Toward a comprehensive catalog of regulatory elements

Akalin A, Fredman D, Arner E et al (2009) Transcriptional features of genomic regulatory blocks. Genome Biol 10:R38. https://doi.org/10.1186/gb-2009-10-4-r38

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alexander RP, Fang G, Rozowsky J et al (2010) Annotating non-coding regions of the genome. Nat Rev Genet 11:559–571. https://doi.org/10.1038/nrg2814

Article  CAS  PubMed  Google Scholar 

Alipanahi B, Delong A, Weirauch MT, Frey BJ (2015) Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nat Biotechnol 33:831–838. https://doi.org/10.1038/nbt.3300

Article  CAS  PubMed  Google Scholar 

Altarejos JY, Montminy M (2011) CREB and the CRTC co-activators: sensors for hormonal and metabolic signals. Nat Rev Mol Cell Biol 12:141–151. https://doi.org/10.1038/nrm3072

Article  CAS  PubMed  PubMed Central  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 

Andersson R, Gebhard C, Miguel-Escalada I et al (2014) An atlas of active enhancers across human cell types and tissues. Nature 507:455–461. https://doi.org/10.1038/nature12787

Article  CAS  PubMed  PubMed Central  Google Scholar 

Andersson R, Sandelin A, Danko CG (2015) A unified architecture of transcriptional regulatory elements. Trends Genet 31:426–433. https://doi.org/10.1016/j.tig.2015.05.007

Article  CAS  PubMed  Google Scholar 

Ardui S, Ameur A, Vermeesch JR, Hestand MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46:2159–2168

Article  CAS  PubMed  PubMed Central  Google Scholar 

Arnold CD, Gerlach D, Stelzer C et al (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 

Asthana S, Noble WS, Kryukov G et al (2007) Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci U S A 104:12410–12415. https://doi.org/10.1073/pnas.0705140104

Article  CAS  PubMed  PubMed Central  Google Scholar 

Avsec Ž, Agarwal V, Visentin D et al (2021a) Effective gene expression prediction from sequence by integrating long-range interactions. Nat Methods 18:1196–1203. https://doi.org/10.1038/s41592-021-01252-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Avsec Ž, Weilert M, Shrikumar A et al (2021b) Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat Genet 53:354–366. https://doi.org/10.1038/s41588-021-00782-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bailey T, Krajewski P, Ladunga I et al (2013) Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol 9:e1003326. https://doi.org/10.1371/journal.pcbi.1003326

Article  CAS  PubMed  PubMed Central  Google Scholar 

Banerji J, Olson L, Schaffner W (1983) A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes. Cell 33:729–740. https://doi.org/10.1016/0092-8674(83)90015-6

Article  CAS  PubMed  Google Scholar 

Batut P, Dobin A, Plessy C et al (2013) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res 23:169–180. https://doi.org/10.1101/gr.139618.112

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baylin SB, Jones PA (2016) Epigenetic determinants of cancer. Cold Spring Harb Perspect Biol. https://doi.org/10.1101/cshperspect.a019505

Article  PubMed  PubMed Central  Google Scholar 

Beagrie RA, Scialdone A, Schueler M et al (2017) Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543:519–524. https://doi.org/10.1038/nature21411

Article  CAS  PubMed  PubMed Central  Google Scholar 

Becker JS, Nicetto D, Zaret KS (2016) H3K9me3-dependent heterochromatin: barrier to cell fate changes. Trends Genet 32:29–41. https://doi.org/10.1016/j.tig.2015.11.001

Article  CAS  PubMed  Google Scholar 

Becker JS, McCarthy RL, Sidoli S et al (2017) Genomic and proteomic resolution of heterochromatin and its restriction of alternate fate genes. Mol Cell 68:1023-1037.e15. https://doi.org/10.1016/j.molcel.2017.11.030

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bender CM, Gonzalgo ML, Gonzales FA et al (1999) Roles of cell division and gene transcription in the methylation of CpG islands. Mol Cell Biol 19:6690–6698. https://doi.org/10.1128/MCB.19.10.6690

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bernstein BE, Mikkelsen TS, Xie X et al (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315–326. https://doi.org/10.1016/j.cell.2006.02.041

Article  CAS  PubMed  Google Scholar 

Bird AP, Taggart MH (1980) Variable patterns of total DNA and rDNA methylation in animals. Nucleic Acids Res 8:1485–1497. https://doi.org/10.1093/nar/8.7.1485

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bird A, Taggart M, Frommer M et al (1985) A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40:91–99. https://doi.org/10.1016/0092-8674(85)90312-5

Article  CAS  PubMed  Google Scholar 

Blackwood EM, Kadonaga JT (1998) Going the distance: a current view of enhancer action. Science 281:60–63. https://doi.org/10.1126/science.281.5373.60

Article  CAS  PubMed  Google Scholar 

Boix CA, James BT, Park YP et al (2021) Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nature 590:300–307. https://doi.org/10.1038/s41586-020-03145-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boyle AP, Davis S, Shulha HP et al (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 et al (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 

Buenrostro JD, Wu B, Litzenburger UM et al (2015) Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523:486–490. https://doi.org/10.1038/nature14590

Article  CAS  PubMed  PubMed Central  Google Scholar 

Burley SK, Roeder RG (1996) Biochemistry and structural biology of transcription factor IID (TFIID). Annu Rev Biochem 65:769–799. https://doi.org/10.1146/annurev.bi.65.070196.004005

Article  CAS  PubMed  Google Scholar 

Cai Y, Zhang Y, Loh YP et al (2021) H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions. Nat Commun 12:719. https://doi.org/10.1038/s41467-021-20940-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carelli FN, Liechti A, Halbert J et al (2018) Repurposing of promoters and enhancers during mammalian evolution. Nat Commun 9:4066. https://doi.org/10.1038/s41467-018-06544-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carleton JB, Berrett KC, Gertz J (2017) Multiplex enhancer interference reveals collaborative control of gene regulation by estrogen receptor α-bound enhancers. Cell Syst 5:333-344.e5

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carninci P, Sandelin A, Lenhard B et al (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38:626–635. https://doi.org/10.1038/ng1789

Article  CAS  PubMed  Google Scholar 

Chan RCW, Libbrecht MW, Roberts EG et al (2018) Segway 2.0: Gaussian mixture models and minibatch training. Bioinformatics 34:669–671. https://doi.org/10.1093/bioinformatics/btx603

Article  CAS  PubMed 

留言 (0)

沒有登入
gif