CAGE™ Preparation Kit : Technology overview
□ Technical Information
CAGE is a novel approach for identifying promoters and gene expression profiling.
CAGE is based on full-length cDNA library technology for next-generation sequencing technologies, where an adaptor is ligated to the 5’ end of each full-length cDNA. By mapping genomic sequences on the CAGE Sequencing reads, transcriptional start sites can be identified. Thus, CAGE can be a powerful tool for discovery of novel genes, genome-wide gene-expression profiling, and promoter analysis.
□Comparison with other gene expression analysis techniques
There are numerous techniques for analyzing gene expression, and each method has its advantages. CAGE differs from other major gene expression analysis techniques in its capability to accurately identify transcriptional start sites in a genome-wide fashion.
Since CAGE enables detailed analyses of the promoter regions of a gene, it is possible to further analyze the expression of a specific gene regulated by each promoter. Therefore, CAGE can serve as a “new-perspective” approach for genome annotation, by elucidating transcriptional signaling cascades, and performing other functions.
CAGE | RNA-seq | SAGE | Microarray | |
---|---|---|---|---|
de novo Gene Finding | good | good | good | N/A |
Gene Expression Quantification |
superior ※ free of PCR bias unaffected by gene size |
good | good | average |
Determining Promoter Site | superior | average | N/A | N/A |
Motif Finding for Transcription Factor Binding Site | superior | average |
average ※ depending on known 5' end sequence information |
average ※ depending on known 5' end sequence information |
Identification of Bidirectional Enhancer RNA | superior | N/A | N/A | N/A |
Determining Transcription Start/1st Exon Site | superior | average | N/A | N/A |
Determining Gene Structure (intron/exon, alternative splicing variants) | N/A |
average ※ depending on sequence depth |
N/A | N/A |
Duration of Work Process | average | average | average | good |
Library Preparation Complicatedness | ※Long Time (8 days) | average | average | easy |
Data Analysis Tools | average | good | average | good |
("N/A" means not applicable)
□ References
□FANTOM main paper
□Others
- Young RS et al, The frequent evolutionary birth and death of functional promoters in mouse and human, Genome Res, 25, 1546-1557 (2015)
- Roy S et al, Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics, Nucleic Acids Res, 43(14), 6969-6982 (2015)
- Yu NY et al, Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium, Nucleic Acids Res, 43(14), 6787-6798 (2015)
- Mina M et al, Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells, Sci Rep, 5, 11999 (2015)
- Ramilowski JA et al, A draft network of ligand-receptor-mediated multicellular signalling in human, Nat Commun, 6, 7866 (2015)
- Aitken S et al, Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response, PLoS Comput Biol, 11(4), e1004217 (2015)
- Haberle V et al, CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses, Nucleic Acids Res, 43(8), e51 (2015)
- Taguchi A et al, Characterization of Novel Transcripts of Human Papillomavirus Type 16 Using Cap Analysis Gene Expression Technology, Journal of Virology, 89(4), 2448-2452 (2015)
- Arner E et al, Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells, Science, 347(6225), 1010-1014 (2015)
- Joshi A et al, Transcription factor, promoter, and enhancer utilization in human myeloid cells, J Leukoc Biol, 97(5), 985-995 (2015)
- Fort A et al, Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify noncoding loci resistant to reprogramming, Cell Cycle, 14(8), 1148-1155 (2015)
- Lizio M et al, Gateways to the FANTOM5 promoter level mammalian expression atlas, Genome Biol, 16, 22 (2015)
- Vitezic M et al, CAGE-defined promoter regions of the genes implicated in Rett Syndrome, BMC Genomics, 15, 1177 (2014)
- Verardo R et al, Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer, Stem Cells, 32(11), 2998-3011 (2014)
- Grison A et al, Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules, BMC Genomics, 15, 729 (2014)
- Fort A et al, Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance, Nature Genetics, 46(6), 558-566 (2014)
- Hasegawa A et al, MOIRAI: a compact workflow system for CAGE analysis, BMC Bioinformatics, 15, 144 (2014)
- Yamaga R et al, Systemic identification of estrogen-regulated genes in breast cancer cells through cap analysis of gene expression mapping, Biochem Biophys Res Commun, 447(3), 531-536 (2014)
- Prasad P et al, High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis, Blood, 123(17), e46-e57 (2014)
- Ohmiya H et al, RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE), BMC Genomics, 15, 269 (2014)
- Kawaji H et al, Comparison of CAGE and RNA-seq transcriptome profiling using a clonally amplified and single molecule next generation sequencing, Genome Res, 24(4), 708-717 (2014)
