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Co-transcriptional splicing has been seen in lower eukaryotes as well as for a few mammalian genes, but the extent to which it affects mammalian gene regulation has been unclear. RNA sequencing now shows that co-transcriptional splicing is widespread in human cells and particularly abundant in the human brain.
The nature of small RNA species derived from gene termini and intron-exon junctions is now further examined. By sequencing transcripts between 12 and 100 nucleotides derived from cells depleted for RNA decay factors as well as those associated with Argonaute proteins, insights into how these RNAs are produced is provided. Moreover, new small RNAs are identified.
Based on genome wide localization of initiating RNA polymerase II, general transcription factors and epigenetic marks in mouse thymocytes, transcription initiation platforms (TIPs) are evidenced, both at promoters and enhancers, as features able to promote tissue-specific expression.
Pioneer transcription factors such as Foxa1 and Foxa2 need to bind to nucleosomal DNA to regulate chromatin structure and gene activation. Now a genome-wide nucleosome mapping in mouse liver shows that the maintenance of nucleosome position and chromatin structure surrounding Foxa23 binding sites is independent of Foxa1/2.
It has long been known that in mammals maternally and paternally inherited genes can be differentially expressed. By generating human parthenogenetic induced pluripotent stem cell lines, the expression of parentally inherited genes is now examined genome wide, uncovering novel imprinted non-coding RNAs and demonstrating the consequences of parthenogenesis on human development.
The lack of sequence-specificity of DNA replication origins in most eukaryotes poses a challenge for its identification. Through BrdU labeling followed by high-throughput sequencing, supported by ChIP-chip to locate ORC1 and CDC6, the origins of replication in Arabidopsis thaliana are now mapped and their contexts analyzed.
APOBEC1 is involved in conversion of a specific C to U in apolipoprotein B mRNA, a classic example of RNA editing. With a comparative RNA-Seq screen, numerous additional targets of APOBEC1 editing are found. Editing sites tend to be located in AU-rich regions of 3′ UTRs, and analysis identifies common features that prove predictive of additional targets.
microRNAs bind Argonaute proteins, guiding silencing of target mRNAs. CLIP-seq has now been used to map microRNA targets bound by Ago2 in a Dicer-dependent fashion in mouse ES cells. The study reveals that certain sets of transcripts, such as TGF-β signaling pathway components, tend to be targeted, and also identifies a G-rich motif in targets that may modulate regulation.
