Temporal Dissection of Rate Limiting Transcriptional Events Using Pol II ChIP and RNA Analysis of Adrenergic Stress Gene Activation

MiR-363-3p attenuates neonatal hypoxic-ischemia encephalopathy by targeting DUSP5

Neonatal hypoxic-ischemia encephalopathy (HIE) refers to hypoxic-ischemic brain damage caused by perinatal asphyxia. Increasing evidence has revealed the crucial roles of microRNAs (miRNAs) in neonatal HIE. In the current research, we aimed to explore the biological role of miR-363-3p in neonatal HIE. For this purpose, we established in vitro models of PC-12 and SH-SY5Y cells subjected to oxygen-glucose deprivation and reperfusion (OGD/R) and an in vivo rat model subjected to middle cerebral artery occlusion/reperfusion (MCAO/R) treatment. First, using H&E staining, TTC staining, and western blot analysis, we observed that DUSP5 knockdown suppressed HIE in vivo. Then, by performing flow cytometric analysis, western blotting, RT-qPCR, and MTT assays, we observed that DUSP5 silencing suppressed OGD/R-induced cell injury in vitro. Subsequently, we explored the potential regulatory mechanism of DUSP5 in OGD/R-treated cells with luciferase reporter assays and RT-qPCR analysis. The results demonstrated that DUSP5 was targeted by miR-363-3p. Next, functional assays, including flow cytometric analysis, MTT assays, western blotting and RT-qPCR, were conducted to explore the biological functions of miR-363-3p in SH-SY5Y and PC-12 cells. Our data showed that miR-363-3p overexpression suppressed OGD/R-induced cell injury. Finally, the results from rescue experiments showed that enhanced DUSP5 expression counteracted the effect of miR-363-3p overexpression. In conclusion, our data suggested that miR-363-3p attenuates neonatal HIE by targeting DUSP5.

PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies

Chromatin immunoprecipitation (ChIP) is the most widely used approach for identification of genome-associated proteins and their modifications. We have previously introduced a microplate-based ChIP platform, Matrix ChIP, where the entire ChIP procedure is done on the same plate without sample transfers. Compared to conventional ChIP protocols, the Matrix ChIP assay is faster and has increased throughput. However, even with microplate ChIP assays, sample preparation and chromatin fragmentation (which is required to map genomic locations) remains a major bottleneck. We have developed a novel technology (termed 'PIXUL') utilizing an array of ultrasound transducers for simultaneous shearing of samples in standard 96-well microplates. We integrated PIXUL with Matrix ChIP ('PIXUL-ChIP'), that allows for fast, reproducible, low-cost and high-throughput sample preparation and ChIP analysis of 96 samples (cell culture or tissues) in one day. Further, we demonstrated that chromatin prepared using PIXUL can be used in an existing ChIP-seq workflow. Thus, the high-throughput capacity of PIXUL-ChIP provides the means to carry out ChIP-qPCR or ChIP-seq experiments involving dozens of samples. Given the complexity of epigenetic processes, the use of PIXUL-ChIP will advance our understanding of these processes in health and disease, as well as facilitate screening of epigenetic drugs.

Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes

BACKGROUND

Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level.

RESULTS

We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses.

CONCLUSIONS

Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.

Gene length as a biological timer to establish temporal transcriptional regulation

Transcriptional timing is inherently influenced by gene length, thus providing a mechanism for temporal regulation of gene expression. While gene size has been shown to be important for the expression timing of specific genes during early development, whether it plays a role in the timing of other global gene expression programs has not been extensively explored. Here, we investigate the role of gene length during the early transcriptional response of human fibroblasts to serum stimulation. Using the nascent sequencing techniques Bru-seq and BruUV-seq, we identified immediate genome-wide transcriptional changes following serum stimulation that were linked to rapid activation of enhancer elements. We identified 873 significantly induced and 209 significantly repressed genes. Variations in gene size allowed for a large group of genes to be simultaneously activated but produce full-length RNAs at different times. The median length of the group of serum-induced genes was significantly larger than the median length of all expressed genes, housekeeping genes, and serum-repressed genes. These gene length relationships were also observed in corresponding mouse orthologs, suggesting that relative gene size is evolutionarily conserved. The sizes of transcription factor and microRNA genes immediately induced after serum stimulation varied dramatically, setting up a cascade mechanism for temporal expression arising from a single activation event. The retention and expansion of large intronic sequences during evolution have likely played important roles in fine-tuning the temporal expression of target genes in various cellular response programs.