GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE103693 Query DataSets for GSE103693
Status Public on Jan 02, 2018
Title The Identification and Characterization of Sindbis Virus RNA:Host Protein Interactions
Organism Homo sapiens
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Arthropod-borne viruses, such as the members of genus Alphavirus, are a significant concern to global public health. As obligate intracellular pathogens, RNA viruses must interact with the host cell machinery to establish, and complete, their viral lifecycles. Despite considerable efforts to define the host/pathogen interactions essential for alphaviral replication, an unbiased and inclusive assessment of alphaviral RNA:protein interactions has not been undertaken. Moreover, the biological and molecular importance of these interactions, in the full context of their molecular function as RNA-binding proteins, has not been fully realized. The data presented here introduces a robust viral RNA:protein discovery method to elucidate the Sindbis virus (SINV) RNA:Protein host interface. Cross-Link Assisted mRNP Purification (CLAMP) assessment reveals an extensive array of host/pathogen interactions centered on the viral RNAs (vRNAs). After prioritization of the host proteins associated with the vRNAs, we identified the site of Protein:vRNA interaction via a CLIP-seq approach and assessed the consequences of the RNA:protein binding event of hnRNP K, hnRNP I, and hnRNP M in regards to viral infection. Herein we demonstrate that mutation of the prioritized hnRNP:vRNA interaction sites effectively disrupted the hnRNP:vRNA interaction. Correlating with disrupted hnRNP:vRNA binding, SINV growth kinetics were reduced relative to wild type parental viral infections in a vertebrate and invertebrate tissue culture models of infection. The molecular mechanism leading to reduced viral growth kinetics was found to be reduced vRNA accumulation and dysregulated structural gene expression. Collectively, this study further defines the scope and importance of the alphavirus host/pathogen vRNA:protein interactions.
Overall design 5 CLIP-Seq samples in TOTAL- 2 Control Samples (Input and Empty), 3 immunoprecitations of hnRNP proteins (hnRNP K, I and M).
Contributor(s) Lapointe AT, Gebhart NN, Meller ME, Hardy RW, Sokoloski KJ
Citation(s) 29321325
Submission date Sep 11, 2017
Last update date Jul 25, 2021
Contact name Kevin J Sokoloski
Organization name University of Louisville
Department Microbiology and Immunology
Lab Sokoloski Lab
Street address 505 S. Hancock St.
City Louisville
State/province KY
ZIP/Postal code 40202
Country USA
Platforms (1)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (5)
GSM2779359 Input Control
GSM2779360 Nonspecific Control
GSM2779361 hnRNP K Library
BioProject PRJNA404068
SRA SRP117254

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE103693_JVI_CLIPSeq_Data_Deposition_with_Summary_Table.xlsx 5.6 Mb (ftp)(http) XLSX
GSE103693_RAW.tar 28.2 Mb (http)(custom) TAR (of BAI, BAM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap