Alternative TSSs are co-regulated in single cells in the mouse brain

Molecular Systems Biology

Volumn 13, Issue 5, 2017, Pages

  Karlsson, Kasper ^a   Lönnerberg, Peter ^b   Linnarsson, Sten ^b  

^a STANFORD CANCER INSTITUTE   (United States)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

alternative TSS usage; neurons; single cell RNA sequencing; transcription; UMI

Indexed keywords

2610017I09RIK PROTEIN; ANDROGEN RECEPTOR; CALY PROTEIN; COX16 PROTEIN; CYSTATIN C; EBF1 PROTEIN; FIS1 PROTEIN; GRM5 PROTEIN; MEG3 PROTEIN; MEMBRANE FUSION PROTEIN; MESSENGER RNA; MYOG PROTEIN; NRXN1 PROTEIN; POLYADENYLATED RNA; PROTEOLIPID PROTEIN; PROTEOLIPID PROTEIN 1; RNA; SNAP25 PROTEIN; SNCA PROTEIN; SPI1 PROTEIN; STAT5A PROTEIN; STAT5B PROTEIN; TRANSCRIPTION FACTOR AP 1; TRANSCRIPTION FACTOR FKHR; UNCLASSIFIED DRUG; CST3 PROTEIN, MOUSE;

3' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; ASTROCYTE; BRAIN CELL; CELL POPULATION; CELL PROLIFERATION; CELL SIZE; ENDOTHELIUM CELL; EPENDYMA CELL; EXON; GENE EXPRESSION; GENETIC CODE; INTERNEURON; MICROGLIA; MOUSE; NERVE CELL; NONHUMAN; OLIGODENDROGLIA; PERICYTE; PRIORITY JOURNAL; PROMOTER REGION; PYRAMIDAL NERVE CELL; RNA DEGRADATION; RNA SEQUENCE; SMOOTH MUSCLE CELL; SOMATOSENSORY CORTEX; START CODON; STOP CODON; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; VASCULAR ENDOTHELIAL CELL; ANIMAL; BRAIN; CYTOLOGY; GENETICS; NUCLEOTIDE SEQUENCE; SINGLE CELL ANALYSIS;

ANIMALS; BASE SEQUENCE; BRAIN; CYSTATIN C; GENE EXPRESSION; MICE; SINGLE-CELL ANALYSIS; TRANSCRIPTION INITIATION SITE;

EID: 85019768711     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.15252/msb.20167374     Document Type: Article

References (24)

1. Akan P, Deloukas P (2008) DNA sequence and structural properties as predictors of human and mouse promoters. Gene 410: 165–176
2. Ayoubi T (2005) Alternative Promoter Usage. In eLS, Chichester: John Wiley & Sons Ltd. http://www.els.net
3. Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR (2013) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res 23: 169–180
4. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y et al (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626–635
5. Deng Q, Ramskold D, Reinius B, Sandberg R (2014) Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343: 193–196
6. Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jorgensen M, Dimont E, Arner E, Schmidl C, Schaefer U et al (2014) A promoter-level mammalian expression atlas. Nature 507: 462–470
7. Huh C, Nagle JW, Kozak CA, Abrahamson M, Karlsson S (1995) Structural organization, expression and chromosomal mapping of the mouse cystatin-C-encoding gene (Cst3). Gene 152: 221–226
8. Islam S, Kjallquist U, Moliner A, Zajac P, Fan JB, Lonnerberg P, Linnarsson S (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 21: 1160–1167
9. Islam S, Kjallquist U, Moliner A, Zajac P, Fan JB, Lonnerberg P, Linnarsson S (2012) Highly multiplexed and strand-specific single-cell RNA 5' end sequencing. Nat Protoc 7: 813–828
10. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lonnerberg P, Linnarsson S (2014) Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods 11: 163–166
11. Karlsson K, Linnarsson S (2017) Single-cell mRNA isoform diversity in the mouse brain. BMC Genom 18: 126
12. Kivioja T, Vaharautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, Taipale J (2012) Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 9: 72–74
13. de Klerk E, t Hoen PA (2015) Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. Trends Genet 31: 128–139
14. Leroith D, Roberts CT Jr (1993) Insulin-like growth factors. Ann N Y Acad Sci 692: 1–9
15. Pelechano V, Wei W, Steinmetz LM (2015) Widespread co-translational RNA decay reveals ribosome dynamics. Cell 161: 1400–1412
16. Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U (2009) Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol 10: R73
17. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S (2006) Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4: e309
18. Raj A, van Oudenaarden A (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135: 216–226
19. Rojas-Duran MF, Gilbert WV (2012) Alternative transcription start site selection leads to large differences in translation activity in yeast. RNA 18: 2299–2305
20. Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A (2013) Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498: 236–240
21. Tang DT, Plessy C, Salimullah M, Suzuki AM, Calligaris R, Gustincich S, Carninci P (2013) Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching. Nucleic Acids Res 41: e44
22. Velten L, Anders S, Pekowska A, Jarvelin AI, Huber W, Pelechano V, Steinmetz LM (2015) Single-cell polyadenylation site mapping reveals 3′ isoform choice variability. Mol Syst Biol 11: 812
23. Xu Y, Ding Y, Li X, Wu X (2015) Cystatin C is a disease-associated protein subject to multiple regulation. Immunol Cell Biol 93: 442–451
24. Zeisel A, Munoz-Manchado AB, Codeluppi S, Lonnerberg P, La Manno G, Jureus A, Marques S, Munguba H, He L, Betsholtz C, Rolny C, Castelo-Branco G, Hjerling-Leffler J, Linnarsson S (2015) Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347: 1138–1142