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Barr, K.

Publications and source records attributed to Barr, K..

13 recordsLinked to original sources

Pannexin 1 Ablation Disrupts Cell Cycle Progression and Compromises the Structure of Melanoma Tumours

Pannexin 1 (PANX1) is a channel-forming glycoprotein that has been implicated in regulating melanoma cell properties such as growth, migration, and invasion. Here we report that the CRISPR-Cas9 mediated ablation of PANX1 or channel inhibition with probenecid shifted A375-P cell cycle distribution towards G2/M, while channel inhibition with spironolactone stalled cell cycle progression at the G1/S checkpoint regardless of PANX1 expression. Bulk RNA sequencing revealed cell cycle related gene expression was downregulated with PANX1 targeting strategies and this was exacerbated when PANX1 deficient cells were treated with spironolactone. When grown as spheroids, we found the deletion and inhibition of PANX1 disrupted spheroid compaction, with spheroids displaying poorly defined borders and reduced circularity. The deletion of PANX1 increased spheroid fragmentation, and this phenotype was intensified when spheroids devoid of PANX1 were treated with spironolactone, highlighting a potential synthetic lethal effect. Using liquid chromatography mass spectrometry, we sought to determine whether PANX1 had binding partners that may act to stabilize spheroid integrity and found that PANX1 co-immunoprecipitated various cell adhesion molecules such as {beta}-actin and F-actin-capping protein subunit -1, suggesting PANX1 and its interacting partners may stabilize cell-cell contacts. When control and PANX1 ablated cells were grown in chick chorioallantoic membrane xenografts to assess their tumour growth characteristics, we discovered that the deletion of PANX1 reduced tumour surface area and viability. Our findings indicate that PANX1 regulates cell cycle progression and the structural architecture of A375-P melanoma tumours, highlighting the therapeutic utility of targeting PANX1 in melanoma.

cancer biology↗

Transcription termination promotes splicing efficiency and fidelity in a compact genome

Splicing of terminal introns is coupled to 3'-end processing by cleavage and polyadenylation (CPA) of mRNAs in mammalian genes. Whether this functional coupling is universally conserved across eukaryotes is unclear. Here we show using long read RNA sequencing in S.cerevisiae that splicing inactivation does not result in widespread CPA impairment. We also show that inactivation of CPA has limited impact on splicing efficiency. The negative impact of CPA inactivation on splicing is mainly due to transcription termination defects that promote readthrough transcription, leading to splicing inhibition for downstream intron-containing genes. Splicing impairment due to 5' extensions is length-dependent and can be detected independently from CPA inactivation for endogenous or synthetic genes, and is likely due to an increased distance of splicing signals to the 5' cap. Finally, we found that deficient termination can promote novel intragenic and long-range intergenic splicing events. These results argue against a broad coupling between splicing and CPA in S.cerevisiae but show that efficient CPA-mediated transcription termination is critical for splicing fidelity and efficiency in a compact genome. Significance StatementAccurate gene expression requires that the enzyme that polymerizes RNA stops at the proper site (termination). In addition multiple RNA processing reactions, including removal of intervening sequences are necessary to produce mature mRNAs. How these different steps in the RNA biogenesis pathways influence each other is not well understood. In this study, we show that inactivation of termination induces mature RNA formation defects, including long RNAs that retain intervening sequences, or chimeric RNAs containing sequences from genes located next to each other on the genome. This study underscores the importance of proper termination to ensure accurate and efficient splicing of adjacent genes, which is particularly critical for compact genomes in which genes are located close to each other.

molecular biology↗

Novel Pannexin 1 isoform is increased in cancer

Alternative translation initiation (ATI) is a process of increasing protein diversity from one transcript, allowing cells to rapidly respond to signals, which is particularly important in cancer cells. Here, we report potential internal translation start sites exist in PANX1 which have implications in trafficking and channel function. Using mouse (mPANX1) constructs for each internal methionine, we saw that these PANX1 isoforms were N-glycosylated, could traffic to the cell surface and mPANX1-M37 formed functional channels activated by C-terminus cleavage or 1-adrenoceptor stimulation. We also identified a ~25 kDa isoform of mPANX1 (mPANX1-25K) endogenously expressed in mouse melanoma cell lines that could be confirmed with a cognate peptide. mPANX1-25K lacks the mPANX1 N-terminus and most likely corresponds to the M210 internal translation start site since we could not identify any alternative transcripts that would produce this ATI product. When we expressed the human equivalent of M210 in Hs578T PANX1 KO cells with and without wildtype human PANX1, we determined M211 exhibits a predominantly intracellular localization, is N-glycosylated and can interact with full-length human PANX1. Collectively, these findings indicate species specific differences in the abundance of PANX1 ATI isoforms which could act independently or in conjunction with the canonical full-length protein in melanoma.