- Rönnerblad M et al, Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation, Blood, 123(17), e79-e89 (2014)
- Motakis E et al, Redefinition of the human mast cell transcriptome by deep-CAGE sequencing, Blood, 123(17), e58-e67 (2014)
- Schmidl C et al, The enhancer and promoter landscape of human regulatory and conventional T cell subpopulations, Blood, 123(17), e68-e78 (2014)
- Schmidl C et al, Transcription and enhancer profiling in human monocyte subsets, Blood, 123(17), e90-e99 (2014)
- Morikawa H et al, Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation, Proc Natl Acad Sci USA, 111(14), 5289-5294 (2014)
- Severin J et al, Interactive visualization and analysis of large-scale NGS data-sets using ZENBU, Nature Biotechnology, 32(3), 217-219 (2014)
- Rye M et al, Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines, BMC Genomics, 15, 120 (2014)
- Murata M et al, Detecting expressed genes using CAGE, Methods Mol Biol, 1164, 67-85 (2014)
- Pascarella G et al, NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements, Front Cell Neurosci, 8, 41 (2014)
- Nepal C et al, Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis, Genome Res, 23(11), 1938-1950 (2013)
- Sompallae R et al, Sompallae RA comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells, Front Genet, 4, 209 (2013)
- Sompallae R, A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells, Front Genet, 4, 209 (2013)
- Harbers M et al, Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation, BMC Genomics, 14, 665 (2013)
- Tang DT et al, Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching, Nucleic Acids Res, 41(3), e44 (2013)
- ENCODE Project Consortium, An integrated encyclopedia of DNA elements in the human genome, Nature, 489(7414), 57-74 (2012)
- Derrien T et al, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res, 22(9), 1775-1789 (2012)
- Djebali S et al, Landscape of transcription in human cells, Nature, 489(7414), 101-108 (2012)
- Itoh M et al, Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer, PLoS One, 7(1), e30809 (2012)
- Takahashi H et al, CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks, Methods Mol Biol, 786, 181-200 (2014)
- Schroder K et al, Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages, Proc Natl Acad Sci USA, 109(16), E944-E953 (2012)
- Plessy C et al, Promoter architecture of mouse olfactory receptor genes, Genome Res, 22(3), 486-497 (2012)
- Takahashi H et al, 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing, Nat Protoc, 7, 542-561 (2012)
- Chien CH et al, Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data, Nucleic Acids Res, 39(21), 9345-9356 (2011)
- Kanamori-Katayama M et al, Unamplified cap analysis of gene expression on a single-molecule sequencer, Genome Res, 21(7), 1150-1159 (2011)
- Hoskins RA et al, Genome-wide analysis of promoter architecture in Drosophila melanogaster, Genome Res, 21(2), 182-192 (2011)
- Salimullah M et al, NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes, Cold Spring Harb Protoc, 2011(1), pdb.prot5559 (2011)
- Schaefer U et al, High sensitivity TSS prediction: estimates of locations where TSS cannot occur, PLoS One, 5(11), e13934 (2010)
- Vitezic M et al, Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE, Nucleic Acids Res, 38(22), 8141-8148 (2010)
- Hestand MS et al, Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies, Nucleic Acids Res, 38(16), e165 (2010)
- Plessy C et al, Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan, Nat Methods, 7(7), 528-534 (2010)
- Atanur SS et al, The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance, Genome Res, 20(6), 791-803 (2010)
- FANTOM Consortium et al, The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line, Nat Genet, 41(5), 553-62 (2009)
- Faulkner GJ et al, The regulated retrotransposon transcriptome of mammalian cells, Nat Genet, 41(5), 563-571 (2009)
- Balwierz PJ et al, Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data, Genome Biol, 10(7), R79 (2009)
- Valen E et al, Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE, Genome Res, 19(2), 255-265 (2009)
- Hofmann O et al, Genome-wide analysis of cancer/testis gene expression, Proc Natl Acad Sci USA, 105(51), 20422-20427 (2008)
- ENCODE Project Consortium et al, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, 447(7146), 799-816 (2007)
- Shimokawa K et al, Large-scale clustering of CAGE tag expression data, BMC Bioinformatics, 8, 161 (2007)
- Kawaji H et al, Dynamic usage of transcription start sites within core promoters, Genome Biol, 7(12), R118 (2006)
- Carninci P et al, Genome-wide analysis of mammalian promoter architecture and evolution, Nat Genet, 38(6), 626-635 (2006)
- Kodzius R et al, CAGE: cap analysis of gene expression, Nat Methods, 3(3), 211-222 (2006)
- Shiraki T et al, Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage, Proc Natl Acad Sci USA, 100(26), 15776-15781 (2003)
- Carninci P et al, High-efficiency full-length cDNA cloning by biotinylated CAP trapper, Genomics, 37(3), 327-336 (1996)