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Internationally, increasing numbers of children and adolescents with gender dysphoria are presenting for care. In response, gender-affirming therapeutic interventions that seek to align bodily characteristics with an individual's gender identity are more commonly being used. Depending on a young person's circumstances and goals, hormonal interventions may aim to achieve full pubertal suppression, modulation of endogenous pubertal sex hormone effects, and/or development of secondary sex characteristics congruent with their affirmed gender. This is a relatively novel therapeutic area and, although short-term outcomes are encouraging, longer term data from prospective longitudinal adolescent cohorts are still lacking, which may create clinical and ethical decision-making challenges. Here, we review current treatment options, reported outcomes, and clinical challenges in the pharmacological management of trans and gender-diverse adolescents.

This cohort study evaluates the prevalence of mental health problems in transgender and gender diverse children aged 9 to 10 years in the US.

PURPOSE: Increasing numbers of transgender adolescents are receiving gender-affirming treatments (GAT). Given GAT can impair reproductive function, clinical guidelines advise prior counselling regarding fertility preservation (FP). For transgender adults assigned male at birth, FP is usually achieved via a masturbatory sample and sperm cryopreservation. This is less straightforward in transgender adolescents, since they may not be developmentally ready to masturbate and/or masturbation may cause unacceptable gender dysphoria. Testicular biopsy represents an alternative method for sperm retrieval in these adolescents, but for those in early/mid puberty, it is difficult to predict whether sperm will be found. The purpose of this study was therefore to identify factors that predict successful sperm retrieval for cryopreservation via testicular biopsy. METHODS: A retrospective cohort study was undertaken at a tertiary-referral pediatric gender service. Subjects were included if they'd received a testicular biopsy in association with the commencement of GAT between 2010 and 2019. The primary outcome measure was successful sperm retrieval, and potential predictors included age, testicular volume and serum testosterone, LH and FSH levels. RESULTS: Of 25 subjects who received a biopsy prior to starting any GAT, 17 had successful sperm retrieval. While age, testosterone, LH and FSH levels showed minimal differences, testicular volume was significantly higher in those with successful sperm retrieval, and a threshold of ≥ 10 mL showed 92% sensitivity and 71% specificity in predicting successful retrieval. An additional 6 patients received a biopsy after starting puberty suppression and before commencement of oestrogen, and one of these individuals had sperm successfully retrieved despite > 2 years of regular puberty suppression. CONCLUSION: These findings suggest that testicular volume is most useful in predicting successful sperm retrieval following testicular biopsy in trans

Heterozygous missense mutations in the human COL7A1 gene - coding for collagen VII - lead to the rare, dominantly inherited skin disorder dominant dystrophic epidermolysis bullosa (DDEB) that is characterized by skin fragility, blistering, scarring and nail dystrophy. To better understand the pathophysiology of DDEB and develop more effective treatments, suitable mouse models for DDEB are required but to date none have existed. We identified the two most common COL7A1 mutations in DDEB patients (p.G2034R and p.G2043R) and used CRISPR to introduce the corresponding mutations into mouse Col7a1 (p.G2028R and p.G2037R). Dominant inheritance of either of these two alleles results in a phenotype that closely resembles that seen in DDEB patients. Specifically, mice carrying these alleles show recurrent blistering that is first observed transiently around the mouth and paws in the early neonatal period and then again around the digits from 5-10 weeks of age. Histologically, the mice show micro-blistering and reduced collagen VII immunostaining. Biochemically, collagen VII from these mice displays reduced thermal stability, which we also observed to be the case for DDEB patients carrying the analogous mutations. Unlike previous rodent models of EB which frequently show early lethality and severe disease, these mouse models which to our knowledge are the first for DDEB show no reduction in growth and survival and - together with a relatively mild phenotype - represent a practically and ethically tractable tool for better understanding and treating EB.