cell biology↗

Pannexin 3 channels regulate architecture, adhesion, barrier function and inflammation in the skin

The channel-forming glycoprotein Pannexin 3 (PANX3) functions in cutaneous wound healing and keratinocyte differentiation, but its role in skin homeostasis through aging is not yet understood. We found that PANX3 is absent in newborn skin but becomes upregulated with age. We characterized the skin of global Panx3 knockout mice (KO) and found that KO dorsal skin showed sex-differences at different ages, but generally had reduced dermal and hypodermal areas compared to aged-matched controls. Transcriptomic analysis of KO epidermis revealed reduced E-cadherin stabilization and Wnt signaling compared to WT, consistent with the inability of primary KO keratinocytes to adhere in culture, and diminished epidermal barrier function in KO mice. We also observed increased inflammatory signaling in KO epidermis and higher incidence of dermatitis in aged KO mice compared to wildtype controls. These findings suggest that during skin aging, PANX3 is critical in the maintenance of dorsal skin architecture, keratinocyte cell-cell and cell-matrix adhesion and inflammatory skin responses.

cell biology↗

Splicing inactivation generates hybrid mRNA-snoRNA transcripts targeted by cytoplasmic RNA decay

Many small nucleolar RNAs (snoRNA)s are processed from introns of host genes, but the importance of splicing for proper biogenesis and the fate of the snoRNAs is not well understood. Here we show that inactivation of splicing factors or mutation of splicing signals leads to the accumulation of partially processed hybrid mRNA-snoRNA transcripts (hmsnoRNA). HmsnoRNAs are processed to the mature 3'-ends of the snoRNAs by the nuclear exosome and bound by snoRNP proteins. HmsnoRNAs are unaffected by translation-coupled RNA quality control pathways, but they are degraded by the major cytoplasmic exonuclease Xrn1p due to their mRNA-like 5'-extensions. These results show that completion of splicing is required to promote complete and accurate processing of intron-encoded snoRNAs and that splicing defects lead to degradation of hybrid mRNA-snoRNA species by cytoplasmic decay, underscoring the importance of splicing for the biogenesis of intron encoded snoRNAs. Significance StatementSmall nucleolar RNAs mediate modifications of nucleosides within ribosomal RNAs, which are necessary for proper ribosomal function and translation. Many snoRNAs are encoded within introns of host genes and accurate biogenesis of these small RNAs is required to produce functional snoRNAs. The work presented here shows that when the splicing reactions are inactivated, snoRNAs undergo a distinct biogenesis pathway which leads to the production of aberrant hybrid RNAs that contain both mRNAs and small RNAs components of the host genes. While snoRNAs are primarily found in the nucleolus, these hybrid RNAs are degraded by the cytoplasmic mRNA degradation pathway. These results demonstrate the importance of splicing to promote accurate snoRNA processing and prevent the production of aberrant mRNA-snoRNA hybrids.

molecular biology↗

Full bandwidth electrophysiology of seizures and epileptiform activity enabled by flexible graphene micro-transistor depth neural probes

Mapping the entire frequency bandwidth of neuronal oscillations in the brain is of paramount importance for understanding physiological and pathological states. The ability to record simultaneously infraslow activity (<0.1 Hz) and higher frequencies (0.1-600 Hz) using the same recording electrode would particularly benefit epilepsy research. However, commonly used metal microelectrode technology is not well suited for recording infraslow activity. Here we use flexible graphene depth neural probes (gDNP), consisting of a linear array of graphene microtransistors, to concurrently record infraslow and high frequency neuronal activity in awake rodents. We show that gDNPs can reliably record and map with high spatial resolution seizures, post-ictal spreading depolarisation, and high frequency epileptic activity through cortical laminae to the CA1 layer of the hippocampus in a mouse model of chemically-induced seizures. We demonstrate functionality of chronically implanted devices over 10 weeks by recording with high fidelity spontaneous spike-wave discharges and associated infraslow activity in a rat model of absence epilepsy. Altogether, our work highlights the suitability of this technology for in vivo electrophysiology research, in particular, to examine the contributions of infraslow activity to seizure initiation and termination.

