Versatility of MicroRNA Biogenesis

MicroRNAs (miRNAs) are short single-stranded RNA molecules that regulate gene expression. MiRNAs originate from large primary (pri) and precursor (pre) transcripts that undergo various processing steps along their biogenesis pathway till they reach their mature and functional form. It is not clear, however, whether all miRNAs are processed similarly. Here we show that the ratio between pre-miRNA and mature miRNA forms varies between different miRNAs. Moreover, over-expression of several factors involved in miRNA biogenesis, including Exportin-5, Drosha, NF90a, NF45 and KSRP, displayed bidirectional effects on pre/mature miRNA ratios, suggesting their intricate biogenesis sensitivity. In an attempt to identify additional factors that might explain the versatility in miRNA biogenesis we have analyzed the contribution of two hnRNP family members, hnRNPH1 and hnRNPR. Knock-down or over-expression of these genes suggested that hnRNPR inhibits, whereas hnRNPH1 facilitates, miRNA processing. Overall, our results emphasize that miRNA biogenesis is versatile

Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle.

Chaperones TAPBPR and tapasin associate with class I major histocompatibility complexes (MHC-I) to promote optimization (editing) of peptide cargo. Here, we use solution NMR to investigate the mechanism of peptide exchange. We identify TAPBPR-induced conformational changes on conserved MHC-I molecular surfaces, consistent with our independently determined X-ray structure of the complex. Dynamics present in the empty MHC-I are stabilized by TAPBPR and become progressively dampened with increasing peptide occupancy. Incoming peptides are recognized according to the global stability of the final pMHC-I product and anneal in a native-like conformation to be edited by TAPBPR. Our results demonstrate an inverse relationship between MHC-I peptide occupancy and TAPBPR binding affinity, wherein the lifetime and structural features of transiently bound peptides control the regulation of a conformational switch located near the TAPBPR binding site, which triggers TAPBPR release. These results suggest a similar mechanism for the function of tapasin in the peptide-loading complex

Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses

G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5'-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NF\u3baB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5'-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place

Conceptualising social justice and sociocultural issues within physical education teacher education: international perspectives

Background: Physical education (PE) and physical education teacher education (PETE) have a substantial literature base that advocates for students to develop a critical consciousness, appreciate multiple perspectives, and engage in actions to enhance social justice (Tinning 2016). Analysing sociocultural issues, critically reflecting on beliefs, knowledge, biography and values, and developing a sense of agency to enact change, have been recognised as an integral part of the PETE knowledge base for some time (Fernández-Balboa 1997). However, there remain differences in how social justice itself is conceptualised and enacted. Social justice is aligned heavily with critical and ‘post’ theories where taking action for justice, democracy and power are central; but social justice is also found in humanist beliefs in student-centredness and equality and has been co-opted by neoliberal forces that promote individual responsibility. While a lack of consensus is not in itself a problem (Bialystok 2014), diverse definitions might contribute to confusion (Randall and Robinson 2016) and lead to uncertainty over what and how to teach for social justice. Purpose: In order to work towards greater certainty around concepts of social justice in the PETE community, this project sought to map variations in definition and conceptualisation of social justice and sociocultural issues among physical education teacher educators (PETEs) and physical education and sport pedagogy (PESP) educators, as part of a wider project on social justice and sociocultural perspectives and practices in PETE. Methods: PETE and PESP faculty (n=72) in North America, Europe, and Australasia engaged in an in-depth interview, during which they were asked how they define social justice and sociocultural issues. Additional information about participants’ social identity was collected. A constant comparative method of analysing participants’ definitions mapped a range of concepts building on the theoretical framework of neoliberal, humanist, critical and ‘post’ approaches to social justice. Findings: The data demonstrate that there are a range of understandings about sociocultural issues and social justice. Most commonly, some participants articulated a humanist approach to social justice by encouraging their pre-service teachers (PSTs) to have awareness of equality of opportunity in relation to gender, sexuality and/or racism. Less prevalent, but strongly stated by those who conceptualised social justice in these terms, was the importance to take action for democracy, empowerment or critical reflection. The terms diversity and equality, framed in neoliberal and humanist discourses, were most commonly used within the United States (US), while critical pedagogy and alignment with critical and ‘post’ theories were more prevalent in Australia and New Zealand. Conclusion: Differences exist in the ways social justice is conceptualised in PETE. While this can be attributed to the influence of local issues, it is also reflective of what intellectual tools, such as humanism or critical theory, are available for problematising social issues. The range of non-critical concepts found raises concern that PSTs are not getting the tools to enact social justice or tackle sociocultural issues.

