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For: Blackwood EM, Kadonaga JT. Going the distance: a current view of enhancer action. Science 1998;281:60-3. [PMID: 9679020 DOI: 10.1126/science.281.5373.60] [Citation(s) in RCA: 555] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
1
Fujioka M, Ke W, Schedl P, Jaynes JB. The homie insulator has sub-elements with different insulating and long-range pairing properties. Genetics 2025;229:iyaf032. [PMID: 39999387 PMCID: PMC12005253 DOI: 10.1093/genetics/iyaf032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 02/12/2025] [Indexed: 02/27/2025]  Open
2
Senapati S, Irshad IU, Sharma AK, Kumar H. Predicting gene expression changes from chromatin structure modification. NPJ Syst Biol Appl 2025;11:34. [PMID: 40234426 PMCID: PMC12000410 DOI: 10.1038/s41540-025-00510-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 03/27/2025] [Indexed: 04/17/2025]  Open
3
Sathian R, Dutta P, Ay F, Davuluri RV. Genomic Language Model for Predicting Enhancers and Their Allele-Specific Activity in the Human Genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.18.644040. [PMID: 40166250 PMCID: PMC11957021 DOI: 10.1101/2025.03.18.644040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
4
Reithofer M, Huber S, Grabherr R. Establishment of the REMBAC-cassette, a rapid, efficient and manifold BacMam tool for recombinant protein expression. J Biotechnol 2025;398:183-192. [PMID: 39755260 DOI: 10.1016/j.jbiotec.2024.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 11/27/2024] [Accepted: 12/24/2024] [Indexed: 01/06/2025]
5
Fujioka M, Ke W, Schedl P, Jaynes JB. The homie insulator has sub-elements with different insulating and long-range pairing properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.02.01.578481. [PMID: 39896478 PMCID: PMC11785010 DOI: 10.1101/2024.02.01.578481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
6
Chandrashekar PB, Chen H, Lee M, Ahmadinejad N, Liu L. DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements. Comput Struct Biotechnol J 2024;23:679-687. [PMID: 38292477 PMCID: PMC10825326 DOI: 10.1016/j.csbj.2023.12.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024]  Open
7
Dekker J, Mirny LA. The chromosome folding problem and how cells solve it. Cell 2024;187:6424-6450. [PMID: 39547207 PMCID: PMC11569382 DOI: 10.1016/j.cell.2024.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 10/15/2024] [Accepted: 10/15/2024] [Indexed: 11/17/2024]
8
Bruner WS, Grant SFA. Translation of genome-wide association study: from genomic signals to biological insights. Front Genet 2024;15:1375481. [PMID: 39421299 PMCID: PMC11484060 DOI: 10.3389/fgene.2024.1375481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 09/24/2024] [Indexed: 10/19/2024]  Open
9
Xu L, Yao S, Ding YE, Xie M, Feng D, Sha P, Tan L, Bei F, Yao Y. Designing and optimizing AAV-mediated gene therapy for neurodegenerative diseases: from bench to bedside. J Transl Med 2024;22:866. [PMID: 39334366 PMCID: PMC11429861 DOI: 10.1186/s12967-024-05661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024]  Open
10
Kwait R, Pinsky ML, Gignoux‐Wolfsohn S, Eskew EA, Kerwin K, Maslo B. Impact of putatively beneficial genomic loci on gene expression in little brown bats (Myotis lucifugus, Le Conte, 1831) affected by white-nose syndrome. Evol Appl 2024;17:e13748. [PMID: 39310794 PMCID: PMC11413065 DOI: 10.1111/eva.13748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 06/06/2024] [Accepted: 06/19/2024] [Indexed: 09/25/2024]  Open
11
Wu P, Yao M, Wang W. Differential impact of quiescent non-coding loci on chromatin entropy. Nucleic Acids Res 2024;52:8778-8799. [PMID: 38908026 PMCID: PMC11347155 DOI: 10.1093/nar/gkae535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/17/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024]  Open
12
AL-Eitan L, Al-Khaldi S, Ibdah RK. ACE gene polymorphism and susceptibility to hypertension in a Jordanian adult population. PLoS One 2024;19:e0304271. [PMID: 38917192 PMCID: PMC11198757 DOI: 10.1371/journal.pone.0304271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/09/2024] [Indexed: 06/27/2024]  Open
13
Iñiguez-Muñoz S, Llinàs-Arias P, Ensenyat-Mendez M, Bedoya-López AF, Orozco JIJ, Cortés J, Roy A, Forsberg-Nilsson K, DiNome ML, Marzese DM. Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements. Cell Mol Life Sci 2024;81:274. [PMID: 38902506 PMCID: PMC11335195 DOI: 10.1007/s00018-024-05314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/07/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024]
14
Gautam P, Sinha SK. The Blueprint of Logical Decisions in a NF-κB Signaling System. ACS OMEGA 2024;9:22625-22634. [PMID: 38826544 PMCID: PMC11137707 DOI: 10.1021/acsomega.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/13/2024] [Accepted: 04/19/2024] [Indexed: 06/04/2024]
15
Yu H, Zhao J, Shen Y, Qiao L, Liu Y, Xie G, Chang S, Ge T, Li N, Chen M, Li H, Zhang J, Wang X. The dynamic landscape of enhancer-derived RNA during mouse early embryo development. Cell Rep 2024;43:114077. [PMID: 38592974 DOI: 10.1016/j.celrep.2024.114077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/10/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024]  Open
16
Yao Z, Song P, Jiao W. Pathogenic role of super-enhancers as potential therapeutic targets in lung cancer. Front Pharmacol 2024;15:1383580. [PMID: 38681203 PMCID: PMC11047458 DOI: 10.3389/fphar.2024.1383580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]  Open
17
Ahmad R, Ullah I, Ullah Z, Alam S, Rady A, Khan SS, Durrani IS. Genomic Exploration: Unraveling the Intricacies of Indica Rice Oryza sativa L. Germin-Like Protein Gene 12-3 (OsGLP12-3) Promoter via Cloning, Sequencing, and In Silico Analysis. ACS OMEGA 2024;9:15271-15281. [PMID: 38585130 PMCID: PMC10993326 DOI: 10.1021/acsomega.3c09670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/21/2024] [Accepted: 03/05/2024] [Indexed: 04/09/2024]
18
Chen M, Guo X, Guo J, Shi C, Wu Y, Chen L, Mao R, Fan Y. Cytoplasmic Accumulation of Histones Induced by BET Inhibition Protects Cells from C9orf72 Poly(PR)-Induced Cell Death. Adv Biol (Weinh) 2024;8:e2300334. [PMID: 38213020 DOI: 10.1002/adbi.202300334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/16/2023] [Indexed: 01/13/2024]
19
Zhigulev A, Norberg Z, Cordier J, Spalinskas R, Bassereh H, Björn N, Pradhananga S, Gréen H, Sahlén P. Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression. Life Sci Alliance 2024;7:e202302244. [PMID: 38228368 PMCID: PMC10796589 DOI: 10.26508/lsa.202302244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]  Open
20
Haug S, Muthusamy S, Li Y, Stewart G, Li X, Treppner M, Köttgen A, Akilesh S. Multi-omic analysis of human kidney tissue identified medulla-specific gene expression patterns. Kidney Int 2024;105:293-311. [PMID: 37995909 PMCID: PMC10843743 DOI: 10.1016/j.kint.2023.10.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 09/21/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
21
Huang Y, Huo Y, Huang L, Zhang L, Zheng Y, Zhang N, Yang M. Super-enhancers: Implications in gastric cancer. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024;793:108489. [PMID: 38355091 DOI: 10.1016/j.mrrev.2024.108489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
22
Randi AM, Jones D, Peghaire C, Arachchillage DJ. Mechanisms regulating heterogeneity of hemostatic gene expression in endothelial cells. J Thromb Haemost 2023;21:3056-3066. [PMID: 37393001 DOI: 10.1016/j.jtha.2023.06.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/30/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023]
23
Keller MP, Hawes EM, Schueler KL, Stapleton DS, Mitok KA, Simonett SP, Oeser JK, Sampson LL, Attie AD, Magnuson MA, O’Brien RM. An Enhancer Within Abcb11 Regulates G6pc2 in C57BL/6 Mouse Pancreatic Islets. Diabetes 2023;72:1621-1628. [PMID: 37552875 PMCID: PMC10588275 DOI: 10.2337/db23-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
24
Marron AO, Sauret‐Güeto S, Rebmann M, Silvestri L, Tomaselli M, Haseloff J. An enhancer trap system to track developmental dynamics in Marchantia polymorpha. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023;116:604-628. [PMID: 37583263 PMCID: PMC10952768 DOI: 10.1111/tpj.16394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/05/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
