More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells

The role of Yamanaka factors as the core regulators in the induction of pluripotency during somatic cell reprogramming has been discovered recently. Our previous study found that Yamanaka factors regulate a developmental signaling network in maintaining embryonic stem （ES） cell pluripotency. Here, we established completely reprogrammed induced pluripotent stem （iPS） cells and analyzed the global promoter occupancy of Yamanaka factors in these cells by ChiP-chip assays. We found that promoters of 565 genes were co-bound by four Yamanaka factors in iPS cells, a 10-fold increase when compared with their binding in ES cells. The promoters occupied by a single Yamanaka factor distributed equally in activated and repressed genes in iPS cells, while in ES cells Oct4, Sox2, or KIf4 distributed mostly in repressed genes and c-Myc in activated ones. Pathway analysis of the ChiP-chip data revealed that Yamanaka factors regulated 16 developmental signaling pathways in iPS cells, among which 12 were common and 4 were unique compared to pathways regulated in ES ChiP-chip dataset in iPS cells and observed similar results, cells. We further analyzed another recently published showing the power of ChiP-chip plus pathway analysis for revealing the nature of pluripotency maintenance and regeneration. Next, we experimentally tested one of the repressive signaling pathways and found that its inhibition indeed improved efficiency of cell reprogramming. Taken together, we proposed that there is a core developmental signaling network necessary for pluripotency, with TGF-β, Hedgehog, Wnt, p53 as repressive （Yin） regulators and Jak-STAT, cell cycle, focal adhesion, adherens junction as active （Yang） ones; and Yamanaka factors synergistically regulate them in a Yin-Yang balanced way to induce pluripotency.

Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana

Chloroplast is a typical plant cell organelle where photosynthesis takes place. In this study, a total of 1 808 chloroplast core proteins in Arabidopsis thaliana were reliably identified by combining the results of previously published studies and our own predictions. We then constructed a chloroplast protein interaction network primarily based on these core protein interactions. The network had 22 925 protein interaction pairs which involved 2 214 proteins. A total of 160 previously uncharacterized proteins were annotated in this network. The subunits of the photosynthetic complexes were modularized, and the functional relationships among photosystem Ⅰ （PSI）, photosystem Ⅱ （PSII）, light harvesting complex of photosystem Ⅰ （LHC Ⅰ） and light harvesting complex of photosystem Ⅰ （LHC Ⅱ） could be deduced from the predicted protein interactions in this network. We further confirmed an interaction between an unknown protein AT1G52220 and a photosynthetic subunit PSI-D2 by yeast two-hybrid analysis. Our chloroplast protein interaction network should be useful for functional mining of photosynthetic proteins and investigation of chloroplast-related functions at the systems biology level in Arabidopsis.

HCCNet： an integrated network database of hepatocellular carcinoma

Dear Editor, As a complex disease, the development and progression of hepatocellular carcinoma （HCC） involves the interactions of multiple proteins, genes and miRNAs in various biological pathways, and it has been extensively studied with different high-throughput techniques. However, efforts to integrate multiple data sources at different levels, especially with regard to biological pathways and interaction networks, are still negligible in the HCC research field.

JMJD3 promotes chondrocyte proliferation and hypertrophy during endochondral bone formation in mice

JMJD3(KDM6B)is an H3K27me3 demethylase and counteracts polycomb-mediated transcription repression.However,the function of JMJD3 in vivo is not well understood.Here we show that JMJD3 is highly expressed in cells of the chondrocyte lineage,especially in prehypertrophic and hypertrophic chondrocytes,during endochondral ossification.Homozygous deletion of Jmjd3 results in severely decreased proliferation and delayed hypertrophy of chondrocytes,and thereby marked retardation of endochondral ossification in mice.Genetically,JMJD3 associates with RUNX2 to promote proliferation and hypertrophy of chondrocytes.Biochemically,JMJD3 associates with and enhances RUNX2 activity by derepression of Runx2 and Ihh transcription throughits H3K27me3 demethylase activity.These results demonstrate that JMJD3 is a key epigenetic regulator in the process of cartilage maturation during endochondral bone formation.

Overview of available methods for diverse RNA-Seq data analyses

RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.

A genealogy data services platform implemented with linked data technologies

Open data becomes not only the responsibility but also a development opportunity for the government, scientific research institutions, libraries and other cultural heritage institutions. The Shanghai Library, starting from the genealogical data, has been dedicated to constructing the historical documents and data services platform through reorganizing its traditional resources by utilizing the Linked Open Data technologies. The genealogy data services platform, through BIBFRAME-based ontology design, data transformation from RDB to RDF, system design on the basis of the four principles of Linked Data as well as the system development based on the framework of semantic technologies, supports bibliographic control in the Internet environment and satisfies general users’ needs for tracing their family roots, and professional researchers’ demands for data mining.

Major Depressive Disorder: Advances in Neuroscience Research and Translational Applications

Major depressive disorder(MDD),also referred to as depression,is one of the most common psychiatric disorders with a high economic burden.The etiology of depression is still not clear,but it is generally believed that MDD is a multifactorial disease caused by the interaction of social,psychological,and biological aspects.Therefore,there is no exact pathological theory that can independently explain its pathogenesis,involving genetics,neurobiology,and neuroimaging.At present,there are many treatment measures for patients with depression,including drug therapy,psychotherapy,and neuromodulation technology.In recent years,great progress has been made in the development of new antidepressants,some of which have been applied in the clinic.This article mainly reviews the research progress,pathogenesis,and treatment of MDD.

Correction to: Major Depressive Disorder: Advances in Neuroscience Research and Translational Applications

Correction to:Neurosci.Bull.2021 https://doi.org/10.1007/sl2264-021-00638-3 The original version of this article unfortunately contained two mistakes.1.In the“Acknowledgements”,the“the National Basic Research”should be changed into“the National Key Research”.