Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes.
AuthorsRheaume BA, Jereen A, Bolisetty M, Sajid MS, Yang Y, Renna K, Sun L, Robson P, Trakhtenberg EF
JournalNat Commun
PubMed ID30018341
'Retinal ganglion cells (RGCs) convey the major output of information collected from the eye to the brain. Thirty subtypes of RGCs have been identified to date. Here, we analyze 6225 RGCs (average of 5000 genes per cell) from right and left eyes by single-cell RNA-seq and classify them into 40 ... More
miR-103 promotes endothelial maladaptation by targeting lncWDR59.
AuthorsNatarelli L, Geißler C, Csaba G, Wei Y, Zhu M, di Francesco A, Hartmann P, Zimmer R, Schober A
JournalNat Commun
PubMed ID29980665
'Blood flow at arterial bifurcations and curvatures is naturally disturbed. Endothelial cells (ECs) fail to adapt to disturbed flow, which transcriptionally direct ECs toward a maladapted phenotype, characterized by chronic regeneration of injured ECs. MicroRNAs (miRNAs) can regulate EC maladaptation through targeting of protein-coding RNAs. However, long noncoding RNAs (lncRNAs), ... More
Long non-coding RNAs influence the transcriptome in pulmonary arterial hypertension: the role of PAXIP1-AS1.
AuthorsJandl K, Thekkekara Puthenparampil H, Marsh LM, Hoffmann J, Wilhelm J, Veith C, Sinn K, Klepetko W, Olschewski H, Olschewski A, Brock M, Kwapiszewska G
JournalJ Pathol
PubMed ID30450722
'In idiopathic pulmonary arterial hypertension (IPAH), global transcriptional changes induce a smooth muscle cell phenotype characterised by excessive proliferation, migration, and apoptosis resistance. Long non-coding RNAs (lncRNAs) are key regulators of cellular function. Using a compartment-specific transcriptional profiling approach, we sought to investigate the link between transcriptional reprogramming by lncRNAs ... More
Detection and Differentiation of Multiple Viral RNAs Using Branched DNA FISH Coupled to Confocal Microscopy and Flow Cytometry.
Authorsvan Buuren N, Kirkegaard K
JournalBio Protoc
PubMed ID30505886
Due to the exceptionally high mutation rates of RNA-dependent RNA polymerases, infectious RNA viruses generate extensive sequence diversity, leading to some of the lowest barriers to the development of antiviral drug resistance in the microbial world. We have previously discovered that higher barriers to the development of drug resistance can ... More
KDM6A and KDM6B play contrasting roles in nuclear transfer embryos revealed by MERVL reporter system.
AuthorsYang L, Song L, Liu X, Bai L, Li G
JournalEMBO Rep
PubMed ID30389724
Despite the success of animal cloning by somatic cell nuclear transfer (SCNT) in many species, the method is limited by its low efficiency. After zygotic genome activation (ZGA) during mouse development, a large number of endogenous retroviruses (ERVs) are expressed, including the murine endogenous retrovirus-L (MuERVL/MERVL). In this study, we ... More
Long-range function of secreted small nucleolar RNAs that direct 2'-
AuthorsRimer JM, Lee J, Holley CL, Crowder RJ, Chen DL, Hanson PI, Ory DS, Schaffer JE
JournalJ Biol Chem
PubMed ID29980600
Small nucleolar RNAs (snoRNAs) are noncoding RNAs that guide chemical modifications of structural RNAs. Whereas snoRNAs primarily localize in the nucleolus, where their canonical function is to target nascent ribosomal RNAs for 2'- ... More
PTBP3 splicing factor promotes hepatocellular carcinoma by destroying the splicing balance of NEAT1 and pre-miR-612.
AuthorsYang X, Qu S, Wang L, Zhang H, Yang Z, Wang J, Dai B, Tao K, Shang R, Liu Z, Li X, Zhang Z, Xia C, Ma B, Liu W, Li H, Dou K
JournalOncogene
PubMed ID30068940
Nuclear-enriched RNA-binding proteins (RBPs) are mainly involved in transcriptional regulation, which is a critical checkpoint to tune gene diversity and expression levels. We analyzed nuclear RBPs in human HCC tissues and matched normal control tissues. Based on the gene expression levels, PTBP3 was identified as top-ranked in the nuclei of ... More
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability.
AuthorsMunschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, Lander ES
JournalNature
PubMed ID30150775
The human genome contains thousands of long non-coding RNAs
Transmission genetics of drug-resistant hepatitis C virus.
Authorsvan Buuren N, Tellinghuisen TL, Richardson CD, Kirkegaard K
JournalElife
PubMed ID29589830
Antiviral development is plagued by drug resistance and genetic barriers to resistance are needed. For HIV and hepatitis C virus (HCV), combination therapy has proved life-saving. The targets of direct-acting antivirals for HCV infection are NS3/4A protease, NS5A phosphoprotein and NS5B polymerase. Differential visualization of drug-resistant and -susceptible RNA genomes ... More
Non-coding RNA Neat1 and Abhd11os expressions are dysregulated in medium spiny neurons of Huntington disease model mice.
AuthorsPark H, Miyazaki H, Yamanaka T, Nukina N
JournalNeurosci Res
PubMed ID30391555
Huntington Disease (HD) is a neurodegenerative disorder caused by expanded CAG repeats in the exon1 of huntingtin gene (HTT). The mutant HTT affects the transcriptional profile of neurons by disrupting the activities of transcriptional machinery and alters expression of many genes. In this study, we identified dysregulated non-coding RNAs (ncRNAs) ... More