Transcriptomic Perturbations Research Articles

Genome-Wide Gene Expression Disturbance by Single A1/C1 Chromosome Substitution in Brassica rapa Restituted From Natural B. napus.

Alien chromosome substitution (CS) lines are treated as vital germplasms for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype “Oro,” after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollinated by RBR. The viability of the substitution and its progeny for the RBR diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis-effect but also prevalent trans-effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in CS related to one naturally evolved allopolyploid.

Integrated ‘omics analysis reveals new drug-induced mitochondrial perturbations in human hepatocytes

We performed a multiple ‘omics study by integrating data on epigenomic, transcriptomic, and proteomic perturbations associated with mitochondrial dysfunction in primary human hepatocytes caused by the liver toxicant valproic acid (VPA), to deeper understand downstream events following epigenetic alterations in the mitochondrial genome. Furthermore, we investigated persistence of cross-omics changes after terminating drug treatment. Upon transient methylation changes of mitochondrial genes during VPA-treatment, increasing complexities of gene-interaction networks across time were demonstrated, which normalized during washout. Furthermore, co-expression between genes and their corresponding proteins increased across time. Additionally, in relation to persistently decreased ATP production, we observed decreased expression of mitochondrial complex I and III–V genes. Persistent transcripts and proteins were related to citric acid cycle and β-oxidation. In particular, we identified a potential novel mitochondrial-nuclear signaling axis, MT-CO2–FN1–MYC–CPT1. In summary, this cross-omics study revealed dynamic responses of the mitochondrial epigenome to an impulse toxicant challenge resulting in persistent mitochondrial dysfunctioning. Moreover, this approach allowed for discriminating between the toxic effect of VPA and adaptation.

In vitro RNA-seq-based toxicogenomics assessment shows reduced biological effect of tobacco heating products when compared to cigarette smoke

The battery of regulatory tests used to evaluate the risk of novel tobacco products such as heated tobacco products (THPs) presents some limitations including a bias towards the apical endpoint tested, and limited information on the mode of action. This is driving a paradigm shift to more holistic systems biology approaches. In this study, we used RNA-sequencing to compare the transcriptomic perturbations following acute exposure of a 3D airway tissue to the aerosols from two commercial THPs and a reference 3R4F cigarette. 2809 RNAs were differentially expressed for the 3R4F treatment and 115 and 2 RNAs for the two THPs (pFDR < 0.05, FC > 1.5), respectively. The relationship between the identified RNA features and gene ontologies were mapped showing a strong association with stress response, xenobiotics metabolism, and COPD-related terms for 3R4F. In contrast, fewer ontologies were found enriched for the THPs aerosols. “Response to wounding” was a common COPD-related term over-represented for the two THPs but at a reduced significance. Quantification of a cytokine panel post-exposure confirmed a pro-inflammatory effect of cigarette smoke but not for THPs. In conclusion, THPs have a reduced impact on gene expression compared to 3R4F.

Mutations of the Atyak1 Kinase Suppress Tor Deficiency in Arabidopsis

The Target Of Rapamycin (TOR) kinase is a conserved energy sensor that regulates growth in response to environmental cues. However, little is known about TOR pathway regulatory elements or substrates in plants. We used Arabidopsis mutants affected in the LST8 gene, a core element of the TOR complex, to search for suppressors of lst8-1-1 (sol) mutants. Two sol lines were isolated, both with mutations in the AtYAK1 gene, which is a member of the dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) family. Atyak1 mutations improved growth and partly rescued the developmental defects observed in lst8-1-1 mutants. They also conferred resistance to AZD-8055, a specific TOR inhibitor. Moreover, atyak1 mutations suppressed the transcriptomic and metabolic perturbations, as well as the ABA hypersensitivity of the lst8-1-1 mutants. Thus, our findings reveal that AtYAK1 is a negative regulatory element of the TOR signaling pathway, which needs to be switched off to activate plant growth.

Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection

The majority of aneuploid fetuses are spontaneously miscarried. Nevertheless, some aneuploid individuals survive despite the strong genetic insult. Here, we investigate if the survival probability of aneuploid fetuses is affected by the genome-wide burden of slightly deleterious variants. We analyzed two cohorts of live-born Down syndrome individuals (388 genotyped samples and 16 fibroblast transcriptomes) and observed a deficit of slightly deleterious variants on Chromosome 21 and decreased transcriptome-wide variation in the expression level of highly constrained genes. We interpret these results as signatures of embryonic selection, and propose a genetic handicap model whereby an individual bearing an extremely severe deleterious variant (such as aneuploidy) could escape embryonic lethality if the genome-wide burden of slightly deleterious variants is sufficiently low. This approach can be used to study the composition and effect of the numerous slightly deleterious variants in humans and model organisms.

