Monday, February 24, 2014

Let Epicentre knock the Sox off your ribosome footprints

SoxB1, Nanog, and Pou5f1 activate zygotic gene expression

Although we are beginning to understand how vertebrate embryos acquire transcriptional competency, the factors that activate specific genes during zygotic genome activation remain unknown. Yale researchers combine loss-of-function analyses, high-throughput sequencing and ribosome footprinting to identify factors that activate the first wave of zygotic transcription to initiate nuclear control of embryonic development.

The translation levels of all maternal mRNAs were investigated using The ARTseq Ribosome Profiling Kit.  50 wild-type embryos injected with Nanog morpholino and SoxB1 morpholino and 50 noninjected embryos were collected at the 64-cell stage. Embryos were lysed and treated with nuclease, and ribosome protected fragments were run, and 28–29-nt fragments were gel purified as previously described.  Total RNA was extracted, and treated with Ribo-Zero Gold kit to deplete rRNA.  TruSeq Illumina RNA sequencing libraries were constructed and run on Illumina HiSeq 2000/2500 to produce single-end 76-nt reads. 

Nanog, Sox19b and Pou5f1 were the most highly translated sequence-specific transcription factors in the pre-maternal-to-zygotic  transcriptome. In zebrafish, Pou5f1 provides temporal control of gene expression and together with SoxB1 regulates dorsal–ventral patterning and neuronal development, whereas Nanog is essential for endoderm formation through regulation of zygotic mxtx2.

The transcriptome analysis provides three major insights. 1) Maternal factors directly regulate hundreds of mRNAs that make up the first wave of zygotic transcription. Transcriptional competence coincides with changes in the chromatin and DNA methylation states of the genome. 2) Nanog, SoxB1 and Pou5f1 contribute to widespread activation of zygotic genes during the maternal-to-zygotic transition. 3) Nanog, SoxB1 and Pou5f1 directly regulate miR-430, which is responsible for clearance of maternal RNAs, helping the transfer of developmental control to the zygotic program.

ResearchBlogging.orgLee MT, et al (2013). Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature, 503 (7476), 360-4 PMID: 24056933

Friday, January 31, 2014

Find your Ribo-Zero™ match with RNAMatchMaker

Will the Ribo-Zero Gold (Human/Mouse/Rat) kit deplete dolphin rRNA? Will it deplete arachnid rRNA? Find the strongest Ribo-Zero match to your favorite ribosomal sequences with free Ribo-Zero RNAMatchMaker software. Simply enter your ribosomal sequence and receive the strongest match from the extensive Ribo-Zero portfolio of options. Save time and money by checking kit compatibility before you start your experiment.