How to cite EaSeq

Our paper introducing EaSeq is published in: Nature Structural & Molecular Biology Volume 23 No 4 (April 2016), 349-357

Please cite this paper and include a link to this site (http://easeq.net) when publishing output from EaSeq. A file for easy import into reference organizing programs is available here.

 

Papers using EaSeq

Histone H4K20 methylation mediated chromatin compaction threshold ensures genome integrity by limiting DNA replication licensing. Shoaib M, Walter D, Gillespie PJ, Izard F, Fahrenkrog B, Lleres D, Lerdrup M, Johansen JV, Hansen K, Julien E, Blow JJ, Sørensen CS. Nat Commun. 2018 Sep 12;9(1):3704. doi: 10.1038/s41467-018-06066-8.

Mechanism of Telapristone acetate (CDB4124) on Progesterone receptor action in breast cancer cells. Davaadelger B, Murphy AR, Clare SE, Lee O, Khan SA, Kim JJ. Endocrinology. 2018 Sep 6. doi: 10.1210/en.2018-00559.

Distinct patterns of histone acetyltransferase and Mediator deployment at yeast protein-coding genes. Bruzzone MJ, Grünberg S, Kubik S, Zentner GE, Shore D. Genes Dev. 2018 Sep 1;32(17-18):1252-1265. doi: 10.1101/gad.312173.118.

Leukemogenic nucleophosmin mutation disrupts the transcription factor hub that regulates granulomonocytic fates. Gu X, Ebrahem Q, Mahfouz RZ, Hasipek M, Enane F, Radivoyevitch T, Rapin N, Przychodzen B, Hu Z, Balusu R, Cotta CV, Wald D, Argueta C, Landesman Y, Martelli MP, Falini B, Carraway H, Porse BT, Maciejewski J, Jha BK, Saunthararajah Y. J Clin Invest. 2018 Aug 27. pii: 97117. doi: 10.1172/JCI97117.

Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription. Kubik S, O’Duibhir E, de Jonge WJ, Mattarocci S, Albert B, Falcone JL, Bruzzone MJ, Holstege FCP, Shore D. Mol Cell. 2018 Jul 5;71(1):89-102.e5. doi: 10.1016/j.molcel.2018.05.030.

Transcription Factor PU.1 Represses and Activates Gene Expression in Early T Cells by Redirecting Partner Transcription Factor Binding. Hosokawa H, Ungerbäck J, Wang X, Matsumoto M, Nakayama KI, Cohen SM, Tanaka T, Rothenberg EV. Immunity. 2018 Jun 19;48(6):1119-1134.e7. doi: 10.1016/j.immuni.2018.04.024.

DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1. Wang X, Srivastava Y, Jankowski A, Malik V, Wei Y, Del Rosario RCH, Cojocaru V, Prabhakar S, Jauch R. Nucleic Acids Res. 2018 Apr 14. doi: 10.1093/nar/gky259.

Regulatory integration of Hox factor activity with T-box factors in limb development. Jain D, Nemec S, Luxey M, Gauthier Y, Bemmo A, Balsalobre A, Drouin J. Development. 2018 Mar 22;145(6). pii: dev159830. doi: 10.1242/dev.159830.

Loss of KDM6A Activates Super-Enhancers to Induce Gender-Specific Squamous-like Pancreatic Cancer and Confers Sensitivity to BET Inhibitors. Andricovich J, Perkail S, Kai Y, Casasanta N, Peng W, Tzatsos A. Cancer Cell. 2018 Mar 12;33(3):512-526.e8. doi: 10.1016/j.ccell.2018.02.003.

Transcriptional regulation mediated by H2A.Z via ANP32e-dependent inhibition of protein phosphatase 2A. Shin H, He M, Yang Z, Jeon YH, Pfleger J, Sayed D, Abdellatif M. Biochim Biophys Acta. 2018 Mar 8. pii: S1874-9399(17)30393-0. doi: 10.1016/j.bbagrm.2018.03.002.

Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2. Højfeldt JW, Laugesen A, Willumsen BM, Damhofer H, Hedehus L, Tvardovskiy A, Mohammad F, Jensen ON, Helin K. Nat Struct Mol Biol. 2018 Feb 26. doi: 10.1038/s41594-018-0036-6.

A Non-catalytic Function of SETD1A Regulates Cyclin K and the DNA Damage Response. Hoshii T, Cifani P, Feng Z, Huang CH, Koche R, Chen CW, Delaney CD, Lowe SW, Kentsis A, Armstrong SA. Cell. 2018 Feb 22;172(5):1007-1021.e17. doi: 10.1016/j.cell.2018.01.032.

Programming of Schwann Cells by Lats1/2-TAZ/YAP Signaling Drives Malignant Peripheral Nerve Sheath Tumorigenesis. Wu LMN, Deng Y, Wang J, Zhao C, Wang J, Rao R, Xu L, Zhou W, Choi K, Rizvi TA, Remke M, Rubin JB, Johnson RL, Carroll TJ, Stemmer-Rachamimov AO, Wu J, Zheng Y, Xin M, Ratner N, Lu QR. Cancer Cell. 2018 Feb 12;33(2):292-308.e7. doi: 10.1016/j.ccell.2018.01.005.