25
Komatsu V, Cooper B, Yim P, Chan K, Gong W, Wheatley L, Rohs R, Fraser SE, Trinh LA. Hand2 represses non-cardiac cell fates through chromatin remodeling at cis- regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.23.559156. [PMID: 37790542 PMCID: PMC10542161 DOI: 10.1101/2023.09.23.559156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
26
Wu P, Wang W. Distinct 3D contacts and phenotypic consequences of adjacent non-coding loci in the epigenetically quiescent regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557110. [PMID: 37745584 PMCID: PMC10515877 DOI: 10.1101/2023.09.11.557110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
27
Bachhav B, de Rossi J, Llanos CD, Segatori L. Cell factory engineering: Challenges and opportunities for synthetic biology applications. Biotechnol Bioeng 2023;120:2441-2459. [PMID: 36859509 PMCID: PMC10440303 DOI: 10.1002/bit.28365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/14/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
28
Kiliti AJ, Sharif GM, Martin MB, Wellstein A, Riegel AT. AIB1/SRC-3/NCOA3 function in estrogen receptor alpha positive breast cancer. Front Endocrinol (Lausanne) 2023;14:1250218. [PMID: 37711895 PMCID: PMC10498919 DOI: 10.3389/fendo.2023.1250218] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]  Open
29
Mirny LA. Chromosome and protein folding: In search for unified principles. Curr Opin Struct Biol 2023;81:102610. [PMID: 37327690 DOI: 10.1016/j.sbi.2023.102610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 06/18/2023]
30
Fan K, Pfister E, Weng Z. Toward a comprehensive catalog of regulatory elements. Hum Genet 2023;142:1091-1111. [PMID: 36935423 DOI: 10.1007/s00439-023-02519-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/03/2023] [Indexed: 03/21/2023]
31
Wang L, Wei C, Wang Y, Huang N, Zhang T, Dai Y, Xue L, Lin S, Wu ZB. Identification of the enhancer RNAs related to tumorgenesis of pituitary neuroendocrine tumors. Front Endocrinol (Lausanne) 2023;14:1149997. [PMID: 37534217 PMCID: PMC10393250 DOI: 10.3389/fendo.2023.1149997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023]  Open
32
Phan LT, Oh C, He T, Manavalan B. A comprehensive revisit of the machine-learning tools developed for the identification of enhancers in the human genome. Proteomics 2023;23:e2200409. [PMID: 37021401 DOI: 10.1002/pmic.202200409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/18/2023] [Accepted: 03/27/2023] [Indexed: 04/07/2023]
33
Wilson AE, Liberles DA. Dosage balance acts as a time-dependent selective barrier to subfunctionalization. BMC Ecol Evol 2023;23:14. [PMID: 37138246 PMCID: PMC10155369 DOI: 10.1186/s12862-023-02116-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/20/2023] [Indexed: 05/05/2023]  Open
34
Chandrashekar PB, Chen H, Lee M, Ahmadinejad N, Liu L. DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.536807. [PMID: 37131697 PMCID: PMC10153112 DOI: 10.1101/2023.04.19.536807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
35
Xue X, Wang M, Zhang X, Ma L, Wang J. PAR-CLIP Assay in Ferroptosis. Methods Mol Biol 2023;2712:29-43. [PMID: 37578694 DOI: 10.1007/978-1-0716-3433-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
36
Gupta K, Wang G, Zhang S, Gao X, Zheng R, Zhang Y, Meng Q, Zhang L, Cao Q, Chen K. StripeDiff: Model-based algorithm for differential analysis of chromatin stripe. SCIENCE ADVANCES 2022;8:eabk2246. [PMID: 36475785 PMCID: PMC9728969 DOI: 10.1126/sciadv.abk2246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/28/2022] [Indexed: 05/27/2023]
37
Liang Y, Xu H, Cheng T, Fu Y, Huang H, Qian W, Wang J, Zhou Y, Qian P, Yin Y, Xu P, Zou W, Chen B. Gene activation guided by nascent RNA-bound transcription factors. Nat Commun 2022;13:7329. [PMID: 36443367 PMCID: PMC9705438 DOI: 10.1038/s41467-022-35041-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022]  Open
38
Yadav Y, Subbaroyan A, Martin OC, Samal A. Relative importance of composition structures and biologically meaningful logics in bipartite Boolean models of gene regulation. Sci Rep 2022;12:18156. [PMID: 36307465 PMCID: PMC9616893 DOI: 10.1038/s41598-022-22654-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/18/2022] [Indexed: 12/31/2022]  Open