MicroRNAs-143 and -145 induce epithelial to mesenchymal transition and modulate the expression of junction proteins.

Transforming growth factor (TGF)-β is one of the major inducers of epithelial to mesenchymal transition (EMT), a crucial program that has a critical role in promoting carcinoma's metastasis formation. MicroRNAs-143 and -145, which are both TGF-β direct transcriptional targets, are essential for the differentiation of vascular smooth muscle cells (VSMC) during embryogenesis, a TGF-β-dependent process reminiscent of EMT. Their role in adult tissues is however less well defined and even ambiguous, as their expression was correlated both positively and negatively with tumor progression. Here we show that high expression of both miRs-143 and -145 in mouse mammary tumor cells expressing constitutively active STAT3 (S3C) is involved in mediating their disrupted cell-cell junctions. Additionally, miR-143 appears to have a unique role in tumorigenesis by enhancing cell migration in vitro and extravasation in vivo while impairing anchorage-independent growth, which may explain the contradictory reports about its role in tumors. Accordingly, we demonstrate that overexpression of either miRNA in the non-transformed mammary epithelial NMuMG cells leads to upregulation of EMT markers and of several endogenous TGF-β targets, downmodulation of a number of junction proteins and increased motility, correlating with enhanced basal and TGF-β-induced SMAD-mediated transcription. Moreover, pervasive transcriptome perturbation consistent with the described phenotype was observed. In particular, the expression of several transcription factors involved in the mitogenic responses, of MAPK family members and, importantly, of several tight junction proteins and the SMAD co-repressor TGIF was significantly reduced. Our results provide important mechanistic insight into the non-redundant role of miRs-143 and -145 in EMT-related processes in both transformed and non-transformed cells, and suggest that their expression must be finely coordinated to warrant optimal migration/invasion while not interfering with cell growth.

Perturbation of IGF2BP1 Transcriptome upon the Interplay between miR-486-5p and let-7a

Perturbation of IGF2BP1 Transcriptome upon the Interplay between miR-486-5p and let-7a

Differential Gene Expression Using RNA Sequencing Profiling in a Reconstituted Airway Epithelium Exposed to Conventional Cigarette Smoke or Electronic Cigarette Aerosols

The use of electronic cigarettes (e-cigarettes) potentially offers a safer alternative to conventional tobacco products. The advance in molecular biology and computational sciences offers new perspective to assess adverse biological responses for product risk assessment by combining omics screens with knowledge-based biological pathways. Our aim was to compare transcriptomic perturbations in MucilAir™, a commercially available lung epithelial tissue, after short repeated exposure to cigarette smoke (3R4F) and e-cigarette (Vype ePen) aerosols. We performed deep RNA sequencing and secreted inflammatory cytokine profiling postexposure. One hundred twenty-three genes were differentially expressed at fold change (FC) >1.5 and p-false discovery rate (pFDR) <0.1 for 3R4F exposure and 0 genes for Vype ePen aerosol exposure. When a relaxed filter pFDR <0.5 and FC >1.5 was applied, 29 genes were identified with e-cigarette aerosol exposure and used for validation of potential candidates by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Gene enrichment analysis was conducted and predicted a response to 3R4F smoke exposure in biological processes involving inflammation and oxidative stress pathways. No enrichment could be performed for Vype ePen aerosol exposure due to the lack of regulated gene candidates at those exposure conditions even after qRT-PCR validation. Of a panel of 33 cytokines screened, 8 were upregulated (FC >1.5 p < 0.05) following 3R4F smoke exposure, which was in agreement with our enrichment analysis. In conclusion, aerosol from the tested e-cigarette caused limited perturbations in gene and inflammatory cytokine expression compared to conventional cigarette smoke, as assessed using next-generation sequencing-based systems biology approaches in 3D commercially available reconstituted lung epithelial tissues.