In rheumatoid arthritis (RA), extracellular vesicles (EVs) are associated with both the propagation and attenuation of joint inflammation and destruction. However, the specific EV content responsible for these processes is largely unknown. Investigations into identifying EV content are confounded by the challenges in obtaining high-quality EV preparations from synovial fluid. Implementing a size exclusion chromatography-based method of EV isolation, coupled with small RNA sequencing, we accurately characterised EV miRNAs in synovial fluid obtained from RA patients and investigated the differences between joints with high- and low-grade inflammation. Synovial fluid was obtained from the joints of 12 RA patients and, based on leukocyte counts, classified as either high (n = 7)- or low (n = 5)-grade inflammation. Using size exclusion chromatography, EVs were purified and small RNA was extracted and sequenced on a NextSeq 500. Sequencing reads were aligned to miRBase v21, and differences in miRNA profiles between RA patients with high- and low-grade joint inflammation were analysed. In total, 1972 distinct miRNAs were identified from RA synovial fluid EVs. miRNAs with less than five reads in fewer than five patients were filtered out, leaving 318 miRNAs for analysis. Analysis of the most abundant miRNAs suggested that they negatively regulate multiple genes relevant to inflammation, including signal transducer and activator of transcription 3 (STAT3), which lies downstream of IL-6 and has a pro-inflammatory role in RA. Synovial fluid from joints with high-grade inflammation contained 3.5-fold more EV miRNA per mL of synovial fluid (p = 0.0017). Seventy-eight EV miRNAs were differentially expressed between RA joints with high- and low-grade inflammation, and pathway analysis revealed that their target genes were commonly involved a variety of processes, including cellular apoptosis, proliferation and migration. Of the 49 miRNAs that were elevated in joints with high-grad

Increasing numbers of trans and gender diverse young people are presenting to health services seeking gender-affirming medical care. While testosterone therapy in transgender males is generally effective in inducing masculinization, some adolescents encounter barriers to accessing such treatment or may not wish to experience all the changes that usually accompany testosterone. Here, we describe the case of a 17 year old trans male who presented with gender dysphoria but was initially unable to start testosterone therapy. Due to a desire for facial hair, he was therefore treated with topical minoxidil, an easily accessible, over-the-counter medication that has been used to treat androgenic alopecia for several decades. In this case, minoxidil was applied regularly to the lower face and, after three months of treatment, he developed obvious pigmented facial hair that was sufficient to help him avoid being misgendered. The only reported side effect was excessive skin dryness. Unexpectedly, despite no direct application to other areas, there was also an increase in pigmented body hair, suggestive of systemic absorption and effect. Given its long-standing use and safety record in the management of alopecia, minoxidil might thus represent a useful treatment option for trans males who desire an increase in facial hair.

OBJECTIVE: Fertility counselling for trans and gender diverse (TGD) adolescents has many complexities, but there is currently little guidance for clinicians working in this area. This study aimed to identify effective strategies for-and qualities of-fertility counselling for TGD adolescents based on clinicians' experiences. DESIGN: We conducted qualitative semi-structured individual interviews in 2019 which explored clinician experiences and fertility counselling practices, perspectives of the young person's experience and barriers and facilitators to fertility preservation access. Data were analysed using thematic analysis. SETTING: This qualitative study examined experiences of clinicians at the Royal Children's Hospital-a tertiary, hospital-based, referral centre and the main provider of paediatric TGD healthcare in Victoria, Australia. PARTICIPANTS: We interviewed 12 clinicians from a range of disciplines (paediatrics, psychology, psychiatry and gynaecology), all of whom were involved with fertility counselling for TGD adolescents. RESULTS: Based on clinician experiences, we identified five elements that can contribute to an effective approach for fertility counselling for TGD adolescents: a multidisciplinary team approach; shared decision-making between adolescents, their parents and clinicians; specific efforts to facilitate patient engagement; flexible personalised care; and reflective practice. CONCLUSIONS: Identification of these different elements can inform and hopefully improve future fertility counselling practices for TGD adolescents, but further studies examining TGD adolescents' experiences of fertility counselling are also required.

Bioethicists are increasingly engaged in considering the ethical issues associated with the care of transgender people. One such issue facing paediatric clinicians is requests for chest surgery from transgender male adolescents. For transgender young people who identify as male but have already progressed through the mid to late stages of puberty, hormone treatment will not reverse breast development. Some of these young people are distressed by their chest, and request surgery to remove this tissue. Demand for this surgery during adolescence is increasing. However, few paediatric hospitals make this intervention available to adolescents. This paper focuses on the following ethical question: Should clinicians make chest surgery available to transgender male adolescents? We argue that making chest surgery available to transgender male adolescents under some circumstances is ethically justifiable for three reasons, based on the concepts of beneficence, privacy, and non-discrimination. Firstly, the limited evidence to date suggests that chest surgery is beneficial to transgender male adolescents who seek this intervention. Secondly, chest surgery protects transgender adolescents' privacy by enabling them to better control disclosure of their transgender identity. Thirdly, chest surgery is already performed on other adolescent males for psychosocial reasons, such as in the case of gynaecomastia; non-discrimination thus provides a further reason for making chest surgery available to transgender male adolescents whose male gender identity is consistent. We suggest that the ethical justifiability of chest surgery in any specific transgender adolescent's case will depend on the individual patient's circumstances.

