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Measuring gene expression in individual cells is crucial for understanding the gene regulatory network controlling human embryonic development. Single-cell RNA sequencing (RNA-Seq) analysis of 124 individual cells from human preimplantation embryos and embryonic stem cells (hESCs) now provides a comprehensive framework of the transcriptome landscapes of human early embryos and hESCs.

A mRNA-interactome capture approach in embryonic stem cells (ESCs) has led to the identification of 283 novel RNA-binding protein (RBP) candidates, of which 68 are preferentially expressed in ESCs. Validation of two known E3 ubiquitin ligases as RBPs reveals an intriguing potential link between RNA biology and protein-modification pathways.

By integrating the expression profiles of long noncoding RNAs (lncRNAs) with clinical outcome and somatic copy-number alteration, the authors identified new lncRNAs that are associated with certain cancer subtypes and clinical prognoses. Experimental validation of the prostate cancer cell growth dependence of two new lncRNAs demonstrates the power of this approach for discovering disease-related lncRNAs.

mRNA-binding proteins have crucial regulatory functions in gene expression. A global analysis in budding yeast now uncovers 120 proteins that cross-link to mRNA, including 66 new mRNA-binding proteins. CLIP analyses of P-body components further identify sites of interaction on specific mRNAs, revealing principles by which these proteins assemble into P-body mRNPs.

Tissue- and disease-specific features of nucleosome positioning have recently been reported. A new study set out to identify features of nucleosome positioning at functional genomic elements during lineage commitment from mouse embryonic stem cells to neural progenitors and embryonic fibroblasts. The results reveal regulatory mechanisms of cell differentiation that involve nucleosome positioning.

A systematic, unbiased screen for general intronic splicing enhancers (ISEs) identified >100 ISEs that promote intron splicing but inhibit splicing in exons. Putative trans-factors for clusters of ISEs were identified, validated and were found to control ISE activity in a context-dependent manner. Altogether, the data provide a comprehensive picture of how ISEs function depending on their location and cognate trans-factors.

The 5-hydroxymethylcytosine (5-hmC) nucleoside is abundant in the brain for unknown reasons. Genome-wide analysis of the distribution of 5-hmC versus 5-methylcytosine (5-mC) in human and mouse tissues now shows that 5-hmC is enriched in genes with synaptic functions. The differential distribution of 5-hmC versus 5-mC at exon-intron boundaries in both human and mouse tissues further suggests a possible role for 5-hmC in pre-mRNA splicing.

RNA 3′-end formation is thought to be crucial in controlling gene expression. Direct RNA sequencing was used to analyze the 3′ ends of Arabidopsis thaliana RNA in unprecedented detail, revealing extreme heterogeneity of RNA 3′ ends, patterns of cleavage and polyadenylation, and previously unrecognized noncoding RNAs.

How metazoans determine where to initiate DNA replication remains mysterious. Now deep sequencing of short nascent strands in different human cell types provides an extensive map of replication origins, identifying cell type–specific signatures and a putative consensus motif with the potential to form G-quadruplex structures.

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.

In fission yeast, the RNAi pathway has been linked to formation of heterochromatin at centromeres. Fusing Dicer to DNA adenine methyltransferase now revealed that Dcr1 also associates with euchromatic regions of the S. pombe genome to mediate co-transcriptional gene silencing.

Antibodies are a primary tool to assess histone post-translational modifications. However, different antibodies and batches might vary in their ability to recognize those modifications, depending on the kind of assay used. Now a systematic analysis of different antibodies and an open database containing the validation results are presented.

Nucleosomes consist of two copies of each histone. H2A.Z is a variant H2A-related histone known to be enriched around transcription start sites. However, an H2A.Z-containing nucleosome could contain contain two copies of H2A.Z (homotypic) or one of H2A.Z and one of canonical H2A (heterotypic). Homotypic and heterotypic H2A.Z nucleosomes are now mapped and their distributions relative to promoters analyzed.