Traumatic Brain Injury Induces Genome-Wide Transcriptomic, Methylomic, and Network Perturbations in Brain and Blood Predicting Neurological Disorders

The complexity of the traumatic brain injury (TBI) pathology, particularly concussive injury, is a serious obstacle for diagnosis, treatment, and long-term prognosis. Here we utilize modern systems biology in a rodent model of concussive injury to gain a thorough view of the impact of TBI on fundamental aspects of gene regulation, which have the potential to drive or alter the course of the TBI pathology. TBI perturbed epigenomic programming, transcriptional activities (expression level and alternative splicing), and the organization of genes in networks centered around genes such as Anax2, Ogn, and Fmod. Transcriptomic signatures in the hippocampus are involved in neuronal signaling, metabolism, inflammation, and blood function, and they overlap with those in leukocytes from peripheral blood. The homology between genomic signatures from blood and brain elicited by TBI provides proof of concept information for development of biomarkers of TBI based on composite genomic patterns. By intersecting with human genome-wide association studies, many TBI signature genes and network regulators identified in our rodent model were causally associated with brain disorders with relevant link to TBI. The overall results show that concussive brain injury reprograms genes which could lead to predisposition to neurological and psychiatric disorders, and that genomic information from peripheral leukocytes has the potential to predict TBI pathogenesis in the brain.

Carcinogenic effects of oil dispersants: A KEGG pathway-based RNA-seq study of human airway epithelial cells

The health impacts of the BP oil spill are yet to be further revealed as the toxicological effects of oil products and dispersants on human respiratory system may be latent and complex, and hence difficult to study and follow up. Here we performed RNA-seq analyses of a system of human airway epithelial cells treated with the BP crude oil and/or dispersants Corexit 9500 and Corexit 9527 that were used to help break up the oil spill. Based on the RNA-seq data, we then systemically analyzed the transcriptomic perturbations of the cells at the KEGG pathway level using two pathway-based analysis tools, GAGE (generally applicable gene set enrichment) and GSNCA (Gene Sets Net Correlations Analysis). Our results suggested a pattern of change towards carcinogenesis for the treated cells marked by upregulation of ribosomal biosynthesis (hsa03008) (p=1.97E−13), protein processing (hsa04141) (p=4.09E−7), Wnt signaling (hsa04310) (p=6.76E−3), neurotrophin signaling (hsa04722) (p=7.73E−3) and insulin signaling (hsa04910) (p=1.16E−2) pathways under the dispersant Corexit 9527 treatment, as identified by GAGE analysis. Furthermore, through GSNCA analysis, we identified gene co-expression changes for several KEGG cancer pathways, including small cell lung cancer pathway (hsa05222, p=9.99E−5), under various treatments of oil/dispersant, especially the mixture of oil and Corexit 9527. Overall, our results suggested carcinogenic effects of dispersants (in particular Corexit 9527) and their mixtures with the BP crude oil, and provided further support for more stringent safety precautions and regulations for operations involving long-term respiratory exposure to oil and dispersants.

Transcriptome profiling of NIH3T3 cell lines expressing opsin and the P23H opsin mutant identifies candidate drugs for the treatment of retinitis pigmentosa

Mammalian cells are commonly employed in screening assays to identify active compounds that could potentially affect the progression of different human diseases including retinitis pigmentosa (RP), a class of inherited diseases causing retinal degeneration with compromised vision. Using transcriptome analysis, we compared NIH3T3 cells expressing wildtype (WT) rod opsin with a retinal disease-causing single P23H mutation. Surprisingly, heterologous expression of WT opsin in NIH3T3 cells caused more than a 2-fold change in 783 out of 16,888 protein coding transcripts. The perturbed genes encoded extracellular matrix proteins, growth factors, cytoskeleton proteins, glycoproteins and metalloproteases involved in cell adhesion, morphology and migration. A different set of 347 transcripts was either up- or down-regulated when the P23H mutant opsin was expressed suggesting an altered molecular perturbation compared to WT opsin. Transcriptome perturbations elicited by drug candidates aimed at mitigating the effects of the mutant protein revealed that different drugs targeted distinct molecular pathways that resulted in a similar phenotype selected by a cell-based high-throughput screen. Thus, transcriptome profiling can provide essential information about the therapeutic potential of a candidate drug to restore normal gene expression in pathological conditions.

Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi.