Gender dysphoria describes the distress associated with having a gender identity that differs from one's birth-assigned sex. To relieve this distress, transgender, and gender diverse (henceforth, trans) individuals commonly undergo medical transition involving hormonal treatments. Current hormonal treatment guidelines cater almost exclusively for those who wish to transition from male to female or vice versa. In contrast, there is a dearth of hormonal options for those trans individuals who identify as non-binary and seek an androgynous appearance that is neither overtly male nor female. Though prolonged puberty suppression with gonadotrophin releasing hormone agonists (GnRHa) could in theory be gender-affirming by preventing the development of unwanted secondary sex characteristics, this treatment option would be limited to pre- or peri-pubertal adolescents and likely have harmful effects. Here, we discuss the theoretical use of Selective Estrogen Receptor Modulators (SERMs) for non-binary people assigned male at birth (AMAB) who are seeking an androgynous appearance through partial feminization without breast growth. Given their unique range of pharmacodynamic effects, SERMs may represent a potential gender-affirming treatment for this population, but there is a lack of knowledge regarding their use and potentially adverse effects in this context.

Small extracellular vesicles (SEVs) such as exosomes are released by multiple cell types. Originally believed to be a mechanism for selectively removing unwanted cellular components, SEVs have received increased attention in recent years for their ability to mediate intercellular communication. Apart from proteins and lipids, SEVs contain RNAs, but how RNAs are selectively loaded into SEVs remains poorly understood. To address this question, we profiled SEV RNAs from mouse dendritic cells using RNA-Seq and identified a long noncoding RNA of retroviral origin, VL30, which is highly enriched (>200-fold) in SEVs compared to parental cells. Bioinformatic analysis revealed that exosome-enriched isoforms of VL30 RNA contain a repetitive 26-nucleotide motif. This repeated motif is itself efficiently incorporated into SEVs, suggesting the likelihood that it directly promotes SEV loading. RNA folding analyses indicate that the motif is likely to form a long double-stranded RNA hairpin and, consistent with this, its overexpression was associated with induction of a potent type I interferon response. Taken together, we propose that preferential loading into SEVs of the VL30 RNA containing this immunostimulatory motif enables cells to remove a potentially toxic RNA and avoid autoinflammation. In this way, the original notion of SEVs as a cellular garbage bin should not be entirely discounted.

OBJECTIVES: Extracellular vesicles (EVs) from rheumatoid arthritis (RA) synovial fluid (SF) have been reported to stimulate the release of pro-inflammatory mediators from recipient cells. We recently developed a size exclusion chromatography (SEC)-based method for EV isolation capable of high-quality enrichments from human SF. Here, we employed this method to accurately characterise the SF EV proteome and investigate potential contributions to inflammatory pathways in RA. METHODS: Using our SEC-based approach, SF EVs were purified from the joints of RA patients classified as having high-level (n = 7) or low-level inflammation (n = 5), and from osteoarthritis (OA) patients (n = 5). Protein profiles were characterised by mass spectrometry. Potential contributions of EV proteins to pathological pathways and differences in protein expression between disease groups were investigated. RESULTS: Synovial fluid EVs were present at higher concentrations in RA joints with high-level inflammation (P-value = 0.004) but were smaller in diameter (P-value = 0.03) than in low-level inflammation. In total, 1058 SF EV proteins were identified by mass spectrometry analysis. Neutrophil and fibroblast markers were overrepresented in all disease groups. Numerous proteins with potential to modulate inflammatory and immunological processes were detected, including nine citrullinated peptides. Forty-five and 135 EV-associated proteins were significantly elevated in RA joints with high-level inflammation than in RA joints with low-level inflammation and OA joints, respectively. Gene ontology analysis revealed significant enrichment for proteins associated with 'neutrophil degranulation' within SF EVs from RA joints with high-level inflammation. CONCLUSION: Our results provide new information about SF EVs and insight into how EVs might contribute to the perpetuation of RA.

