Development of GRO-cap (GRO-seq followed by 5'-cap enrichment) to map transcription start sites in C. elegans
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Barbara Meyer
PROVIDER: E-GEOD-43085 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.
Kruesi William S WS Core Leighton J LJ Waters Colin T CT Lis John T JT Meyer Barbara J BJ
eLife 20130618
The X-chromosome gene regulatory process called dosage compensation ensures that males (1X) and females (2X) express equal levels of X-chromosome transcripts. The mechanism in Caenorhabditis elegans has been elusive due to improperly annotated transcription start sites (TSSs). Here we define TSSs and the distribution of transcriptionally engaged RNA polymerase II (Pol II) genome-wide in wild-type and dosage-compensation-defective animals to dissect this regulatory mechanism. Our TSS-mapping stra ...[more]
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Details on the probe design strategy, but for eelpout (Zoarces viviparus), and transcript selection strategy are described elsewhere (Kristiansson et al., 2009; Cuklev et al., 2011). However, in the present study, singletons and non-annotated expressed sequence tags (ESTs) were replaced by newly well-annotated ESTs in rainbow trout. When available, transcripts at GenBank (http://www.ncbi.nlm.nih.gov/nucleotide) were used. In our lab, results from similar microarrays using the same platform have shown good correlation with quantitative polymerase chain reaction (qPCR) data (Gunnarsson et al., 2009b; Kristiansson et al., 2009; Cuklev et al., 2011; Lennquist et al., 2011). To reduce variation in estrogen-responsive genes, only males were used for the subsequent gene expression analyses. Biotinylated antisense RNA (aRNA) was synthesized using MessageAmpM-bM-^DM-" II-Biotin Enhanced Single Round aRNA Amplification Kit (AmbionM-BM-.). 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