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For: Vo Ngoc L, Cassidy CJ, Huang CY, Duttke SH, Kadonaga JT. The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters. Genes Dev 2017;31:6-11. [PMID: 28108474 DOI: 10.1101/gad.293837.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/19/2016] [Indexed: 12/19/2022]
Number Cited by Other Article(s)
1
Hajheidari M, Sunyaev S, de Meaux J. Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression. PLANT & CELL PHYSIOLOGY 2025;66:444-460. [PMID: 39626022 PMCID: PMC12085094 DOI: 10.1093/pcp/pcae140] [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] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 11/17/2024] [Accepted: 11/29/2024] [Indexed: 05/18/2025]
2
Krchlikova V, Lu Y, Sauter D. Viral influencers: deciphering the role of endogenous retroviral LTR12 repeats in cellular gene expression. J Virol 2025;99:e0135124. [PMID: 39887236 PMCID: PMC11853044 DOI: 10.1128/jvi.01351-24] [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] [Indexed: 02/01/2025]  Open
3
Pavlu S, Nikumbh S, Kovacik M, An T, Lenhard B, Simkova H, Navratilova P. Core promoterome of barley embryo. Comput Struct Biotechnol J 2024;23:264-277. [PMID: 38173877 PMCID: PMC10762323 DOI: 10.1016/j.csbj.2023.12.003] [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: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024]  Open
4
Cochran K, Yin M, Mantripragada A, Schreiber J, Marinov GK, Shah SR, Yu H, Lis JT, Kundaje A. Dissecting the cis-regulatory syntax of transcription initiation with deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596138. [PMID: 38853896 PMCID: PMC11160661 DOI: 10.1101/2024.05.28.596138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
5
Chivu AG, Basso BA, Abuhashem A, Leger MM, Barshad G, Rice EJ, Vill AC, Wong W, Chou SP, Chovatiya G, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito IL, Ruiz-Trillo I, Hadjantonakis AK, Lis JT, Lewis JJ, Danko CG. Evolution of promoter-proximal pausing enabled a new layer of transcription control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.19.529146. [PMID: 39416036 PMCID: PMC11482795 DOI: 10.1101/2023.02.19.529146] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
6
He AY, Danko CG. Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.583868. [PMID: 38559255 PMCID: PMC10979970 DOI: 10.1101/2024.03.13.583868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
7
Liu LL, Song CC, Abu-Elala N, Tan XY, Zhao T, Zheng H, Yang H, Luo Z. Transcriptional regulation of Znt family members znt4, znt5 and znt10 and their function in zinc transport in yellow catfish (Pelteobagrus fulvidraco). BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024;1867:195041. [PMID: 38740364 DOI: 10.1016/j.bbagrm.2024.195041] [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: 08/13/2023] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
8
Sloutskin A, Itzhak D, Vogler G, Pozeilov H, Ideses D, Alter H, Adato O, Shachar H, Doniger T, Shohat-Ophir G, Frasch M, Bodmer R, Duttke SH, Juven-Gershon T. From promoter motif to cardiac function: a single DPE motif affects transcription regulation and organ function in vivo. Development 2024;151:dev202355. [PMID: 38958007 DOI: 10.1242/dev.202355] [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: 09/18/2023] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
9
Villani RM, McKenzie ME, Davidson AL, Spurdle AB. Regional-specific calibration enables application of computational evidence for clinical classification of 5' cis-regulatory variants in Mendelian disease. Am J Hum Genet 2024;111:1301-1315. [PMID: 38815586 PMCID: PMC11267523 DOI: 10.1016/j.ajhg.2024.05.002] [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: 12/21/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024]  Open
10
Duttke SH, Guzman C, Chang M, Delos Santos NP, McDonald BR, Xie J, Carlin AF, Heinz S, Benner C. Position-dependent function of human sequence-specific transcription factors. Nature 2024;631:891-898. [PMID: 39020164 PMCID: PMC11269187 DOI: 10.1038/s41586-024-07662-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: 03/29/2022] [Accepted: 06/04/2024] [Indexed: 07/19/2024]
11
Adato O, Sloutskin A, Komemi H, Brabb I, Duttke S, Bucher P, Unger R, Juven-Gershon T. ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements. Bioinformatics 2024;40:btae110. [PMID: 38407414 PMCID: PMC10950481 DOI: 10.1093/bioinformatics/btae110] [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: 11/14/2023] [Revised: 02/04/2024] [Accepted: 02/23/2024] [Indexed: 02/27/2024]  Open