In this article, we analyse the novel case of Phoenix, a non-binary adult requesting ongoing puberty suppression (OPS) to permanently prevent the development of secondary sex characteristics, as a way of affirming their gender identity. We argue that (1) the aim of OPS is consistent with the proper goals of medicine to promote well-being, and therefore could ethically be offered to non-binary adults in principle; (2) there are additional equity-based reasons to offer OPS to non-binary adults as a group; and (3) the ethical defensibility of facilitating individual requests for OPS from non-binary adults also depends on other relevant considerations, including the balance of potential benefits over harms for that specific patient, and whether the patient's request is substantially autonomous. Although the broadly principlist ethical approach we take can be used to analyse other cases of non-binary adults requesting OPS apart from the case we evaluate, we highlight that the outcome will necessarily depend on the individual's context and values. However, such clinical provision of OPS should ideally be within the context of a properly designed research study with long-term follow-up and open publication of results.

INTRODUCTION: Being transgender is frequently accompanied by gender dysphoria, which often coexists with mental health concerns. Increased referrals of transgender and gender diverse (TGD) youth to gender clinics have been observed in many countries. Nevertheless, there are limited empirical data on the presentation and outcomes of these patients, and there is an urgent need for more evidence to ensure optimal medical and psychosocial interventions. Here, we describe Trans20, a longitudinal study of TGD patients attending a multidisciplinary paediatric gender service in Melbourne, Australia. Trans20 aims to understand the demographic and clinical characteristics of these patients, to document the natural history of gender diversity presenting in childhood and to investigate long-term outcomes for those receiving interventions. METHODS AND ANALYSIS: Trans20 is a prospective cohort study based on children and adolescents first seen at the Royal Children's Hospital Gender Service (RCHGS) between February 2017 and February 2020. Current estimates indicate the final sample size will be approximately 600. Patients and their parents complete online questionnaires prior to the first appointment with RCHGS and regularly thereafter as part of routine clinical care. On discharge from RCHGS, patients are invited to continue undertaking questionnaires biennially. In this way, a naturally forming cohort study has been created. The primary outcomes include gender dysphoria, physical and mental health, schooling, family functioning and quality of life. Subgroup analyses based on factors such as gender identity, birth-assigned sex and treatment received will be performed using bivariate and multivariate modelling as appropriate, and relevant statistical methods will be applied for the repeated measures over time. ETHICS AND DISSEMINATION: The Royal Children's Hospital Human Research Ethics Committee approved this study (#36323). Findings from Trans20 will have translational impact b

Purpose: The presence of a disorder of sexual development (DSD) acts as a diagnostic specifier for gender dysphoria (GD) under DSM-5, while the International Classification of Diseases (ICD)-10 specifically states that its equivalent diagnosis, gender identity disorder (GID), must not be the result of a chromosomal abnormality. For these reasons, routine karyotyping has been previously advocated in the clinical work-up of children and adolescents with suspected GD or GID. However, the utility of such testing remains unclear. Methods: The results of routine molecular karyotyping were analyzed in 128 patients attending our Australian statewide pediatric gender service from 2013 to 2016. Karyotyping was performed using an Illumina BeadChip platform and provided information on both sex chromosome composition and copy number variation (CNV). Results: No sex chromosome abnormalities directly suggestive of a DSD were discovered. The rate of CNVs among our patient cohort was 8.6% (11/128), similar to that previously reported for the general population. Unexpectedly, three trans male patients shared the same CNV, involving an almost identical 400 kbp deletion on chromosome 15q11.2. The frequency of this deletion within birth-assigned females in our cohort (3/69; 4.3%) was significantly higher than that within local control populations (0.3%; Fisher's exact test p-value=0.002), suggesting a possible association between 15q11.2 deletions and trans male identity. Conclusion: Routine molecular karyotyping failed to detect any occult DSD and indicated that the rate of CNVs was similar to that of the general population. Given these findings, we suggest that molecular karyotyping has minimal clinical utility in the routine management of children and adolescents with GD.

