Using Synthetic DNA Libraries to Investigate Chromatin and Gene Regulation

Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS (2016) A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell 167:1867–1882.e21. https://doi.org/10.1016/j.cell.2016.11.048

Article  CAS  PubMed  PubMed Central  Google Scholar 

Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, de Ridder J, Berns A, Wessels LFA, van Lohuizen M, van Steensel B (2013) Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 154:914–927. https://doi.org/10.1016/j.cell.2013.07.018

Article  CAS  PubMed  Google Scholar 

Andersson R, Sandelin A (2020) Determinants of enhancer and promoter activities of regulatory elements. Nat Rev Genet 21:71–87. https://doi.org/10.1038/s41576-019-0173-8

Article  CAS  PubMed  Google Scholar 

Andrilenas KK, Penvose A, Siggers T (2015) Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes. Brief Funct Genomics 14:17–29. https://doi.org/10.1093/bfgp/elu046

Article  CAS  PubMed  Google Scholar 

Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A (2013) Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339:1074–1077. https://doi.org/10.1126/science.1232542

Article  CAS  PubMed  Google Scholar 

Arnold CD, Gerlach D, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A (2014) Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nat Genet 46:685–692. https://doi.org/10.1038/ng.3009

Article  CAS  PubMed  PubMed Central  Google Scholar 

Arnold CD, Zabidi MA, Pagani M, Rath M, Schernhuber K, Kazmar T, Stark A (2017) Genome-wide assessment of sequenceintrinsic enhancer responsiveness at singlebase- pair resolution. Nat Biotechnol 35:136–144. https://doi.org/10.1038/nbt.3739

Article  CAS  PubMed  Google Scholar 

Arnone MI, Davidson EH (1997) The hardwiring of development: organization and function of genomic regulatory systems. Development 124:1851–1864. https://doi.org/10.1242/dev.124.10.1851

Article  CAS  PubMed  Google Scholar 

Arnosti DN, Kulkarni MM (2005) Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? J Cell Biochem 94:890–898. https://doi.org/10.1002/jcb.20352

Article  CAS  PubMed  Google Scholar 

Arora A, Castro-Gutierrez R, Moffatt C, Eletto D, Becker R, Brown M, Moor AE, Russ HA, Taliaferro JM (2022) High throughput identification of RNA localization elements in neuronal cells. Nucleic Acids Res 50:10626–10642. https://doi.org/10.1093/nar/gkac763

Article  CAS  PubMed  PubMed Central  Google Scholar 

Audic Y, Hartley RS (2004) Post-transcriptional regulation in cancer. Biol Cell 96:479–498. https://doi.org/10.1016/j.biolcel.2004.05.002

Article  CAS  PubMed  Google Scholar 

Bai L, Morozov AV (2010) Gene regulation by nucleosome positioning. Trends Genet 26:476–483. https://doi.org/10.1016/j.tig.2010.08.003

Article  CAS  PubMed  Google Scholar 

Bai L, Charvin G, Siggia ED, Cross FR (2010) Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Dev Cell 18:544–555. https://doi.org/10.1016/j.devcel.2010.02.007

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bai L, Ondracka A, Cross FR (2011) Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter. Mol Cell 42:465–476. https://doi.org/10.1016/j.molcel.2011.03.028

Article  CAS  PubMed  PubMed Central  Google Scholar 

Banerji J, Rusconi S, Schaffner W (1981) Expression of a β-globin gene is enhanced by remote SV40 DNA sequences. Cell 27:299–308. https://doi.org/10.1016/0092-8674(81)90413-X

Article  CAS  PubMed  Google Scholar 

Barakat TS, Halbritter F, Zhang M, Rendeiro AF, Perenthaler E, Bock C, Chambers I (2018) Functional dissection of the enhancer repertoire in human embryonic stem cells. Cell Stem Cell 23:276–288.e278. https://doi.org/10.1016/j.stem.2018.06.014

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bergman DT, Jones TR, Liu V, Ray J, Jagoda E, Siraj L, Kang HY, Nasser J, Kane M, Rios A et al (2022) Compatibility rules of human enhancer and promoter sequences. Nature 607:176–184. https://doi.org/10.1038/s41586-022-04877-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132:311–322. https://doi.org/10.1016/j.cell.2007.12.014

Article  CAS  PubMed  PubMed Central  Google Scholar 

Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10:1213–1218. https://doi.org/10.1038/nmeth.2688

Article  CAS  PubMed  PubMed Central  Google Scholar 

Burke TW, Kadonaga JT (1997) The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAF II 60 of Drosophila. Genes Dev 11:3020–3031. https://doi.org/10.1101/gad.11.22.3020

Article  CAS  PubMed  PubMed Central  Google Scholar 

Butler JEF, Kadonaga JT (2001) Enhancer–promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 15:2515–2519. https://doi.org/10.1101/gad.924301

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cai Y, Yu X, Hu S, Yu J (2009) A brief review on the mechanisms of miRNA regulation. Genom Proteom Bioinform 7:147–154. https://doi.org/10.1016/S1672-0229(08)60044-3

Article  CAS  Google Scholar 

Calhoun VC, Stathopoulos A, Levine M (2002) Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex. Proc Natl Acad Sci USA 99:9243–9247. https://doi.org/10.1073/pnas.142291299

Article  CAS  PubMed  PubMed Central  Google Scholar 

Calo E, Wysocka J (2013) Modification of enhancer chromatin: what, how, and why? Mol Cell 49:825–837. https://doi.org/10.1016/j.molcel.2013.01.038

Article  CAS  PubMed  Google Scholar 

Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP et al (2015) BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527:192–197. https://doi.org/10.1038/nature15521

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cao J, Novoa EM, Zhang Z, Chen WCW, Liu D, Choi GCG, Wong ASL, Wehrspaun C, Kellis M, Lu TK (2021) High-throughput 5’ UTR engineering for enhanced protein production in non-viral gene therapies. Nat Commun 12:4138. https://doi.org/10.1038/s41467-021-24436-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Catarino RR, Stark A (2018) Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. Genes Dev 32:202–223. https://doi.org/10.1101/gad.310367.117

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chaudhari HG, Cohen BA (2018) Local sequence features that influence AP-1 cis -regulatory activity. Genome Res 28:171–181. https://doi.org/10.1101/gr.226530.117

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle MPR, Iyer E, Lin S, Kiani S, Guzman CD, Wiegand DJ et al (2015) Highly efficient Cas9-mediated transcriptional programming. Nat Methods 12:326–328. https://doi.org/10.1038/nmeth.3312

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen C-Y, Morris Q, Mitchell JA (2012) Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. BMC Genomics 13:152. https://doi.org/10.1186/1471-2164-13-152

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen L, Fish AE, Capra JA (2018) Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLOS Computational Biology 14:e1006484. https://doi.org/10.1371/journal.pcbi.1006484

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen H, Kharerin H, Dhasarathy A, Kladde M, Bai L (2022a) Partitioned usage of chromatin remodelers by nucleosome-displacing factors. Cell Rep 40:111250. https://doi.org/10.1016/j.celrep.2022.111250

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M et al (2022b) Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. Cell Reports 41:111630. https://doi.org/10.1016/j.celrep.2022.111630

留言 (0)

沒有登入
gif