neuroscience↗

Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation

Dynamic and temporally specific gene regulatory changes may underlie unexplained genetic associations with complex disease. During a dynamic process such as cellular differentiation, the overall cell type composition of a tissue (or an in vitro culture) and the gene regulatory profile of each cell can both experience significant changes over time. To identify these dynamic effects in high resolution, we collected single-cell RNA-sequencing data over a differentiation time course from induced pluripotent stem cells to cardiomyocytes, sampled at 7 unique time points in 19 human cell lines. We employed a flexible approach to map dynamic eQTLs whose effects vary significantly over the course of bifurcating differentiation trajectories, including many whose effects are specific to one of these two lineages. Our study design allowed us to distinguish true dynamic eQTLs affecting a specific cell lineage from expression changes driven by potentially non-genetic differences between cell lines such as cell composition. Additionally, we used the cell type profiles learned from single-cell data to deconvolve and re-analyze data from matched bulk RNA-seq samples. Using this approach, we were able to identify a large number of novel dynamic eQTLs in single cell data while also attributing dynamic effects in bulk to a particular lineage. Overall, we found that using single cell data to uncover dynamic eQTLs can provide new insight into the gene regulatory changes that occur among heterogeneous cell types during cardiomyocyte differentiation.

genomics↗

Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees

Comparative functional genomic studies have shown that differences in gene expression between species can often be explained by corresponding inter-species differences in genetic and epigenetic regulatory mechanisms. In the quest to understand gene regulatory evolution in primates, the role of co-transcriptional regulatory mechanisms, such as alternative polyadenylation (APA), have so far received little attention. To begin addressing this gap, we studied APA in lymphoblastoid cell lines from six humans and six chimpanzees, and estimated usage for 44,432 polyadenylation sites (PAS) in 9,518 genes in both species. While APA is largely conserved in humans and chimpanzees, we identified 1,705 genes with significantly different PAS usage (FDR of 0.05) between the two species. We found that genes with divergent APA patterns are enriched among differentially expressed genes, as well as among genes that show differences in protein translation between species. In particular, differences in APA between humans and chimpanzees can explain a subset of observed inter-species protein expression differences that do not display corresponding differences at the transcript level. Finally, we focused on genes that have a dominant PAS, namely a PAS that is used more often than all others. Dominant PAS are highly conserved, and inter-species differences in dominant PAS are particularly enriched for genes that also show expression differences between the species. This study establishes APA as another key mechanism underlying the genetic regulation of transcript and protein expression levels in primates.

genomics↗

Reach and Grasp Altered in Pantomime String-Pulling: A Test of the Action/Perception Theory in a Bilateral Reaching Task

The action/perception theory of cortical organization is supported by the finding that pantomime hand movements of reaching and grasping are different from real movements. Frame-by-frame video analysis and MATLAB(R) based tracking examined real/pantomime differences in a bilaterally movement, string-pulling, pulling down a rope with hand-over-hand movements. Sensory control of string-pulling varied from visually-direct when cued, visually-indirect when non cued and somatosensory controlled in the absence of vision. Cued grasping points were visual tracked and the pupils dilated in anticipation of the grasp, but when noncued, visual tracking and pupil responses were absent. In real string-pulling, grasping and releasing the string featured an arpeggio movement in which the fingers close and open in the sequence 5 through 1 (pinki first, thumb last); in pantomime, finger order was reversed, 1 through 5. In real string-pulling, the hand is fully opened and closed to grasp and release; in pantomime, hand opening was attenuated and featured a gradual opening centered on the grasp. The temporal structure of arm movements in real string-pulling featured up-arm movements that were faster than down-arm movement. In pantomime, up/down movements had similar speed. In real string-pulling, up/down arm movements were direct and symmetric; in pantomime, they were more circular and asymmetric. That pantomime string-pulling featured less motoric and temporal complexity than real string-pulling is discussed in relation to the action/perception theory and in relation to the idea that pantomimed string-pulling may feature the substitution of gestures for real movement.\n\nSignificant StatementMost laboratory studies investigating hand movements made by humans feature single hand movements, the current study presents a novel string-pulling task to study bimanual coordination of left and right hands in real and pantomime conditions. The results show that pantomime string-pulling featured less motoric and temporal complexity than real string-pulling. These findings are relevant to the contemporary theory of action and perception that the dorsal stream (parietal cortex) is related to actions and the ventral stream (temporal cortex) is related to perception.