As a complex biological fluid, human synovial fluid (SF) presents challenges for extracellular vesicle (EV) enrichment using standard methods. In this study of human SF, a size exclusion chromatography (SEC)-based method of EV enrichment is shown to deplete contaminants that remain after standard ultracentrifugation-based enrichment methods. Specifically, considerable levels of serum albumin, the high-density lipoprotein marker, apolipoprotein A-I, fibronectin and other extracellular proteins and debris are present in EVs prepared by differential ultracentrifugation. While the addition of a sucrose density gradient purification step improved purification quality, some contamination remained. In contrast, using a SEC-based approach, SF EVs were efficiently separated from serum albumin, apolipoprotein A-I and additional contaminating proteins that co-purified with high-speed centrifugation. Finally, using high-resolution mass spectrometry analysis, we found that residual contaminants which remain after SEC, such as fibronectin and other extracellular proteins, can be successfully depleted by proteinase K. Taken together, our results highlight the limitations of ultracentrifugation-based methods of EV isolation from complex biological fluids and suggest that SEC can be used to obtain higher purity EV samples. In this way, SEC-based methods are likely to be useful for identifying EV-enriched components and improving understanding of EV function in disease.

Past research suggests more variation in sexual attraction in Autism Spectrum Disorder (ASD) using clinical samples. This study utilised a population representative group of 14/15 year olds from the Longitudinal Study of Australian Children. Ninety-four adolescents (73 males, 21 females) with ASD and 3454 (1685 males, 1675 females) without self-reported on sexual attraction and past sexual relationships. Females with ASD reported lower rates of heterosexual preference (adjusted odds ratio: 0.14, p < .001), higher rates of bisexuality (adjusted odds ratio: 6.05, p < .001) and uncertainty in attraction (adjusted odds ratio: 10.44, p < .001) compared with non-ASD females. ASD males reported fewer prior boyfriends/girlfriends. Findings confirm female adolescents with ASD have differences in sexual attraction compared with non-ASD females.

OBJECTIVE: Helper T (Th) cell responses are critical for the pathogenesis of Helicobacter pylori-induced gastritis. Th22 cells represent a newly discovered Th cell subset, but their relevance to H. pylori-induced gastritis is unknown. DESIGN: Flow cytometry, real-time PCR and ELISA analyses were performed to examine cell, protein and transcript levels in gastric samples from patients and mice infected with H. pylori. Gastric tissues from interleukin (IL)-22-deficient and wild-type (control) mice were also examined. Tissue inflammation was determined for pro-inflammatory cell infiltration and pro-inflammatory protein production. Gastric epithelial cells and myeloid-derived suppressor cells (MDSC) were isolated, stimulated and/or cultured for Th22 cell function assays. RESULTS: Th22 cells accumulated in gastric mucosa of both patients and mice infected with H. pylori. Th22 cell polarisation was promoted via the production of IL-23 by dendritic cells (DC) during H. pylori infection, and resulted in increased inflammation within the gastric mucosa. This inflammation was characterised by the CXCR2-dependent influx of MDSCs, whose migration was induced via the IL-22-dependent production of CXCL2 by gastric epithelial cells. Under the influence of IL-22, MDSCs, in turn, produced pro-inflammatory proteins, such as S100A8 and S100A9, and suppressed Th1 cell responses, thereby contributing to the development of H. pylori-associated gastritis. CONCLUSIONS: This study, therefore, identifies a novel regulatory network involving H. pylori, DCs, Th22 cells, gastric epithelial cells and MDSCs, which collectively exert a pro-inflammatory effect within the gastric microenvironment. Efforts to inhibit this Th22-dependent pathway may therefore prove a valuable strategy in the therapy of H. pylori-associated gastritis.