BackgroundAvocado (Persea americana Mill.) is a commercially important fruit crop worldwide. A major limitation to production is the oomycete Phytophthora cinnamomi, which causes root rot leading to branch-dieback and tree death. The decline of orchards infected with P. cinnamomi occurs much faster when exposed to flooding, even if flooding is only transient. Flooding is a multifactorial stress compromised of several individual stresses, making breeding and selection for tolerant varieties challenging. With more plantations occurring in marginal areas, with imperfect irrigation and drainage, understanding the response of avocado to these stresses will be important for the industry.ResultsMaintenance of energy production was found to be central in the response to flooding, as seen by up-regulation of transcripts related to glycolysis and induction of transcripts related to ethanolic fermentation. Energy-intensive processes were generally down-regulated, as evidenced by repression of transcripts related to processes such as secondary cell-wall biosynthesis as well as defence-related transcripts. Aquaporins were found to be down-regulated in avocado roots exposed to flooding, indicating reduced water-uptake under these conditions.ConclusionsThe transcriptomic response of avocado to flooding and P. cinnamomi was investigated utilizing microarray analysis. Differences in the transcriptome caused by the presence of the pathogen were minor compared to transcriptomic perturbations caused by flooding. The transcriptomic response of avocado to flooding reveals a response to flooding that is conserved in several species. This data could provide key information that could be used to improve selection of stress tolerant rootstocks in the avocado industry.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0893-2) contains supplementary material, which is available to authorized users.

Characterization of circular RNAs landscape in multiple system atrophy brain.

Circular RNAs (circRNAs) have been recently identified as a naturally occurring family of widespread and diverse endogenous non-coding RNAs that may regulate gene expression in mammals. They are unusually stable RNA molecules with cell type- or developmental stage-specific expression patterns. However, the role of circRNAs in pathology of complex disease is entirely unknown. Here, we report the specific circular transcriptome in the multiple system atrophy (MSA) brain as determined by RNA sequencing. Five circRNAs, namely IQCK, MAP4K3, EFCAB11, DTNA, and MCTP1, were identified and validated as specifically over-expressed in MSA frontal cortex. The expression levels of linear transcripts were not significantly altered and thus did not follow the pattern of their circular counterparts. Further analysis of expression of five MSA-specific circRNAs revealed their over-expression in the white matter of the MSA cortical tissue. Together, this is the first report describing perturbation of circular transcriptome in α-synucleinopathies.

Abstract 1964: NcRNAs fingerprints in colon cancer in vitro model by EGCG, genistein and their combinatorial effects

Abstract INTRODUCTION Epidemiological studies have associated green tea intake with reduced risk in cancer. Up to date, thirty-five clinical trials use green tea polyphenol epigallocathechin-3-O-gallate (EGCG) in cancer treatment. The mechanism responsible for apoptosis and the perturbation of the noncoding transcriptome after polyphenols are largely unknown. Our aim was to examine the combined effects of two compounds, EGCG and Genistein alone or in various combinations, on two colon cancer cell lines on the expression of noncodingRNAs. MATERIAL AND METHODS The experiments were performed on two colon cancer cell lines RKO (p53+ wild type) and HCT116 (Ras mutated and transforming growth factor beta 1 (TGF beta 1) and beta 2 (TGF beta 2) expression positive) In order to establish the IC50 dose we performed MTT assay. For future analysis, cells were treated for 48 h either with Genistein and EGCG with established IC50 doses for both cell lines or the following combinations: 30 μM EGCG and 10 μM Genistein and 30 μM Genistein and 10 μM EGCG. We performed genome-wide profiling with a non-codingRNA array composed by probes for about 1500 human miRNAs and about 3500 lncRNAs, and ncRNA microarray analyses were performed. RESULTS After 48h exposer, both compounds effectively reduced cell viability in a dose-dependent manner in RKO and HCT116 cells. In the combined treatment the most interesting results were obtained at 30 μM EGCG and 10 μM Genistein and 30 μM Genistein and 10 μM EGCG, in both cell lines. Were we observed a 80% decrease of cell viability in the first situation and more than 80% of the cells maintained their viability in thesecond one. Bioinformatic analysis was performed using R (version 3.0.1) and Bioconductor (h&amp;gt;p:// www.bioconductor.org/). The raw intensity for each probe is the median feature pixel intensity with the median background subtracted. We found eighteen miRNAs and six lncRNAs commonly DE in HCT 116 cells and 56 miRNAs and 14 lncRNAs commonly DE in RKO cells by various treatments. Among the former genes we identified the oncogenic miR-18 and miR-222, as well as the long-non-codingRNAs CCAT2 that we previously identified as oncogenic in colon cancer, and MALAT-1. Furthermore, we recognized multiple ncRNA transcripts specifically disregulated by one specific type of treatment. The expression of specific miRNAs was negatively correlated with some lncRNAs supporting a potential direct interaction by sequence complementarity, while for other miRNA-lncRNA pairs the expression was positively correlated suggesting common transcriptional mechanisms. We confirmed the array data by qRT- PCR and a restricted panel of confirmed ncRNAs was tested on the phenotypic effects in colon cancer cells. CONCLUSION This is the first study to prove that EGCG and /or genistein alone or in combination affect the expression of multiple types of noncodingRNAs in a correlated manner; their transcriptomic effects are more extensive as initially expected. Citation Format: Ioana Berindan Neagoe, Valentina Pileczki, Cornelia Braicu, Cristina Ivan, Xinna Zhang, George Adrian Calin. NcRNAs fingerprints in colon cancer in vitro model by EGCG, genistein and their combinatorial effects. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1964.

