A5112905610- RNA modifications and cancer
- RNA Research and Splicing
- Circular RNAs in diseases
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- CRISPR and Genetic Engineering
- Immune cells in cancer
- Cancer, Hypoxia, and Metabolism
- RNA and protein synthesis mechanisms
- RNA regulation and disease
- Cancer-related gene regulation
- Virus-based gene therapy research
- Epigenetics and DNA Methylation
- Analytical chemistry methods development
- Analytical Chemistry and Chromatography
- Advanced biosensing and bioanalysis techniques
- TGF-β signaling in diseases
- Chemokine receptors and signaling
- RNA Interference and Gene Delivery
- Plant Gene Expression Analysis
- Phagocytosis and Immune Regulation
- Plant Molecular Biology Research
- Adipose Tissue and Metabolism
- Insect Resistance and Genetics
- Ubiquitin and proteasome pathways
Children's Hospital of Fudan University
2023-2025
Sichuan Animal Science Academy
2019-2025
Chinese Academy of Sciences
2015-2025
Fudan University
2016-2025
Zhejiang Cancer Hospital
2024-2025
Pudong Medical Center
2025
Southern Medical University
2023-2024
Third Affiliated Hospital of Zhengzhou University
2022-2024
Chongqing University
2014-2024
Shanxi Medical University
2015-2024
From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation still needed characterize how used help produce functional organism (see Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for Caenorhabditis elegans genome, and The modENCODE Consortium 1787 Drosophila melanogaster full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites,...
Circular RNAs (circRNAs) derived from back-spliced exons have been widely identified as being co-expressed with their linear counterparts. A single gene locus can produce multiple circRNAs through alternative back-splice site selection and/or splice selection; however, a detailed map of back-splicing/splicing in is lacking. Here, the upgraded CIRCexplorer2 pipeline, we systematically annotated different types back-splicing and splicing events various cell lines. Compared cognate RNAs,...
The human 8q24 gene desert contains multiple enhancers that form tissue-specific long-range chromatin loops with the MYC oncogene, but how looping at locus is regulated remains poorly understood. Here we demonstrate a long noncoding RNA (lncRNA), CCAT1-L, transcribed specifically in colorectal cancers from 515 kb upstream of MYC. This lncRNA plays role transcriptional regulation and promotes looping. Importantly, CCAT1-L located within strong super-enhancer spatially close to Knockdown...
Steady-state circular RNAs (circRNAs) have been mapped to thousands of genomic loci in mammals. We studied circRNA processing using metabolic tagging nascent with 4-thiouridine (4sU). Strikingly, the efficiency from pre-mRNA is extremely low endogenously. Additional studies revealed that back-splicing outcomes correlate fast RNA Polymerase II elongation rate and are tightly controlled by cis-elements vivo. Additionally, prolonged 4sU labeling cells shows circRNAs largely processed...
Abstract Background RNAs can be physically classified into poly(A)+ or poly(A)- transcripts according to the presence absence of a poly(A) tail at their 3' ends. Current deep sequencing approaches largely depend on enrichment with tail, and therefore offer little insight nature expression that lack tails. Results We have used explore repertoire both from HeLa cells H9 human embryonic stem (hESCs). Using stringent criteria, we found while majority are poly(A)+, significant portion either...
Uniform processing and detailed annotation of human, worm fly RNA-sequencing data reveal ancient, conserved features the transcriptome, shared co-expression modules (many enriched in developmental genes), matched expression patterns across development similar extent non-canonical, non-coding transcription; furthermore, are used to create a single, universal model predict gene-expression levels for all three organisms from chromatin at promoter. In this paper modENCODE consortium reports on...
Drosophila melanogaster cell lines are important resources for biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals 25 lines. Unannotated transcription is substantial (typically 19% euchromatic signal). Conservatively, identify 1405 novel transcribed regions; 684 these appear to be new exons neighboring, often distant, genes. Sixty-four percent genes expressed detectably in at least one line, but only 21% detected all Each line expresses, on...
Abstract Circular RNAs (circRNAs) from back-splicing of exon(s) have been recently identified to be broadly expressed in eukaryotes, tissue- and species-specific manners. Although functions most circRNAs remain elusive, some are shown functional gene expression regulation potentially relate diseases. Due their stability, can also used as biomarkers for diagnosis. Profiling by integrating among different samples thus provides molecular basis further study potential application clinic. Here,...