Background: We aimed to characterize the content of leading YouTube videos related to alcohol intoxication and to examine factors associated with alcohol intoxication in videos that were assessed positively by viewers. Methods: We systematically captured the 70 most relevant and popular videos on YouTube related to alcohol intoxication. We employed an iterative process to codebook development which resulted in 42 codes in 6 categories: video characteristics, character socio demographics, alcohol depiction, degree of alcohol use, characteristics associated with alcohol, and consequences of alcohol. Results: There were a total of 333,246,875 views for all videos combined. While 89% of videos involved males, only 49% involved females. The videos had a median of 1,646 (interquartile range [IQR] 300 to 22,969) "like" designations and 33 (IQR 14 to 1,261) "dislike" designations each. Liquor was most frequently represented, followed by beer and then wine/champagne. Nearly one-half (44%) of videos contained a brand reference. Humor was juxtaposed with alcohol use in 79% of videos, and motor vehicle use was present in 24%. There were significantly more likes per dislike, indicating more positive sentiment, when there was representation of liquor (29.1 vs. 11.4, p = 0.008), brand references (32.1 vs. 19.2, p = 0.04), and/or physical attractiveness (67.5 vs. 17.8, p < 0.001). Conclusions: Internet videos depicting alcohol intoxication are heavily viewed. Nearly, half of these videos involve a brand-name reference. While these videos commonly juxtapose alcohol intoxication with characteristics such as humor and attractiveness, they infrequently depict negative clinical outcomes. The popularity of this site may provide an opportunity for public health intervention.

T cell responses are characterized by the phenomenon of immunodominance (ID), whereby peptide-specific T cells are elicited in a reproducible hierarchy of dominant and subdominant responses. However, the mechanisms that give rise to ID are not well understood. We investigated the effect of viral dose on primary CD8(+) T cell (T(CD8+)) ID by injecting mice i.p. with various doses of influenza A virus and assessing the primary T(CD8+) response to five dominant and subdominant peptides. Increasing viral dose enhanced the overall strength of the T(CD8+) response, and it altered the ID hierarchy: specifically, NP(366-374) T(CD8+) were dominant at low viral doses but were supplanted by PA(224-233) T(CD8+) at high doses. To understand the basis for this reversal, we mathematically modeled these T(CD8+) responses and used Bayesian statistics to obtain estimates for Ag presentation, T(CD8+) precursor numbers, and avidity. Interestingly, at low viral doses, Ag presentation most critically shaped ID hierarchy, enabling T(CD8+) specific to the more abundantly presented NP(366-374) to dominate. By comparison, at high viral doses, T(CD8+) avidity and precursor numbers appeared to be the major influences on ID hierarchy, resulting in PA(224-233) T(CD8+) usurping NP(366-374) cells as the result of higher avidity and precursor numbers. These results demonstrate that the nature of primary T(CD8+) responses to influenza A virus is highly influenced by Ag dose, which, in turn, determines the relative importance of Ag presentation, T(CD8+) avidity, and precursor numbers in shaping the ID hierarchy. These findings provide valuable insights for future T(CD8+)-based vaccination strategies.

In mammals, thousands of long non-protein-coding RNAs (ncRNAs) (>200 nt) have recently been described. However, the biological significance and function of the vast majority of these transcripts remain unclear. We have constructed a public repository, the Noncoding RNA Expression Database (NRED), which provides gene expression information for thousands of long ncRNAs in human and mouse. The database contains both microarray and in situ hybridization data, much of which is described here for the first time. NRED also supplies a rich tapestry of ancillary information for featured ncRNAs, including evolutionary conservation, secondary structure evidence, genomic context links and antisense relationships. The database is available at http://jsm-research.imb.uq.edu.au/NRED, and the web interface enables both advanced searches and data downloads. Taken together, NRED should significantly advance the study and understanding of long ncRNAs, and provides a timely and valuable resource to the scientific community.

The assumption that RNA can be readily classified into either protein-coding or non-protein-coding categories has pervaded biology for close to 50 years. Until recently, discrimination between these two categories was relatively straightforward: most transcripts were clearly identifiable as protein-coding messenger RNAs (mRNAs), and readily distinguished from the small number of well-characterized non-protein-coding RNAs (ncRNAs), such as transfer, ribosomal, and spliceosomal RNAs. Recent genome-wide studies have revealed the existence of thousands of noncoding transcripts, whose function and significance are unclear. The discovery of this hidden transcriptome and the implicit challenge it presents to our understanding of the expression and regulation of genetic information has made the need to distinguish between mRNAs and ncRNAs both more pressing and more complicated. In this Review, we consider the diverse strategies employed to discriminate between protein-coding and noncoding transcripts and the fundamental difficulties that are inherent in what may superficially appear to be a simple problem. Misannotations can also run in both directions: some ncRNAs may actually encode peptides, and some of those currently thought to do so may not. Moreover, recent studies have shown that some RNAs can function both as mRNAs and intrinsically as functional ncRNAs, which may be a relatively widespread phenomenon. We conclude that it is difficult to annotate an RNA unequivocally as protein-coding or noncoding, with overlapping protein-coding and noncoding transcripts further confounding this distinction. In addition, the finding that some transcripts can function both intrinsically at the RNA level and to encode proteins suggests a false dichotomy between mRNAs and ncRNAs. Therefore, the functionality of any transcript at the RNA level should not be discounted.

