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.

Tuesday, December 17, 2013

Select the Right Tool for your Molecular Biology Project

Select the right tool for your molecular biology project with the new Molecular Biology Selection Guide. This guide enables you to see all your available options for each step of your workflow. Tools are available for sequencing, microarrays, PCR, cloning, and more. 

Wednesday, November 6, 2013

RNA aptamers:  A new paradigm in cancer diagnosis and treatment

RNA aptamers are small, single-stranded RNA molecules that are functionally analogous to antibodies.  Interestingly, they are emerging as a class of molecules with potential in the diagnosis and treatment of human diseases.

Epicentre will host a Free Webinar on Nov 7/13 that will focus on the use of RNA aptamers for developing cancer diagnostics and treatments:

  • Selecting and using RNA aptamers as therapeutic agents
  • Targeted delivery of therapeutics such as siRNA
  • Development of biosensors/diagnostics for early cancer detection

We hope you can join us for this informative session. 

Wednesday, October 23, 2013

Visit Epicentre at ASHG

Epicentre will be attending ASHG to be held October 23-25, in Boston, MA. Stop by Booth #528 to learn more about our products for Methyl-Seq, ribosome profiling, and more.

In addition, we will be presenting the following posters:

  • 477F: Whole genome methylation analysis using a novel bisulfite sequencing scheme.
  • 622F: Understanding translational regulation using RNA-Seq of Ribosome Protected mRNA fragments.

We hope to see you at the conference! If you're not attending, and would like more information about the products highlighted at the conference, please contact us by e-mail or call 1 (800) 284-8474 within the US.

Wednesday, October 2, 2013

EpiGnome™ Methyl-Seq Kit: Informatics Guide Now Available

Sequencing-based DNA methylation analysis applies the coverage density and flexibility enabled by next-generation sequencing to enhance epigenetic studies. Analysis of the sequencing data is an important step of the procedure and so an Informatics Guide is available to get started. The guide produces an output file that can be viewed in a genome viewer and contains sequence information.

Click here for the Informatics Guide

EpiGnome™ Methyl-Seq Kit: Sample Data Set Now Available

The following test data set may be downloaded for use with the Methyl-Seq BioInformatics Guide. This data set was generated using EpiGnome Methyl-Seq Kit with 50 ng of Coriell gDNA (GM12878) as input into bisulfite conversion. The libraries were sequenced PE 75 bp reads. The data set contains 10,000 reads from Read 1 and Read 2.

Click here for the sample data set

Thursday, September 5, 2013

Complete methylome analysis from only 50 ng

Epicentre's new Methyl-Seq Kit produces whole genome bisulfite sequencing libraries from only 50 ng of genomic DNA. EpiGnome™ follows a unique "post-bisulfite conversion" library construction method which yields highly diverse libraries with uniform coverage.

  • Highly diverse libraries
  • Uniform CpG, CHG, and CHH coverage
  • 1-day procedure
  • Only 50 ng into bisulfite-conversion