neuroscience↗

Fully Interpretable Deep Learning Model of Transcriptional Control

The universal expressibility assumption of Deep Neural Networks (DNNs) is the key motivation behind recent work in the system biology community to employ DNNs to solve important problems in functional genomics and molecular genetics. Because of the black box nature of DNNs, such assumptions, while useful in practice, are unsatisfactory for scientific analysis. In this paper, we give an example of a DNN in which every layer is interpretable. Moreover, this DNN is biologically validated and predictive. We derive our DNN from a systems biology model that was not previously recognized as having a DNN structure. This DNN is concerned with a key unsolved biological problem, which is to understand the DNA regulatory code which controls how genes in multicellular organisms are turned on and off. Although we apply our DNN to data from the early embryo of the fruit fly Drosophila, this system serves as a testbed for analysis of much larger data sets obtained by systems biology studies on a genomic scale.

systems biology↗

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

Cellular heterogeneity in gene expression is driven by cellular processes such as cell cycle and cell-type identity, and cellular environment such as spatial location. The cell cycle, in particular, is thought to be a key driver of cell-to-cell heterogeneity in gene expression, even in otherwise homogeneous cell populations. Recent advances in single-cell RNA-sequencing (scRNA-seq) facilitate detailed characterization of gene expression heterogeneity, and can thus shed new light on the processes driving heterogeneity. Here, we combined fluorescence imaging with scRNA-seq to measure cell cycle phase and gene expression levels in human induced pluripotent stem cells (iPSCs). Using these data, we developed a novel approach to characterize cell cycle progression. While standard methods assign cells to discrete cell cycle stages, our method goes beyond this, and quantifies cell cycle progression on a continuum. We found that, on average, scRNA-seq data from only five genes predicted a cells position on the cell cycle continuum to within 14% of the entire cycle, and that using more genes did not improve this accuracy. Our data and predictor of cell cycle phase can directly help future studies to account for cell-cycle-related heterogeneity in iPSCs. Our results and methods also provide a foundation for future work to characterize the effects of the cell cycle on expression heterogeneity in other cell types.

genomics↗

Skip-mers: increasing entropy and sensitivity to detect conserved genic regions with simple cyclic q-grams

Bioinformatic analyses and tools make extensive use of k-mers (fixed contiguous strings of k nucleotides) as an informational unit. K-mer analyses are both useful and fast, but are strongly affected by single-nucleotide polymorphisms or sequencing errors, effectively hindering direct-analyses of whole regions and decreasing their usability between evolutionary distant samples.\n\nWe introduce a concept of skip-mers, a cyclic pattern of used-and-skipped positions of k nucleotides spanning a region of size S [&ge;] k, and show how analyses are improved compared to using k-mers. The entropy of skip-mers increases with the larger span, capturing information from more distant positions and increasing the specificity, and uniqueness, of larger span skip-mers within a genome. In addition, skip-mers constructed in cycles of 1 or 2 nucleotides in every 3 (or a multiple of 3) lead to increased sensitivity in the coding regions of genes, by grouping together the more conserved nucleotides of the protein-coding regions.\n\nWe implemented a set of tools to count and intersect skip-mers between different datasets. We used these tools to show how skip-mers have advantages over k-mers in terms of entropy and increased sensitivity to detect conserved coding sequence, allowing better identification of genic matches between evolutionarily distant species. We also highlight potential applications to problems such as whole-genome alignment and multi-genome evolutionary analyses.\n\nSoftware availabilitythe skm-tools implementing the methods described in this manuscript are available under MIT license at http://github.com/bioinfologics/skm-tools/

bioinformatics↗

W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data

Producing high-quality whole-genome shotgun de novo assemblies from plant and animal species with large and complex genomes using low-cost short read sequencing technologies remains a challenge. But when the right sequencing data, with appropriate quality control, is assembled using approaches focused on robustness of the process rather than maximization of a single metric such as the usual contiguity estimators, good quality assemblies with informative value for comparative analyses can be produced. Here we present a complete method described from data generation and qc all the way up to scaffold of complex genomes using Illumina short reads and its application to data from plants and human datasets. We show how to use the w2rap pipeline following a metric-guided approach to produce cost-effective assemblies. The assemblies are highly accurate, provide good coverage of the genome and show good short range contiguity. Our pipeline has already enabled the rapid, cost-effective generation of de novo genome assemblies from large, polyploid crop species with a focus on comparative genomics.\n\nAvailabilityw2rap is available under MIT license, with some subcomponents under GPL-licenses. A ready-to-run docker with all software pre-requisites and example data is also available.\n\nhttp://github.com/bioinfologics/w2rap\n\nhttp://github.com/bioinfologics/w2rap-contigger

bioinformatics↗