12
Archuleta SR, Goodrich JA, Kugel JF. Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle. Biomolecules 2024;14:176. [PMID: 38397413 PMCID: PMC10886972 DOI: 10.3390/biom14020176] [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: 12/21/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024]  Open
13
Uemura K, Ohyama T. Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function. Int J Mol Sci 2024;25:1487. [PMID: 38338773 PMCID: PMC10855393 DOI: 10.3390/ijms25031487] [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: 12/08/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024]  Open
14
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y. Structural visualization of transcription initiation in action. Science 2023;382:eadi5120. [PMID: 38127763 DOI: 10.1126/science.adi5120] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023]
15
Kharytonchyk S, Burnett C, GC K, Telesnitsky A. Transcription start site heterogeneity and its role in RNA fate determination distinguish HIV-1 from other retroviruses and are mediated by core promoter elements. J Virol 2023;97:e0081823. [PMID: 37681957 PMCID: PMC10537674 DOI: 10.1128/jvi.00818-23] [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: 06/02/2023] [Accepted: 07/07/2023] [Indexed: 09/09/2023]  Open
16
Mcdonald BR, Picard C, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559415. [PMID: 37808859 PMCID: PMC10557634 DOI: 10.1101/2023.09.25.559415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
17
Fisher MJ, Luse DS. Promoter-proximal nucleosomes attenuate RNA polymerase II transcription through TFIID. J Biol Chem 2023;299:104928. [PMID: 37330174 PMCID: PMC10404688 DOI: 10.1016/j.jbc.2023.104928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023]  Open
18
Sloutskin A, Itzhak D, Vogler G, Ideses D, Alter H, Shachar H, Doniger T, Frasch M, Bodmer R, Duttke SH, Juven-Gershon T. A single DPE core promoter motif contributes to in vivo transcriptional regulation and affects cardiac function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.544490. [PMID: 37398300 PMCID: PMC10312617 DOI: 10.1101/2023.06.11.544490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
19
Volkening JD, Spatz SJ, Ponnuraj N, Akbar H, Arrington JV, Vega-Rodriguez W, Jarosinski KW. Viral proteogenomic and expression profiling during productive replication of a skin-tropic herpesvirus in the natural host. PLoS Pathog 2023;19:e1011204. [PMID: 37289833 PMCID: PMC10284419 DOI: 10.1371/journal.ppat.1011204] [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: 02/14/2023] [Revised: 06/21/2023] [Accepted: 05/29/2023] [Indexed: 06/10/2023]  Open
20
Kharytonchyk S, Burnett C, Gc K, Telesnitsky A. Transcription start site heterogeneity and its role in RNA fate determination distinguish HIV-1 from other retroviruses and are mediated by core promoter elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541776. [PMID: 37292892 PMCID: PMC10245945 DOI: 10.1101/2023.05.22.541776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
21
Vo Ngoc L, Rhyne TE, Kadonaga JT. Analysis of the Drosophila and human DPR elements reveals a distinct human variant whose specificity can be enhanced by machine learning. Genes Dev 2023;37:377-382. [PMID: 37163335 PMCID: PMC10270198 DOI: 10.1101/gad.350572.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/06/2023] [Indexed: 05/11/2023]
22
van den Elzen AMG, Watson MJ, Thoreen CC. mRNA 5' terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay. PLoS Genet 2022;18:e1010532. [PMID: 36441824 PMCID: PMC9731452 DOI: 10.1371/journal.pgen.1010532] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/08/2022] [Accepted: 11/15/2022] [Indexed: 11/30/2022]  Open
23
Chou SP, Alexander AK, Rice EJ, Choate LA, Danko CG. Genetic dissection of the RNA polymerase II transcription cycle. eLife 2022;11:e78458. [PMID: 35775732 PMCID: PMC9286732 DOI: 10.7554/elife.78458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/30/2022] [Indexed: 11/20/2022]  Open
24
Hou TY, Kraus WL. Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression. Cell Rep 2022;39:110944. [PMID: 35705040 PMCID: PMC9246336 DOI: 10.1016/j.celrep.2022.110944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/12/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2022]  Open
25
Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases. Nat Rev Mol Cell Biol 2022;23:603-622. [PMID: 35505252 DOI: 10.1038/s41580-022-00476-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 02/07/2023]
26
Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM, Fatima R, Gil L, Goldfarb T, Gonzalez JM, Haddad D, Hardy M, Hunt T, Jackson J, Joardar VS, Kay M, Kodali VK, McGarvey KM, McMahon A, Mudge JM, Murphy DN, Murphy MR, Rajput B, Rangwala SH, Riddick LD, Thibaud-Nissen F, Threadgold G, Vatsan AR, Wallin C, Webb D, Flicek P, Birney E, Pruitt KD, Frankish A, Cunningham F, Murphy TD. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature 2022;604:310-315. [PMID: 35388217 PMCID: PMC9007741 DOI: 10.1038/s41586-022-04558-8] [Citation(s) in RCA: 268] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/07/2022] [Indexed: 12/25/2022]
27
Duttke SH, Beyhan S, Singh R, Neal S, Viriyakosol S, Fierer J, Kirkland TN, Stajich JE, Benner C, Carlin AF. Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA. mSystems 2022;7:e0140421. [PMID: 35076277 PMCID: PMC8788335 DOI: 10.1128/msystems.01404-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/04/2022] [Indexed: 01/07/2023]  Open
28
Rojas DA, Urbina F, Valenzuela-Pérez L, Leiva L, Miralles VJ, Maldonado E. Initiator-Directed Transcription: Fission Yeast Nmtl Initiator Directs Preinitiation Complex Formation and Transcriptional Initiation. Genes (Basel) 2022;13:genes13020256. [PMID: 35205301 PMCID: PMC8871863 DOI: 10.3390/genes13020256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023]  Open
29
Fiszbein A, McGurk M, Calvo-Roitberg E, Kim G, Burge CB, Pai AA. Widespread occurrence of hybrid internal-terminal exons in human transcriptomes. SCIENCE ADVANCES 2022;8:eabk1752. [PMID: 35044812 PMCID: PMC8769537 DOI: 10.1126/sciadv.abk1752] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/23/2021] [Indexed: 06/12/2023]
30
Identification and characterization of the promoter and transcription factors regulating the expression of cerebral sodium/calcium exchanger 2 (NCX2) gene. Cell Calcium 2022;102:102542. [DOI: 10.1016/j.ceca.2022.102542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/30/2021] [Accepted: 01/22/2022] [Indexed: 11/22/2022]
31
Sloutskin A, Shir-Shapira H, Freiman RN, Juven-Gershon T. The Core Promoter Is a Regulatory Hub for Developmental Gene Expression. Front Cell Dev Biol 2021;9:666508. [PMID: 34568311 PMCID: PMC8461331 DOI: 10.3389/fcell.2021.666508] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022]  Open
32
Zinghirino F, Pappalardo XG, Messina A, Nicosia G, De Pinto V, Guarino F. VDAC Genes Expression and Regulation in Mammals. Front Physiol 2021;12:708695. [PMID: 34421651 PMCID: PMC8374620 DOI: 10.3389/fphys.2021.708695] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022]  Open
33
Shamie I, Duttke SH, Karottki KJLC, Han CZ, Hansen AH, Hefzi H, Xiong K, Li S, Roth SJ, Tao J, Lee GM, Glass CK, Kildegaard HF, Benner C, Lewis NE. A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genom Bioinform 2021;3:lqab061. [PMID: 34268494 PMCID: PMC8276764 DOI: 10.1093/nargab/lqab061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/29/2021] [Accepted: 06/14/2021] [Indexed: 01/05/2023]  Open
34
Grencewicz DJ, Romigh T, Thacker S, Abbas A, Jaini R, Luse D, Eng C. Redefining the PTEN promoter: Identification of novel upstream transcription start regions. Hum Mol Genet 2021;30:2135-2148. [PMID: 34218272 DOI: 10.1093/hmg/ddab175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 11/14/2022]  Open
35
Zhang M, Chaney HL, Current JZ, Yao J. Identification of the core promoter of ZNFO, an oocyte-specific maternal effect gene in cattle. Gene 2021;791:145717. [PMID: 33991649 DOI: 10.1016/j.gene.2021.145717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 01/26/2023]
36
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y. Structural insights into preinitiation complex assembly on core promoters. Science 2021;372:science.aba8490. [PMID: 33795473 DOI: 10.1126/science.aba8490] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 02/01/2021] [Accepted: 03/25/2021] [Indexed: 12/24/2022]
37
Conservation of the HBV RNA element epsilon in nackednaviruses reveals ancient origin of protein-primed reverse transcription. Proc Natl Acad Sci U S A 2021;118:2022373118. [PMID: 33753499 DOI: 10.1073/pnas.2022373118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
38