Loss of Tet1-Associated 5-Hydroxymethylcytosine Is Concomitant with Aberrant Promoter Hypermethylation in Liver Cancer.

Aberrant hypermethylation of CpG islands (CGI) in human tumors occurs predominantly at repressed genes in the host tissue, but the preceding events driving this phenomenon are poorly understood. In this study, we temporally tracked epigenetic and transcriptomic perturbations that occur in a mouse model of liver carcinogenesis. Hypermethylated CGI events in the model were predicted by enrichment of the DNA modification 5-hydroxymethylcytosine (5hmC) and the histone H3 modification H3K27me3 at silenced promoters in the host tissue. During cancer progression, selected CGIs underwent hypo-hydroxymethylation prior to hypermethylation, while retaining H3K27me3. In livers from mice deficient in Tet1, a tumor suppressor involved in cytosine demethylation, we observed a similar loss of promoter core 5hmC, suggesting that reduced Tet1 activity at CGI may contribute to epigenetic dysregulation during hepatocarcinogenesis. Consistent with this possibility, mouse liver tumors exhibited reduced Tet1 protein levels. Similar to humans, DNA methylation changes at CGI in mice did not appear to be direct drivers of hepatocellular carcinoma progression, rather, dynamic changes in H3K27me3 promoter deposition correlated strongly with tumor-specific activation and repression of transcription. Overall, our results suggest that loss of promoter-associated 5hmC in liver tumors licenses reprograming of DNA methylation at silent CGI during progression. Cancer Res; 76(10); 3097-108. ©2016 AACR.

Systems Pharmacology Approach to Identify Potential Therapeutic Small‐Molecules for Treatment of Diabetic Peripheral Neuropathy

Diabetic peripheral neuropathy (DPN) is one of the most common complications of diabetes. Despite extensive research the underlying mechanisms leading to this complication are not fully understood, and there are no specific treatments or means to predict DPN onset or progression. In this study, we employed a systems pharmacology approach to identify DPN‐related transcriptional networks and pathways conserved across various animal models and species, to identify drug‐candidates with therapeutic potentials.From our Diabetic Neuropathy Microarray Knowledge‐Base (DNMKB), we selected DPN‐related microarray data performed in sciatic nerve samples from type 1 diabetes (streptozotocin‐treated) and type 2 diabetes (db/db, ob/ob, high‐fat diet fed) murine models and human subjects with non‐progressive and progressive DPN. Differentially expressed genes (DEGs) were identified between non‐diabetic and diabetic samples in murine models, and between non‐progressive and progressive samples in human. Our in‐house literature mining program, SciMiner, was used to construct a transcriptional network for each DEG set, based on the sentence‐level gene‐gene co‐citation information in the complete PubMed abstracts. These networks were then compared using a network‐comparison program TALE (tool for approximate large graph matching) to identify overlapping relations between networks. These comparisons indicated that genes involved in the reelin signaling pathway, matrix metalloproteinases inhibition, and proliferation regulation to be differentially expressed and conserved between datasets.The genes that demonstrate the most dramatic fold change while overlapping across species and various DPN models were defined as the representative gene expression signature of DPN. This DPN signature was searched against the drug‐perturbed gene expression profile data from the Library of Integrated Network‐based Cellular Signatures (LINCS) database. LINCS, aiming to create a network‐based understanding of gene expression when cells are exposed to different perturbing agents, have extensively profiled the transcriptomic perturbations of over 20,000 small‐molecules in various cell lines and primary cells. Our expression profile‐based comparison analysis identified over 50 potential small‐molecule compounds with potential of reversing the direction of expression changes identified in the central pathways involved in our DPN networks. The top candidates included methyltransferase inhibitors and metabotropic glutamate inhibitors.A systems pharmacology approach, integrating of multiple bio/chem‐informatics analyses, identified DPN‐associated pathways that are highly conserved across various murine models and across species, as well as potential small‐molecules for DPN.Support or Funding InformationThe study was supported by the Diabetic Complications Consortium (DiaComp) Pilot &amp; Feasiblity Grant (to J.H.), and the American Diabetes Association (to E.L.F).