39
Leung AKY, Yao L, Yu H. Functional genomic assays to annotate enhancer-promoter interactions genome wide. Hum Mol Genet 2022;31:R97-R104. [PMID: 36018818 PMCID: PMC9585677 DOI: 10.1093/hmg/ddac204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/14/2022]  Open
40
Gao L, Rong H. Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma. Sci Rep 2022;12:16545. [PMID: 36192427 PMCID: PMC9529949 DOI: 10.1038/s41598-022-20824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022]  Open
41
Nair SJ, Suter T, Wang S, Yang L, Yang F, Rosenfeld MG. Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures. Trends Genet 2022;38:1019-1047. [PMID: 35811173 PMCID: PMC9474616 DOI: 10.1016/j.tig.2022.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023]
42
Butt AH, Alkhalifah T, Alturise F, Khan YD. A machine learning technique for identifying DNA enhancer regions utilizing CIS-regulatory element patterns. Sci Rep 2022;12:15183. [PMID: 36071071 PMCID: PMC9452539 DOI: 10.1038/s41598-022-19099-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022]  Open
43
Huang R, Huang D, Wang S, Xian S, Liu Y, Jin M, Zhang X, Chen S, Yue X, Zhang W, Lu J, Liu H, Huang Z, Zhang H, Yin H. Repression of enhancer RNA PHLDA1 promotes tumorigenesis and progression of Ewing sarcoma via decreasing infiltrating T‐lymphocytes: A bioinformatic analysis. Front Genet 2022;13:952162. [PMID: 36092920 PMCID: PMC9453160 DOI: 10.3389/fgene.2022.952162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022]  Open
44
Saito T, Asai S, Tanaka N, Nohata N, Minemura C, Koma A, Kikkawa N, Kasamatsu A, Hanazawa T, Uzawa K, Seki N. Genome-Wide Super-Enhancer-Based Analysis: Identification of Prognostic Genes in Oral Squamous Cell Carcinoma. Int J Mol Sci 2022;23:ijms23169154. [PMID: 36012427 PMCID: PMC9409227 DOI: 10.3390/ijms23169154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/29/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022]  Open
45
Wang K, Escobar M, Li J, Mahata B, Goell J, Shah S, Cluck M, Hilton I. Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions. Nucleic Acids Res 2022;50:7842-7855. [PMID: 35849129 PMCID: PMC9371918 DOI: 10.1093/nar/gkac582] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 12/29/2022]  Open
46
Popay TM, Dixon JR. Coming full circle: On the origin and evolution of the looping model for enhancer-promoter communication. J Biol Chem 2022;298:102117. [PMID: 35691341 PMCID: PMC9283939 DOI: 10.1016/j.jbc.2022.102117] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/05/2022]  Open
47
Heurtaux T, Bouvier DS, Benani A, Helgueta Romero S, Frauenknecht KBM, Mittelbronn M, Sinkkonen L. Normal and Pathological NRF2 Signalling in the Central Nervous System. Antioxidants (Basel) 2022;11:1426. [PMID: 35892629 PMCID: PMC9394413 DOI: 10.3390/antiox11081426] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]  Open
48
Mishra GP, Jha A, Ahad A, Sen K, Sen A, Podder S, Prusty S, Biswas VK, Gupta B, Raghav SK. Epigenomics of conventional type-I dendritic cells depicted preferential control of TLR9 versus TLR3 response by NCoR1 through differential IRF3 activation. Cell Mol Life Sci 2022;79:429. [PMID: 35849243 PMCID: PMC9293861 DOI: 10.1007/s00018-022-04424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/28/2022] [Accepted: 06/13/2022] [Indexed: 11/26/2022]
49
Huang G, Luo W, Zhang G, Zheng P, Yao Y, Lyu J, Liu Y, Wei DQ. Enhancer-LSTMAtt: A Bi-LSTM and Attention-Based Deep Learning Method for Enhancer Recognition. Biomolecules 2022;12:995. [PMID: 35883552 PMCID: PMC9313278 DOI: 10.3390/biom12070995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/03/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023]  Open
50
Liu J, Jia J, Wang S, Zhang J, Xian S, Zheng Z, Deng L, Feng Y, Zhang Y, Zhang J. Prognostic Ability of Enhancer RNAs in Metastasis of Non-Small Cell Lung Cancer. Molecules 2022;27:molecules27134108. [PMID: 35807355 PMCID: PMC9268450 DOI: 10.3390/molecules27134108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/15/2022] [Accepted: 06/23/2022] [Indexed: 02/01/2023]  Open
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