromosomes and displayed random X-inactivation. This effect was exacerbated in embryos lacking both maternal and zygotic EED (Eedmz-/-), suggesting that zygotic EED can also contribute to the onset of imprinted X-inactivation. Xist expression dynamics in Eedm-/- embryos resemble that of early human embryos, which lack oocyte-derived maternal PRC2 and only undergo random X-inactivation. Thus, expression of PRC2 in the oocyte and transmission of the gene products to the embryo may dictate the occurrence of imprinted X-inactivation in mammals.

X-chromosome inactivation is a dosage compensation mechanism that equalizes X-linked gene expression between male and female mammals through the transcriptional silencing of most genes on one of the two X-chromosomes in females. With a few key exceptions, once the X-chromosome is inactivated replicated copies of that X-chromosome are maintained as inactive in all descendant cells. X-inactivation is therefore a paradigm of epigenetic inheritance. Imprinted X-inactivation is a specialized form of X-inactivation that results in the silencing of the paternally derived X-chromosome. Due to its parent-of-origin-specific pattern of inactivation, imprinted X-inactivation is a model of mitotic as well as meiotic, i.e., transgenerational, epigenetic inheritance. All cells of the early mouse embryo undergo imprinted X-inactivation, a pattern that is subsequently maintained in extraembryonic cell types in vivo and in vitro. Here, we describe both high- and low-throughput approaches to interrogate imprinted X-inactivation in the mouse embryo as well in cultured extraembryonic stem cells.

Chronic pain affects approximately 19% of adults, and negatively impacts on quality of life;1 pharmacological, psychological, and physical therapies are the recommended management. Despite limited evidence of efficacy and long-term harms, opioid prescribing has increased. Non-compliance in chronic-pain patients is problematic; underuse contributes to insufficient relief and opioid diversion. Overuse may cause adverse events, tolerance, and dependence. The Scottish Intercollegiate Guidelines Network 136 recommends annual opioid review, with continuation only if demonstrated efficacy. Increased risk of opioid-related death with concomitant opioid gabapentinoid use has been reported. The aims of this study were to (i) assess the effectiveness, side-effects, and compliance to opioid prescription in Lothian Chronic Pain Service (LCPS) patients; (ii) compare opioid management within LCPS to Scottish Intercollegiate Guidelines Network 136 recommendations; (iii) assess changes in opioid management since a 2006 service evaluation; and (iv) identify patients prescribed opioids and gabapentinoids. Patients attending LCPS (multidisciplinary pain management provider) clinics were screened for opioid use. Patients reporting opioids completed an opioid use questionnaire (self-reported opioid use, efficacy, and side-effects) and the brief pain inventory short form (pain severity and interference). The current analgesic prescription was recorded. Responses were compared with a 2006 service evaluation. Oral swabs were taken to assess medication compliance; non-compliance was defined as a mismatch between opioid prescription and self-reported opioid use or oral swab. 64.1% (202/315) patients attending LCPS reported opioid use. In patients prescribed opioids, the median age was 53 yr (18–91) and pain duration was 7.0 yr (0.17–60). 43.3% (87/202) had taken opioids for longer than 5 yr; 30.0% (61/202) reported opioid and gabapentinoid use. From the Brief Pain Inventory (BPI), 79.9% (151/189) reported moderate/severe pain (>6/10); the interference score was 7.57 (range: 0.42–10). 28.5% (57/202) reported acceptable pain relief; 58.7% (118/202) reported side-effects; 65.1% (127/202) reported medication review within the past year; 26.2% (53/202) were non-compliant with overuse more than underuse (16.3% vs 12.9%). Underusers had a longer pain duration (P=0.015) and were less likely to report that opioids reduced pain (P=0.04). 26.0% (82/315) of those screened reported strong opioid use compared with 18.9% (79/419) screened in 2006 (P=0.033). Despite chronic opioid use, the LCPS patients had moderate/severe pain with high functional interference; reducing opioid use and alternative pain management warrant consideration. Concomitant opioid gabapentinoid use was prevalent, amid reports of increased risk of opioid-related death. Non-compliance occurs; oral swabs can identify non-compliance not detected by patient reporting. Strong opioid use has increased since 2006, despite recommendations to limit long-term use. 1.Breivik H, Collett B, Ventafridda V, et al. Eur J Pain 2005; 10: 287–333

The origins of the South Asian microlithic is hotly debated, with introduction by colonizing Homo sapiens or local adaptive response to climate change, contributing the two main competing models. Here we review the lithic evidence from two regions (the Jurreru Valley and the Middle Son Valley) where well-dated sites spanning 85-6 ka provide detailed records of local technological change. From these recently compiled records, it is clear that technological change from the Middle Paleolithic to the microlithic is continuous and gradual and that elements that are dominant in the microlithic can be seen to have antecedents in the Middle Paleolithic. Furthermore, the oldest sites are found in inland riverine settings rather than coastal settings, with increases in the prevalence of microlithic technology not taking place until climatic conditions worsened. We argue that current evidence better supports the gradual and staged introduction of the microlithic as climate deteriorated, thus favoring the adaptive model.

Background: Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression broadly, it remains unclear why some but not other PRC2 target genes require PRC2 and H3K27me3 for silencing. Results: Here we define the transcriptional and chromatin features that predict which PRC2 target genes require PRC2/H3K27me3 for silencing by interrogating imprinted mouse X-chromosome inactivation. H3K27me3 is enriched at promoters of silenced genes across the inactive X chromosome. To abrogate PRC2 function, we delete the core PRC2 protein EED in F1 hybrid trophoblast stem cells (TSCs), which undergo imprinted inactivation of the paternally inherited X chromosome. Eed(-/-) TSCs lack H3K27me3 and Xist lncRNA enrichment on the inactive X chromosome. Despite the absence of H3K27me3 and Xist RNA, only a subset of the inactivated X-linked genes is derepressed in Eed(-/-) TSCs. Unexpectedly, in wild-type (WT) TSCs these genes are transcribed and are enriched for active chromatin hallmarks on the inactive-X, including RNA PolII, H3K27ac, and H3K36me3, but not the bivalent mark H3K4me2. By contrast, PRC2 targets that remain repressed in Eed(-/-) TSCs are depleted for active chromatin characteristics in WT TSCs. Conclusions: A comparative analysis of transcriptional and chromatin features of inactive X-linked genes in WT and Eed(-/-) TSCs suggests that PRC2 acts as a brake to prevent induction of transcribed genes on the inactive X chromosome, a mode of PRC2 function that may apply broadly.

Fluorescence in situ hybridization (FISH) enables the detection of specific nucleic acid sequences within single cells. For example, RNA FISH provides information on both the expression level and localization of RNA transcripts and, when combined with detection of associated proteins and chromatin modifications, can lend essential insights into long noncoding RNA (lncRNA) function. Epigenetic effects have been postulated for many lncRNAs, but shown for only a few. Advances in in situ techniques and microscopy, however, now allow for visualization of lncRNAs that are expressed at very low levels or are not very stable. FISH-based detections of RNA and DNA coupled with immunological staining of proteins/histone modifications offer the possibility to connect lncRNAs to epigenetic effects. Here, we describe an integrated set of protocols to detect, individually or in combination, specific RNAs, DNAs, proteins, and histone modifications in single cells at a high level of sensitivity using conventional fluorescence microscopy.

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.