DNA Methylation Profiling of MYC, SMAD2/3 and DNMT3A in Colorectal Cancer

Epigenetic modifications particularly DNA methylation is a common place and remarkable factor in carcinogenesis transformation. Conspicuously, previous findings have presented a cluster of irregular promoter methylation alterationsrelated with silencing of TSG (tumor suppressor genes), little is accepted regarding their sequential DNA methylation (Hypo and Hyper) modifications during the cancer progression. In this way, fluctuations of DNA methylation of many certain genes especially MYC, SMAD2/3 and DNMT3A have an impressive central key role in many different cancers like colorectal (CRC)one. CRC is distinguished by DNA methylation, which is related with tumorigenesis and also genomic instability. Importantly, molecular heterogeneity between multiple adenomas in different patients with CRC may show diverse developmental phenotypes for these kinds of tumors. Conclusively, studying of factors which are involved in CRC carcinogenesis, especially the alterations in epigenetic elements, such as DNA methylation besides the RNA remodeling, histone modification, histone acetylation and histone phosphorylation can be influential in order to find new therapeutic and diagnostic biomarkers in this type of malignancy. In this account, we tried to discuss and address the potential significant methylated modifications of these genes and their importance during the development of CRC carcinogenesis.

Ligands with poly-fluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities

The interaction of nucleic acids with their molecular targets often involves structural reorganization that may traverse a complex folding landscape. With the more recent recognition that many RNAs, both coding and noncoding, may regulate cellular activities by interacting with target molecules, it becomes increasingly important to understand the means by which nucleic acids interact with their targets and how drugs might be developed that can influence critical folding transitions. We have extensively investigated the interaction of the Spinach2 and Broccoli aptamers with a library of small molecule ligands modified by various extensions from the imido nitrogen of DFHBI (3,5-difluoro-4-hydroxybenzylidene imidazolinone) that reach out from the Spinach2 ligand binding pocket. Studies of the interaction of these compounds with the aptamers revealed that poly-fluorophenyl-modified ligands initiate a slow change in aptamer affinity that takes an extended time (half-life of ~40 min) to achieve. The change in affinity appears to involve an initial disruption of the entrance to the ligand binding pocket followed by a gradual lockdown for which the most likely driving force is an interaction of the gateway adenine with a nearby 2'OH group. These results suggest that poly-fluorophenyl modifications might increase the ability of small molecule drugs to disrupt local structure and promote RNA remodeling.

THE DEAD-BOX PROTEIN CSHA FROM Staphylococcus aureus Mu 50 EXHIBITS RIBONUCLEASE ACTIVITY

DEAD-box proteins play important roles in many RNA processes ranging from RNA synthesis to RNA decay. Furthermore, it has been reported that some bacterial DEAD-box proteins known to be components of the RNA degradosome do not cleave RNA substrates directly. However, the role of DEAD-box proteins in RNA degradation is poorly understood. The present study demonstrated that the DEAD-box protein CshA from the vancomycin-resistant Staphylococcus aureus strain Mu50 possesses RNA degradation activity, ribonuclease activity. Despite having RNA-dependent ATPase activity, CshA did not exhibit RNA helicase activity in vitro. Instead, CshA catalyzed the degradation of single-stranded RNAs of various duplex RNA substrates to form blunt-end RNA products. Thus, we suggest that the ribonuclease activity of the DEAD-box protein CshA may contribute to RNA remodeling in the bacterial RNA degradosome. To our knowledge, this study is the first to report that a DEAD-box protein from a pathogenic bacterium is implicated in multiple ATP-independent activity on RNA, such as degradation.

The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2

Understanding human neurogenesis is critical toward regenerative medicine for neurodegeneration. However, little is known how neural differentiation is regulated by RNA helicases, which comprise a diverse class of RNA remodeling enzymes. We show here that expression of the DEAD box-containing RNA helicases DDX5 and DDX17 is abundant throughout retinoic acid-induced neural differentiation of the human pluripotent stem cell (hPSC) line NTERA2, and is mostly localized within the nucleus. Using ChIP-seq, we identify that the two RNA helicases occupy chromatin genome-wide at regions associated with neurogenesis- and differentiation-related genes in both hPSCs and their neural derivatives. Further, RNA-seq analyses indicate both DDX5 and DDX17 are mutually required for controlling transcriptional expression of these genes. We show that the two RNA helicases are not important for maintenance of stem cell state of hPSCs. In contrast, they facilitate early neural differentiation of hPSCs, generation of neurospheres from the stem cells, and expression of key neurogenic transcription factors during neural differentiation. Importantly, DDX5 and DDX17 are important for differentiation of hPSCs toward NESTIN- and TUBB3-positive cells, which represent neural progenitors and mature neurons. Collectively, our findings suggest the role of DDX5 and DDX17 in transcriptional regulation of genes involved in neurogenesis, and hence in neural differentiation of hPSCs.

Early-life undernutrition induces enhancer RNA remodeling in mice liver

Background Maternal protein restriction diet (PRD) increases the risk of metabolic dysfunction in adulthood, the mechanisms during the early life of offspring are still poorly understood. Apart from genetic factors, epigenetic mechanisms are crucial to offer phenotypic plasticity in response to environmental situations and transmission. Enhancer-associated noncoding RNAs (eRNAs) transcription serves as a robust indicator of enhancer activation, and have potential roles in mediating enhancer functions and gene transcription. Results Using global run-on sequencing (GRO-seq) of nascent RNA including eRNA and total RNA sequencing data, we show that early-life undernutrition causes remodeling of enhancer activity in mouse liver. Differentially expressed nascent active genes were enriched in metabolic pathways. Besides, our work detected a large number of high confidence enhancers based on eRNA transcription at the ages of 4 weeks and 7 weeks, respectively. Importantly, except for ~ 1000 remodeling enhancers, the early-life undernutrition induced instability of enhancer activity which decreased in 4 weeks and increased in adulthood. eRNA transcription mainly contributes to the regulation of some important metabolic enzymes, suggesting a link between metabolic dysfunction and enhancer transcriptional control. We discovered a novel eRNA that is positively correlated to the expression of circadian gene Cry1 with increased binding of epigenetic cofactor p300. Conclusions Our study reveals novel insights into mechanisms of metabolic dysfunction. Enhancer activity in early life acts on metabolism-associated genes, leading to the increased susceptibility of metabolic disorders.

Dual-level autoregulation of the E. coli DeaD RNA helicase via mRNA stability and Rho-dependent transcription termination

ABSTRACTDEAD-box proteins (DBPs) are RNA remodeling factors associated with RNA helicase activity that are found in nearly all organisms. Despite extensive studies on the mechanisms used by DBPs to regulate RNA function, very little is known about how DBPs themselves are regulated. In this work, we have analyzed the expression and regulation of DeaD/CsdA, the largest of the DBPs in Escherichia coli (E. coli). We show that deaD transcription initiates 838 nts upstream of the start of the coding region. We have also found that DeaD is autoregulated through a negative feedback mechanism that operates both at the level of mRNA stability and Rho-dependent transcription termination, and this regulation is dependent upon the 5’ untranslated region (5’ UTR). These findings suggest that DeaD might be regulating the conformation of its own mRNA through its RNA helicase activity to facilitate ribonuclease and Rho access to its 5’UTR.