A U1 snRNP-specific assembly pathway reveals the SMN complex as a versatile hub for RNP exchange.

Despite their equal stoichiometry in spliceosomes, U1 snRNP (U1) is typically the most abundant snRNP in vertebrates. What regulates U1 over-abundance and snRNP repertoire in general is unknown. Sm core assembly is a key step in snRNP biogenesis mediated by the SMN complex. All pre-snRNAs are delivered by the snRNA-specific RNA-binding protein (RBP) Gemin5 to join SMN-Gemin2-recruited Sm proteins. Here, we find that the U1-specific RBP U1-70K bridges pre-U1 to SMN-Gemin2-Sm, establishing an additional, Gemin5-independent Sm core assembly pathway. We show that U1-70K hijacks SMN-Gemin2-Sm, enhancing U1’s and inhibiting other snRNAs’ Sm core assembly, thereby promoting U1 over-abundance and regulating snRNP repertoire. Ubiquitous SMN-Gemin2’s surprising ability to facilitate transactions between different RBPs and RNAs explains its puzzling multi-RBP valency and myriad transcriptome perturbations associated with SMN’s deficiency in neurodegenerative spinal muscular atrophy. We propose that SMN-Gemin2 is a versatile RNP exchange that functions broadly in RNA metabolism.

Genome-wide gene expression perturbation induced by loss of C2 chromosome in allotetraploid Brassica napus L.

Aneuploidy with loss of entire chromosomes from normal complement disrupts the balanced genome and is tolerable only by polyploidy plants. In this study, the monosomic and nullisomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome. The monosomics gave a plant phenotype very similar to the original donor, but the nullisomics had much smaller stature and also shorter growth period. By the comparative analyses on the global transcript profiles with the euploid donor, genome-wide alterations in gene expression were revealed in two aneuploids, and their majority of differentially expressed genes (DEGs) resulted from the trans-acting effects of the zero and one copy of C2 chromosome. The higher number of up-regulated genes than down-regulated genes on other chromosomes suggested that the genome responded to the C2 loss via enhancing the expression of certain genes. Particularly, more DEGs were detected in the monosomics than nullisomics, contrasting with their phenotypes. The gene expression of the other chromosomes was differently affected, and several dysregulated domains in which up- or downregulated genes obviously clustered were identifiable. But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss. Some genes and their expressions on C2 were correlated with the phenotype deviations in the aneuploids. These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference

Genome control is operated by transcription factors (TFs) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRNs). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse engineer the GRNs of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types and inferred a coexpression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5,632 direct target genes through 24,926 enhancers. Using this network, we found network motifs, cis-regulatory codes, and regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general cofactor in the eye network, being bound to thousands of nucleosome-free regions.

Transcriptome analysis of grey and white matter cortical tissue in multiple system atrophy.

Multiple system atrophy (MSA) is a distinct member of a group of neurodegenerative diseases known as α-synucleinopathies, which are characterized by the presence of aggregated α-synuclein in the brain. MSA is unique in that the principal site for α-synuclein deposition is in the oligodendrocytes rather than neurons. The cause of MSA is unknown, and the pathogenesis of MSA is still largely speculative. Brain transcriptome perturbations during the onset and progression of MSA are mostly unknown. Using RNA sequencing, we performed a comparative transcriptome profiling analysis of the grey matter (GM) and white matter (WM) of the frontal cortex of MSA and control brains. The transcriptome sequencing revealed increased expression of the alpha and beta haemoglobin genes in MSA WM, decreased expression of the transthyretin (TTR) gene in MSA GM and numerous region-specific long intervening non-coding RNAs (lincRNAs). In contrast, we observed only moderate changes in the expression patterns of the α-synuclein (SNCA) gene, which confirmed previous observations by other research groups. Our study suggests that at the transcriptional level, MSA pathology may be related to increased iron levels in WM and perturbations of the non-coding fraction of the transcriptome.