One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor.   However, until now, this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or “recipe”, and a user interface with inter-operating software tools to identify protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from a RNA-Seq e ..read more

Researchers find some neurons in the autistic brain preferentially express the copy of a gene inherited from one parent over the other. Many researchers have assumed that most cells express both copies of a gene equally. Studies in cultured cells suggest this might not always be the case. The new study is the first to provide evidence of this phenomenon in the brains of mice and monkeys. “This really can shape how mutated genes are expressed at the cellular level,” says lead researcher Christopher Gregg, assistant professor of neurobiology and anatomy at the University of Utah in Salt Lake C ..read more

In 2004, oncologist Gideon Rechavi at Tel Aviv University in Israel and his colleagues compared all the human genomic DNA sequences then available with their corresponding messenger RNAs — the molecules that carry the information needed to make a protein from a gene. They were looking for signs that one of the nucleotide building blocks in the RNA sequence, called adenosine (A), had changed to another building block called inosine (I). This ‘A-to-I editing’ can alter a protein’s coding sequence, and, in humans, is crucial for keeping the innate immune response in check. “It sounds simple, but ..read more

from Genetic Engineering News by Jeffrey S. Buguliskis, Ph.D. The Use of RNA-Seq Has Enormous Applicability toward the Development of Clinical Diagnostics DNA→RNA→Protein. This flow of genetic information has been the framework of modern biology since it was first enunciated by Francis Crick in 1958. However, in recent years researchers have begun to assemble a more comprehensive picture surrounding the “central dogma” of molecular biology, leading to the revelation that RNA is not just a simple genetic messenger—a middleman so to speak—but rather a complex signaling molecule that is present ..read more

Highlights    Defined open chromatin regions in sorted human α- and β-cells using ATAC-seq.    Detected type 2 diabetes-associated risk loci in human α- and β-cell open chromatin.    Classified human α- and β-cell-specific transcripts using mRNA-seq.    Discovered novel human α- and β-cell signature proteins.    Identified potential gene regulatory regions by integrating ATAC- and mRNA-seq data. Although glucagon-secreting α-cells and insulin-secreting β-cells have opposing functions in regulating plasma glucose levels, the two cell types sha ..read more

Advances in next-generation sequencing platforms have reshaped the landscape of functional genomic and epigenomic research as well as human genetics studies. Annotation of noncoding regions in the genome with genomic and epigenomic data has facilitated the generation of new, testable hypotheses regarding the functional consequences of genetic variants associated with human complex traits. Large consortia, such as the US National Institutes of Health (NIH) Roadmap Epigenomics Consortium and ENCODE, have generated tens of thousands of sequencing-based genome-wide data sets, creating a useful re ..read more

from NatureJobs Employer: Johns Hopkins University Location: Posted: June 28, 2014 Expires: August 22, 2014 The laboratory of Human Environmental Epigenomes of Dr. Zhibin Wang at Johns Hopkins University is looking for one or two postdoctoral fellow(s) to join a hot field of human epigenomes. The Wang laboratory has been pioneering with their developed ChIP-seq method and other deep sequencing methods (for example, RNA-seq and BS-seq) to answer how epigenetic codes are involved in the pathogenesis of human diseases. Current research efforts are centered on: 1) How DNA methylation patterns co ..read more

Despite the prevalent studies of DNA/Chromatin related epigenetics, such as, histone modifications and DNA methylation, RNA epigenetics has not drawn deserved attention until a new affinity-based sequencing approach MeRIP-Seq was developed and applied to survey the global mRNA N6-methyladenosine (m6A) in mammalian cells. As a marriage of ChIP-Seq and RNA-Seq, MeRIP-Seq has the potential to study the transcriptome-wide distribution of various post-transcriptional RNA modifications. Researchers at Xi’an Jiaotong-Liverpool University have previously developed an R/Bioconductor package ‘exomePeak ..read more

from Zone in with Zon by Jerry Zon Methylated riboA and riboC are the most commonly detected nucleobases in epigenetics research Powerful new analytical methods are key tools for progress Promising PacBio sequencing and novel “Pan Probes” reported    In a Grand Challenge Commentary published in Nature Chemical Biology in 2010, Prof. Chuan He at the University of Chicago opined that “[p]ost-transcriptional RNA modifications can be dynamic and might have functions beyond fine-tuning the structure and function of RNA. Understanding these RNA modification pathways and their functions m ..read more