RNAdb is a comprehensive database of mammalian non-protein-coding RNAs (ncRNAs). There is increasing recognition that ncRNAs play important regulatory roles in multicellular organisms, and there is an expanding rate of discovery of novel ncRNAs as well as an increasing allocation of function. In this update to RNAdb, we provide nucleotide sequences and annotations for tens of thousands of non-housekeeping ncRNAs, including a wide range of mammalian microRNAs, small nucleolar RNAs and larger mRNA-like ncRNAs. Some of these have documented functions and/or expression patterns, but the majority remain of unclear significance, and include PIWI-interacting RNAs, ncRNAs identified from the latest rounds of large-scale cDNA sequencing projects, putative antisense transcripts, as well as ncRNAs predicted on the basis of structural features and alignments. Improvements to the database comprise not only new and updated ncRNA datasets, but also provision of microarray-based expression data and closer interface with more specialized ncRNA resources such as miRBase and snoRNA-LBME-db. To access RNAdb, visit http://research.imb.uq.edu.au/RNAdb.

Non-protein-coding RNAs (ncRNAs) are increasingly being recognized as having important regulatory roles. Although much recent attention has focused on tiny 22- to 25-nucleotide microRNAs, several functional ncRNAs are orders of magnitude larger in size. Examples of such macro ncRNAs include Xist and Air, which in mouse are 18 and 108 kilobases (Kb), respectively. We surveyed the 102,801 FANTOM3 mouse cDNA clones and found that Air and Xist were present not as single, full-length transcripts but as a cluster of multiple, shorter cDNAs, which were unspliced, had little coding potential, and were most likely primed from internal adenine-rich regions within longer parental transcripts. We therefore conducted a genome-wide search for regional clusters of such cDNAs to find novel macro ncRNA candidates. Sixty-six regions were identified, each of which mapped outside known protein-coding loci and which had a mean length of 92 Kb. We detected several known long ncRNAs within these regions, supporting the basic rationale of our approach. In silico analysis showed that many regions had evidence of imprinting and/or antisense transcription. These regions were significantly associated with microRNAs and transcripts from the central nervous system. We selected eight novel regions for experimental validation by northern blot and RT-PCR and found that the majority represent previously unrecognized noncoding transcripts that are at least 10 Kb in size and predominantly localized in the nucleus. Taken together, the data not only identify multiple new ncRNAs but also suggest the existence of many more macro ncRNAs like Xist and Air.

Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown. Current catalogues of mammalian proteins exhibit an artefactual discontinuity at a length of 100 aa, so that protein abundance peaks just above this length and falls off sharply below it. To clarify the abundance of short proteins, we identify proteins in the FANTOM collection of mouse cDNAs by analysing synonymous and non-synonymous substitutions with the computer program CRITICA. This analysis confirms that there is no real discontinuity at length 100. Roughly 10% of mouse proteins are shorter than 100 aa, although the majority of these are variants of proteins longer than 100 aa. We identify many novel short proteins, including a "dark matter" subset containing ones that lack detectable homology to other known proteins. Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway.

In recent years, there have been increasing numbers of transcripts identified that do not encode proteins, many of which are developmentally regulated and appear to have regulatory functions. Here, we describe the construction of a comprehensive mammalian noncoding RNA database (RNAdb) which contains over 800 unique experimentally studied non-coding RNAs (ncRNAs), including many associated with diseases and/or developmental processes. The database is available at http://research.imb.uq.edu.au/RNAdb and is searchable by many criteria. It includes microRNAs and snoRNAs, but not infrastructural RNAs, such as rRNAs and tRNAs, which are catalogued elsewhere. The database also includes over 1100 putative antisense ncRNAs and almost 20,000 putative ncRNAs identified in high-quality murine and human cDNA libraries, with more to be added in the near future. Many of these RNAs are large, and many are spliced, some alternatively. The database will be useful as a foundation for the emerging field of RNomics and the characterization of the roles of ncRNAs in mammalian gene expression and regulation.