Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements （TEs） have no longer been totally considered as ＂junk DNA＂ for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Tech- nologies based on 3C （chromosome conformation capture） have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions （hESC： r= 0.9, P〈 2.2 × 10^16; IMRg0 fibroblasts： r= 0.94, P 〈 2.2 ×10^16） and also have asignificant positive correlation with some remote functional DNA elements like enhancers and promoters （Enhancer： hESC： r= 0.997, P= 2.3× 10^-4; IMR90： r- 0.934, P= 2 × 10^-2; Promoter： hESC： r= 0.995, P= 3.8 × 10^-4; IMR90： r= 0.996, P = 3.2 × 10^-4）. Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes.

Char Plant:A De Novo Open Chromatin Region Prediction Tool for Plant Genomes

Chromatin accessibility is a highly informative structural feature for understanding gene transcription regulation,because it indicates the degree to which nuclear macromolecules such as proteins and RNAs can access chromosomal DNA.Studies have shown that chromatin accessibility is highly dynamic during stress response,stimulus response,and developmental transition.Moreover,physical access to chromosomal DNA in eukaryotes is highly cell-specific.Therefore,current technologies such as DNase-seq,ATAC-seq,and FAIRE-seq reveal only a portion of the open chromatin regions(OCRs)present in a given species.Thus,the genome-wide distribution of OCRs remains unknown.In this study,we developed a bioinformatics tool called Char Plant for the de novo prediction of OCRs in plant genomes.To develop this tool,we constructed a three-layer convolutional neural network(CNN)and subsequently trained the CNN using DNase-seq and ATACseq datasets of four plant species.The model simultaneously learns the sequence motifs and regulatory logics,which are jointly used to determine DNA accessibility.All of these steps are integrated into Char Plant,which can be run using a simple command line.The results of data analysis using Char Plant in this study demonstrate its prediction power and computational efficiency.To our knowledge,Char Plant is the first de novo prediction tool that can identify potential OCRs in the whole genome.The source code of Char Plant and supporting files are freely available from https://github.com/Yin-Shen/Char Plant.

Path from schizophrenia genomics to biology:gene regulation and perturbation in neurons derived from induced pluripotent stem cells and genome editing

Schizophrenia（SZ） is a devastating mental disorder afflicting 1% of the population. Recent genome-wide association studies（GWASs） of SZ have identified 〉100 risk loci. However,the causal variants/genes and the causal mechanisms remain largely unknown,which hinders the translation of GWAS fi ndings into disease biology and drug targets. Most risk variants are noncoding,thus likely regulate gene expression. A major mechanism of transcriptional regulation is chromatin remodeling,and open chromatin is a versatile predictor of regulatory sequences. Micro RNA-mediated post-transcriptional regulation plays an important role in SZ pathogenesis. Neurons differentiated from patient-specifi c induced pluripotent stem cells（i PSCs） provide an experimental model to characterize the genetic perturbation of regulatory variants that are often specifi c to cell type and/or developmental stage. The emerging genome-editing technology enables the creation ofisogenic i PSCs and neurons to effi ciently characterize the effects of SZ-associated regulatory variants on SZ-relevant molecular and cellular phenotypes involving dopaminergic,glutamatergic,and GABAergic neurotransmissions. SZ GWAS fi ndings equipped with the emerging functional genomics approaches provide an unprecedented opportunity for understanding new disease biology and identifying novel drug targets.

Individual variation in buffalo somatic cell cloning efficiency is related to glycolytic metabolism

Mammalian individuals differ in their somatic cell cloning efficiency,but the mechanisms leading to this variation is poorly understood.Here we found that high cloning efficiency buffalo fetal fibroblasts(BFFs)displayed robust energy metabolism,looser chromatin structure,high H3 K9 acetylation and low heterochromatin protein 1α(HP1α)expression.High cloning efficiency BFFs had more H3 K9 ac regions near to the upstream of glycolysis genes by Ch IP-seq,and involved more openness loci related to glycolysis genes through ATAC-seq.The expression of these glycolysis genes was also found to be higher in high cloning efficiency BFFs by q RT-PCR.Two key enzymes of glycolysis,PDKs and LDH,were confirmed to be associated with histone acetylation and chromatin openness of BFFs.Treatment of low cloning efficiency BFFs with PS48(activator of PDK1)resulted in an increase in the intracellular lactate production and H3 K9 acetylation,decrease in histone deacetylase activity and HP1αexpression,less condensed chromatin structure and more cloning embryos developing to blastocysts.These results indicate that the cloning efficiency of buffalo somatic cells is associated with their glycolytic metabolism and chromatin structure,and can be improved by increasing glycolytic metabolism.