By studying the genomes of fruit flies, scientists from the Zaugg and Furlong groups at EMBL Heidelberg have identified a set of genomic features that can predict how much the expression of a gene varies between individuals in a species. Their...
Read More »RNA-Seq Reveals An Aging-Related Effect on the Circadian Clock
Some genes controlled by the body’s circadian clock are more active in older fruit flies compared to younger ones. And oxidative stress can induce the expression of these genes in young flies, according to a study published today (February 21) ...
Read More »TEtools – facilitates big data expression analysis of transposable elements
Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. ...
Read More »Published reference genomes should be re-annotated before use as references for RNA-Seq experiments
RNA-seq based on short reads generated by next generation sequencing technologies has become the main approach to study differential gene expression. Until now, the main applications of this technique have been to study the variation of gene expression in a ...
Read More »Optimization of next generation sequencing transcriptome annotation for species lacking sequenced genomes
Next generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods ...
Read More »Developmental Analysis of Spliceosomal snRNA Isoform Expression with RNA-Seq
Pre-mRNA splicing is a critical step in eukaryotic gene expression that contributes to proteomic, cellular and developmental complexity. Small nuclear (sn)RNAs are core spliceosomal components, however, the extent to which differential expression of snRNA isoforms regulates splicing is completely unknown. ...
Read More »Biases during read mapping can be avoided by mapping reads to two alternative genomes
Genetic variation in cis-regulatory elements is an important cause of variation in gene expression. Cis-regulatory variation can be detected by using high-throughput RNA sequencing (RNA-seq) to identify differences in the expression of the two alleles of a gene. This requires ...
Read More »Quality assessment and control of tissue specific RNA-seq libraries
RNA-sequencing (RNA-seq) is rapidly emerging as the technology of choice for whole-transcriptome studies. However, RNA-seq is not a bias free technique. It requires large amounts of RNA and library preparation can introduce multiple artifacts, compounded by problems from later stages ...
Read More »RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins
Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of ...
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