Replication confers β cell immaturity. Puri S, Roy N, Russ HA, Leonhardt L, French EK, Roy R, Bengtsson H, Scott DK, Stewart AF, Hebrok M. Nat Commun. 2018 Feb 2;9(1):485. doi: 10.1038/s41467-018-02939-0.

Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate. Mayran A, Khetchoumian K, Hariri F, Pastinen T, Gauthier Y, Balsalobre A, Drouin J. Nat Genet. 2018 Jan 22. doi: 10.1038/s41588-017-0035-2.

Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis. Stelloo S, Nevedomskaya E, Kim Y, Hoekman L, Bleijerveld OB, Mirza T, Wessels LFA, van Weerden WM, Altelaar AFM, Bergman AM, Zwart W. Oncogene. 2017 Sep 18. doi: 10.1038/onc.2017.330.

Maternal expression of the JMJD2A/KDM4A histone demethylase is critical for pre-implantation development. Sankar A, Kooistra SM, Gonzalez JM, Ohlsson C, Poutanen M, Helin K. Development. 2017 Aug 21. pii: dev.155473. doi: 10.1242/dev.155473.

Pitx1 directly modulates the core limb development program to implement hindlimb identity. Nemec S, Luxey M, Jain D, Sung AH, Pastinen T, Drouin J. Development. 2017 Aug 14. pii: dev.154864. doi: 10.1242/dev.154864.

GATA4 loss of function in liver cancer impedes precursor to hepatocyte transition. Enane FO, Shuen WH, Gu X, Quteba E, Przychodzen B, Makishima H, Bodo J, Ng J, Chee CL, Ba R, Seng Koh L, Lim J, Cheong R, Teo M, Hu Z, Ng KP, Maciejewski J, Radivoyevitch T, Chung A, Ooi LL, Tan YM, Cheow PC, Chow P, Chan CY, Lim KH, Yerian L, Hsi E, Toh HC, Saunthararajah Y. J Clin Invest. 2017 Jul 31. pii: 93488. doi: 10.1172/JCI93488.

Direct targets of pSTAT5 signalling in erythropoiesis. Gillinder KR, Tuckey H, Bell CC, Magor GW, Huang S, Ilsley MD, Perkins AC. PLoS One. 2017 Jul 21;12(7):e0180922. doi: 10.1371/journal.pone.0180922.

Identification of novel dysregulated key genes in Breast cancer through high throughput ChIP-Seq data analysis. Raj U, Aier I, Semwal R, Varadwaj PK. Sci Rep. 2017 Jun 12;7(1):3229. doi: 10.1038/s41598-017-03534-x.

Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2. Tchasovnikarova IA, Timms RT, Douse CH, Roberts RC, Dougan G, Kingston RE, Modis Y, Lehner PJ. Nat Genet. 2017 Jun 5. doi: 10.1038/ng.3878.

The accessible chromatin landscape during conversion of human embryonic stem cells to trophoblast by bone morphogenetic protein 4. Liu Y, Ding D, Liu H, Sun X. Biol Reprod. 2017 Jun 1;96(6):1267-1278. doi: 10.1093/biolre/iox028.

Krüppel-like factors compete for promoters and enhancers to fine-tune transcription. Ilsley MD, Gillinder KR, Magor GW, Huang S, Bailey TL, Crossley M, Perkins AC. Nucleic Acids Res. 2017 May 24. doi: 10.1093/nar/gkx441

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization Nora EP, Goloborodko A, Valton A-L, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Cell. 2017 May 18; 169(5), 930–944, doi: 10.1016/j.cell.2017.05.004

Crebbp loss cooperates with Bcl2 overexpression to promote lymphoma in mice. García-Ramírez I, Tadros S, González-Herrero I, Martín-Lorenzo A, Rodríguez-Hernández G, Moore D, Ruiz-Roca L, Blanco O, Alonso-López D, Rivas JL, Hartert K, Duval R, Klinkebiel D, Bast M, Vose J, Lunning M, Fu K, Greiner T, Rodrigues-Lima F, Jiménez R, Criado FJG, Cenador MBG, Brindle P, Vicente-Dueñas C, Alizadeh A, Sánchez-García I, Green MR. Blood. 2017 May 11;129(19):2645-2656. doi: 10.1182/blood-2016-08-733469. Epub 2017 Mar 13.

DDK Promotes Tumor Chemoresistance and Survival via Multiple Pathways. Sasi NK1, Bhutkar A2, Lanning NJ3, MacKeigan JP3, Weinreich M4. Neoplasia. 2017 May;19(5):439-450. doi: 10.1016/j.neo.2017.03.001. Epub 2017 Apr 25.

Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency. Yang Y, Liu B, Xu J, Wang J, Wu J, Shi C, Xu Y, Dong J, Wang C, Lai W, Zhu J, Xiong L, Zhu D, Li X, Yang W, Yamauchi T, Sugawara A, Li Z, Sun F, Li X, Li C, He A, Du Y, Wang T, Zhao C, Li H, Chi X, Zhang H, Liu Y, Li C, Duo S, Yin M, Shen H, Belmonte JC, Deng H. Cell. 2017 Apr 6;169(2):243-257.e25. doi: 10.1016/j.cell.2017.02.005.

MAP3K4 Controls the Chromatin Modifier HDAC6 during Trophoblast Stem Cell Epithelial-to-Mesenchymal Transition. Mobley RJ, Raghu D, Duke LD, Abell-Hart K, Zawistowski JS, Lutz K, Gomez SM, Roy S, Homayouni R, Johnson GL, Abell AN. Cell Rep. 2017 Mar 7;18(10):2387-2400. doi: 10.1016/j.celrep.2017.02.030.

Loss of the histone methyltransferase EZH2 induces resistance to multiple drugs in acute myeloid leukemia. Göllner S, Oellerich T, Agrawal-Singh S, Schenk T, Klein HU, Rohde C, Pabst C, Sauer T, Lerdrup M, Tavor S, Stölzel F, Herold S, Ehninger G, Köhler G, Pan KT, Urlaub H, Serve H, Dugas M, Spiekermann K, Vick B, Jeremias I, Berdel WE, Hansen K, Zelent A, Wickenhauser C, Müller LP, Thiede C, Müller-Tidow C. Nat Med. 2017 Jan;23(1):69-78. doi: 10.1038/nm.4247.

 ATF7IP-Mediated Stabilization of the Histone Methyltransferase SETDB1 Is Essential for Heterochromatin Formation by the HUSH Complex. Timms RT, Tchasovnikarova IA, Antrobus R, Dougan G, Lehner PJ. Cell Rep. 2016 Oct 11;17(3):653-659. doi: 10.1016/j.celrep.2016.09.050.

 Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Loubiere V, Delest A, Thomas A, Bonev B, Schuettengruber B, Sati S, Martinez AM, Cavalli G. Nat Genet. 2016 Sep 19. doi: 10.1038/ng.3671

 Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Dahl JA, Jung I, Aanes H, Greggains GD, Manaf A, Lerdrup M, Li G, Kuan S, Li B, Lee AY, Preissl S, Jermstad I, Haugen MH, Suganthan R, Bjørås M, Hansen K, Dalen KT, Fedorcsak P, Ren B, Klungland A. Nature. 2016 Sep 14;537(7621):548-552. doi: 10.1038/nature19360.

Jmjd2/Kdm4 demethylases are required for expression of Il3ra and survival of acute myeloid leukemia cells. Agger K, Miyagi S, Pedersen MT, Kooistra SM, Johansen JV, Helin K. Genes Dev. 2016 Jun 1;30(11):1278-88. doi: 10.1101/gad.280495.116. Epub 2016 Jun 2.

An interactive environment for agile analysis and visualization of ChIP-sequencing data. Lerdrup M, Johansen JV, Agrawal-Singh S, Hansen K. Nat Struct Mol Biol. 2016 Apr;23(4):349-57. doi: 10.1038/nsmb.3180. Epub 2016 Feb 29.

 β-Catenin Regulates Primitive Streak Induction through Collaborative Interactions with SMAD2/SMAD3 and OCT4. Funa NS, Schachter KA, Lerdrup M, Ekberg J, Hess K, Dietrich N, Honoré C, Hansen K, Semb H. Cell Stem Cell. 2015 Jun 4;16(6):639-52. doi: 10.1016/j.stem.2015.03.008. Epub 2015 Apr 23.

 Dopamine signaling leads to loss of Polycomb repression and aberrant gene activation in experimental parkinsonism. Södersten E, Feyder M, Lerdrup M, Gomes AL, Kryh H, Spigolon G, Caboche J, Fisone G, Hansen K. PLoS Genet. 2014 Sep 25;10(9):e1004574. doi: 10.1371/journal.pgen.1004574. eCollection 2014 Sep.

 DNA methylation changes are a late event in acute promyelocytic leukemia and coincide with loss of transcription factor binding. Schoofs T, Rohde C, Hebestreit K, Klein HU, Göllner S, Schulze I, Lerdrup M, Dietrich N, Agrawal-Singh S, Witten A, Stoll M, Lengfelder E, Hofmann WK, Schlenke P, Büchner T, Hansen K, Berdel WE, Rosenbauer F, Dugas M, Müller-Tidow C. Blood. 2013 Jan 3;121(1):178-87. doi: 10.1182/blood-2012-08-448860. Epub 2012 Nov 14.

REST-mediated recruitment of polycomb repressor complexes in mammalian cells. (precursing algorithms and plots) Dietrich N, Lerdrup M, Landt E, Agrawal-Singh S, Bak M, Tommerup N, Rappsilber J, Södersten E, Hansen K. PLoS Genet. 2012;8(3):e1002494. doi: 10.1371/journal.pgen.1002494. Epub 2012 Mar 1.

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