Skopenkova VV, Egorova TV, Bardina MV. Muscle-Specific Promoters for Gene Therapy. Acta Naturae 2021;13:47-58. [PMID: 33959386 PMCID: PMC8084301 DOI: 10.32607/actanaturae.11063] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022]  Open
39
Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture. Nat Commun 2020;11:5963. [PMID: 33235186 PMCID: PMC7687912 DOI: 10.1038/s41467-020-19829-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022]  Open
40
Srinivasachar Badarinarayan S, Shcherbakova I, Langer S, Koepke L, Preising A, Hotter D, Kirchhoff F, Sparrer KMJ, Schotta G, Sauter D. HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression. Nucleic Acids Res 2020;48:10890-10908. [PMID: 33021676 PMCID: PMC7641743 DOI: 10.1093/nar/gkaa832] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]  Open
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Luse DS, Parida M, Spector BM, Nilson KA, Price DH. A unified view of the sequence and functional organization of the human RNA polymerase II promoter. Nucleic Acids Res 2020;48:7767-7785. [PMID: 32597978 PMCID: PMC7641323 DOI: 10.1093/nar/gkaa531] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/31/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]  Open
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Identification of the human DPR core promoter element using machine learning. Nature 2020;585:459-463. [PMID: 32908305 PMCID: PMC7501168 DOI: 10.1038/s41586-020-2689-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/16/2020] [Indexed: 01/31/2023]
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Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020;21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022]  Open
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Qiu C, Jin H, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Visbisky AM, Schwartz SL, Cui P, Čabart P, Han KH, Lai WKM, Metz RP, Johnson CD, Sze SH, Pugh BF, Nickels BE, Kaplan CD. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biol 2020;21:132. [PMID: 32487207 PMCID: PMC7265651 DOI: 10.1186/s13059-020-02040-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/08/2020] [Indexed: 12/15/2022]  Open
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Dubaisi S, Fang H, Caruso JA, Gaedigk R, Vyhlidal CA, Kocarek TA, Runge-Morris M. Developmental Expression of SULT1C4 Transcript Variants in Human Liver: Implications for Discordance Between SULT1C4 mRNA and Protein Levels. Drug Metab Dispos 2020;48:515-520. [PMID: 32303576 PMCID: PMC7250359 DOI: 10.1124/dmd.120.090829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/20/2020] [Indexed: 01/11/2023]  Open
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Policastro RA, Raborn RT, Brendel VP, Zentner GE. Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Res 2020;30:910-923. [PMID: 32660958 PMCID: PMC7370879 DOI: 10.1101/gr.261545.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
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Catizone AN, Uzunbas GK, Celadova P, Kuang S, Bose D, Sammons MA. Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. Nucleic Acids Res 2020;48:4195-4213. [PMID: 32133495 PMCID: PMC7192610 DOI: 10.1093/nar/gkaa147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/27/2020] [Accepted: 02/26/2020] [Indexed: 01/03/2023]  Open
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Lee Q, Padula MP, Pinello N, Williams SH, O'Rourke MB, Fumagalli MJ, Orkin JD, Song R, Shaban B, Brenner O, Pimanda JE, Weninger W, de Souza WM, Melin AD, Wong JJL, Crim MJ, Monette S, Roediger B, Jolly CJ. Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys. PLoS Pathog 2020;16:e1008262. [PMID: 31971979 PMCID: PMC6999912 DOI: 10.1371/journal.ppat.1008262] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/04/2020] [Accepted: 12/08/2019] [Indexed: 12/21/2022]  Open
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Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes. Nat Commun 2019;10:5636. [PMID: 31822664 PMCID: PMC6904561 DOI: 10.1038/s41467-019-13561-z] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/12/2019] [Indexed: 01/14/2023]  Open
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Duttke SH, Chang MW, Heinz S, Benner C. Identification and dynamic quantification of regulatory elements using total RNA. Genome Res 2019;29:1836-1846. [PMID: 31649059 PMCID: PMC6836739 DOI: 10.1101/gr.253492.119] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022]
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