Implicit and explicit pedagogical practices related to sociocultural issues and social justice in physical education teacher education programs

Background: For many years, scholars in PETE have argued for the importance of educating pre-service teachers (PSTs) about equality (e.g., Evans 1990), sociocultural perspectives and issues (e.g., Cliff, Wright and Clarke, 2009; Author 2014) and critical pedagogy (e.g., Fernandez-Balboa 1997; Philpot 2015). Despite this advocacy, we would argue that there are significant differences in how faculty teach about sociocultural issues, and for, social justice. The pedagogical actions through which Physical Education Teacher Educators (PETEs) do this work is the focus of this paper. Purpose: We investigated the pedagogical approaches and strategies used by PETE faculty to address and educate PSTs about social justice and sociocultural issues related to gender, race, sexuality, (dis)ability, socioeconomic status and religion in their individual PETE programs. In this study, we draw on transformational pedagogy (Ukpokodu 2009; Ovens 2017) as a framework for theorizing the data. Through this study, we highlight the pedagogical practices espoused as those that engender transformative learning. Data collection and analysis: Data for this interpretive qualitative research study was collected primarily through in-depth semi-structured interviews with over 70 PETEs who work in 48 PETE programs across Australia, Canada, England, Ireland New Zealand, Sweden, and the United States. Furthermore, an informational survey was used to gather demographic data of the participants. The participants, all current PETEs, had a wide range of professional experiences, which included the length of time in the profession, the type of institution employed, educational backgrounds and courses taught. Data analysis was completed using the processes of content analysis and the constant comparative method (Corbin and Strauss 2008). Findings: Three major themes represent the findings. In the first theme, ‘Intentional and Explicit Pedagogies’ we provide descriptions of the approaches and strategies used by PETEs in this study that were planned in advance of the learning experiences. In the second theme, ‘Teachable Moments’ we provide examples of how PETEs utilized ‘teachable moments’ in implicit and explicit ways to educate PSTs about sociocultural issues. The third theme, ‘Resistance and Constraints’ captures the individual challenges PETE faculty faced within their courses if, and when, they teach for equity and social justice. The findings suggest that social justice struggles to find an explicit presence within many PETE programs and that educating PSTs about sociocultural issues and social justice is lacking in many PETE programs

Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis

Mutations causing aberrant splicing are frequently implicated in human diseases including cancer. Here, we establish a high-throughput screen of randomly mutated minigenes to decode the cis-regulatory landscape that determines alternative splicing of exon 11 in the proto-oncogene MST1R (RON). Mathematical modelling of splicing kinetics enables us to identify more than 1000 mutations affecting RON exon 11 skipping, which corresponds to the pathological isoform RON Delta 165. Importantly, the effects correlate with RON alternative splicing in cancer patients bearing the same mutations. Moreover, we highlight heterogeneous nuclear ribonucleoprotein H (HNRNPH) as a key regulator of RON splicing in healthy tissues and cancer. Using iCLIP and synergy analysis, we pinpoint the functionally most relevant HNRNPH binding sites and demonstrate how cooperative HNRNPH binding facilitates a splicing switch of RON exon 11. Our results thereby offer insights into splicing regulation and the impact of mutations on alternative splicing in cancer.Institute of Molecular Biology Core Facilities; DFG [ZA 881/2-1, KO 4566/4-1, LE 3473/2-1]; LOEWE program Ubiquitin Networks (Ub-Net) of the State of Hesse (Germany); Deutsche Forschungsgemeinschaft [SFB902 B13]; EMBO [3057]; Fundacao para a Ciencia e a Tecnologia, Portugal (FCT Investigator Starting Grant) [IF/00595/2014]; German Federal Ministry of Research (BMBF; e:bio junior group program) [FKZ: 0316196]; Boehringer Ingelheim Foundation; [INST 47/870-1 FUGG

Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay

BACKGROUND: In addition to acting as an RNA quality control pathway, nonsense-mediated mRNA decay (NMD) plays roles in regulating normal gene expression. In particular, the extent to which alternative splicing is coupled to NMD and the roles of NMD in regulating uORF containing transcripts have been a matter of debate. RESULTS: In order to achieve a greater understanding of NMD regulated gene expression we used 2D-DiGE proteomics technology to examine the changes in protein expression induced in HeLa cells by UPF1 knockdown. QPCR based validation of the corresponding mRNAs, in response to both UPF1 knockdown and cycloheximide treatment, identified 17 bona fide NMD targets. Most of these were associated with bioinformatically predicted NMD activating features, predominantly upstream open reading frames (uORFs). Strikingly, however, the majority of transcripts up-regulated by UPF1 knockdown were either insensitive to, or even down-regulated by, cycloheximide treatment. Furthermore, the mRNA abundance of several down-regulated proteins failed to change upon UPF1 knockdown, indicating that UPF1`s role in regulating mRNA and protein abundance is more complex than previously appreciated. Among the bona fide NMD targets, we identified a highly conserved AS-NMD event within the 3` UTR of the HNRNPA2B1 gene. Overexpression of GFP tagged hnRNP A2 resulted in a decrease in endogenous hnRNP A2 and B1 mRNA with a concurrent increase in the NMD sensitive isoforms. CONCLUSIONS: Despite the large number of changes in protein expression upon UPF1 knockdown, a relatively small fraction of them can be directly attributed to the action of NMD on the corresponding mRNA. From amongst these we have identified a conserved AS-NMD event within HNRNPA2B1 that appears to mediate autoregulation of HNRNPA2B1 expression levels