Epigenetic reprogramming provides valuable resources for customized pluripotent stem cells generation, which are thought to be important bases of future regenerative medicine. Here we review the commonly used methods for epigenetic reprogramming: somatic cell nuclear transfer, cell fusion, cell extract treatment, inducing pluripotency by defined molecules, and briefly discuss their advantages and limitations. Finally we propose that mechanisms underlying epigenetic reprogramming and safety evaluation platform will be future research directions.

Host pattern recognition receptors (PRRs) recognize invading viral pathogens and initiate a series of signaling cascades that lead to the expression of type I interferons (IFNs) and inflammatory cytokines. During the past decade, significant progresses have been made to characterize PRRs such as Toll-like receptors (TLRs) and RIG-I-like receptors (RLRs) and elucidate the molecular mechanisms of TLR- and RLR-mediated signaling. To avoid excessive and harmful immune effects caused by over-activation of these signaling pathways, host cells adopt a number of strategies to regulate them. In addition, invading viruses also employ a variety of mechanisms to inhibit the production of type I IFNs, thereby evading the supervision and clearance by the host. In this review, we briefly summarize the TLR- and RLR-mediated type I IFN signaling and then focus on the mechanisms by which host cellular and viral components regulate the expression of type I IFNs.

MicroRNAs (miRNAs) are a highly conserved class of small (18–24 nucleotides) non-coding RNAs that regulate a broad spectrum of biological processes. Aberrations or corruptions of miRNA functions may lead to deregulated cell proliferation, tumorigenesis, and ultimately, cancer. Increasing evidences suggested that a large fraction of miRNAs is regulated at the post-transcriptional stage, which impacts on the level and function of miRNAs during cell development and human diseases. Recently, several distinct mechanisms are emerging to regulate the biogenesis, stability and function of miRNAs at post-transcriptional level, such as specific binding to terminal loops of miRNA precursors (pri-miRNAs or pre-miRNAs) by RNA-binding proteins and 3’-terminal modifications by particular enzymes. Signaling cascades and post-translational modifications of the core components of RNA machinery also take part in the post-transcriptional regulation of miRNAs.

Embryonic stem (ES) cells distinct themselves from other cell type populations by their pluripotent ability. The unique features of ES cells are controlled by both genetic and epigenetic factors. Studies have shown that the methylation status of DNA and histones in ES cells is quite different from that of differentiated cells and somatic stem cells. Herein, we summarized recent advances in DNA and histone methylation studies of mammalian ES cells. The methylation status of several key pluripotent regulatory genes is also discussed.

Dendritic spines are the major targets of excitatory synaptic input. They exist in a wide variety of shapes and sizes, from thin to mushroom-shaped to stubby. One of the striking characteristics of dendritic spines is their motile nature. Spines can undergo various structural modifications such as changes in density, shape, size, and motility. During development, spines are highly dynamic and many spines are formed and eliminated. As animals mature, most spines become stable and the vast majority of them can last throughout life. However, spine morphology can still undergo progressive changes. Structural dynamics of dendritic spines is thought to play important roles in synapse plasticity and information processing. Abnormal spine structures are often associated with malfunction of the nervous system.

Both thymocytes and tumor cells express M2 type isoenzyme of pyruvate kinase (M2PK), which is different from R type isoenzyme of pyruvate kinase (RPK) that is expressed in erythrocytes. In this report, the effect of RPK and M2PK on the transcription of human immunodeficiency virus type 1 (HIV-1) was tested. The results indicated that M2PK could enhance HIV-1 transcription from its long terminal repeat (LTR) promoter, while RPK did not have such an effect. Specific down-regulation of M2PK could inhibit HIV-1 transcription from its LTR region. Furthermore, it was found that the C terminal region of M2PK is responsible for this effect. Collectively, the cellular factor M2PK that is expressed in thymocytes could facilitate the transcription of HIV-1.

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA (sRNA) targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORs (ARFs) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5′ rapid amplification of cDNA ends (RLM 5′-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.