Publication

ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment

Jeffery D. Steimle, Chul Kim, Rangarajan D. Nadadur, Zhezhen Wang, Andrew D. Hoffmann, Erika Hanson, Junghun Kweon, Tanvi Sinha, Kyunghee Choi, Brian L. Black, John M. Cunningham, Kohta Ikegami*, Ivan P. Moskowitz*

*Corresponding author

bioRxiv https://www.biorxiv.org/content/10.1101/2021.06.25.449981v1

Nuclear lamin phosphorylation: an emerging role in gene regulation and pathogenesis of laminopathies

Liu SY, Ikegami K

Nucleus (2020) review PMID: 33030403 

Transcriptional patterning of the ventricular cardiac conduction system

Burnicka-Turek O, Broman M, Steimle JD, Boukens B, Ikegami K, Nadadaru R, Qiao Y, Arnolds D, Yang XH, Patel V, Nobrega M, Efimov I, Moskowitz IP 

Circulation Research (2020) PMID: 32290757

Phosphorylated Lamin A/C in the nuclear interior binds active enhancers associated with abnormal transcription in progeria

Ikegami K*,  Secchia S,  Almakki O, Lieb JD, Moskowitz IP (*Corresponding author)

Developmental Cell (2020) PMID: 32208162

Commented by: Manzo SG, van Steensel B: Phosphorylated Lamins in Euchromatin: New Clues to Progeria. Dev Cell (2020)

Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans

Stutzman AV, Liang AS, Beilinson V, Ikegami K

Epigenetics & Chromatin (2020) PMID: 31918747

Evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development

Steimle JD, Rankin SA, Slagle CE, Bekeny J, Rydeen AB, Chan SS, Kweon J, Yang XH, Ikegami K, Nadadur RD, Rowton M, Hoffmann AD, Lazarevic S, Thomas W, Boyle Anderson EAT, Horb ME, Luna-Zurita L, Ho RK, Kyba M, Jensen B, Zorn AM, Conlon FL, Moskowitz IP

Proceedings of the National Academy of Sciences (2018) PMID: 30352852

Caenorhabditis elegans RSD-2 and RSD-6 promote germ cell immortality by maintaining small interfering RNA populations 

Sakaguchi A, Sarkies P, Simon M, Goldstein L, Hedges A, Ikegami K, Alvares S, Yang L, LaRocque LR, Hall J, Miska EA, Ahmed S.

Proceedings of the National Academy of Sciences  (2014) PMID: 25258416

Comparative analysis of metazoan chromatin organization 

Ho JWK, Liu T, Jung YL, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SCJ, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dosé AC, Duan X, Epstein CB, Ercan S, Feingold EA, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta, V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SCR, Ahringer J, Liu XS, Karpen GH, Lieb JD, Park PJ (Co-second author) 

Nature (2014) PMID: 25164756

Commented by: Muerdter F, Stark A: Hiding in plain sight. Nature (2014)

Reduced insulin/IGF-1 signaling restores germ cell immortality to Caenorhabditis elegans Piwi mutants 

Simon M, Sarkies P, Ikegami K, Doebley A, Goldstein LD, Mitchell J, Sakaguchi A, Miska EA, Ahmed S

Cell Reports (2014) PMID: 24767993

Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans 

González-Aguilera C, Ikegami K, Ayuso C, de Luis A, Íñiguez M, Cabello J, Lieb JD, Askjaer P

Genome Biology (2014) PMID: 24490688

TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination

Berkseth M*, Ikegami K*, Arur S, Lieb JD, Zarkower D (*Co-first author)

Proceedings of the National Academy of Sciences (2013) PMID: 24046365

Integral Nuclear Pore Proteins Bind to Pol III-Transcribed Genes and Are Required for Pol III Transcript Processing in C. elegans 

Ikegami K, Lieb JD 

Molecular Cell (2013) PMID: 24011592

Commented by: Schuldt A: Processing at the pore. Nature Reviews Molecular Cell Biology (2013); Maraia RJ, Arimbasseri AG: It’s Sno’ing on Pol III at nuclear pores. Genome Biology (2013)

Cover image by Sophia Tintori

Promoter- and RNA polymerase II-dependent hsp-16 gene association with nuclear pores in Caenorhabditis elegans

Rohner S, Kalck V, Wang X, Ikegami K, Lieb JD, Gasser SM, Meister P

Journal of Cell Biology (2013) PMID: 23460676

Broad chromosomal domains of histone modification patterns in C. elegans

Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung M-S, Ercan S, Ikegami K, Jensen M, Kolasinska-Zwierz P, Rosenbaum H, Shin H, Taing S, Takasaki T, Iniguez AL, Desai A, Dernburg AF, Kimura H, Lieb JD, Ahringer J, Strome S, Liu XS

Genome Research 21, 227–236. (2011) PMID: 21177964

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project 

Gerstein MB*, Lu ZJ*, Van Nostrand EL*, Cheng C*, Arshinoff BI*, Liu T*, Yip KY*, Robilotto R*, Rechtsteiner A*, Ikegami K*, Alves P*, Chateigner A*, Perry M*, Morris M*, Auerbach RK*, Feng X*, Leng J*, Vielle A*, Niu W*, Rhrissorrakrai K*, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung M-S, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi S-L, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan K-K, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH (*Co-first author)

Science (2010) PMID: 21177976

Commented by: Blaxter M: Genetics. Revealing the dark matter of the genome. Science (2010); Rusk N: What makes flies and worms tick. Nature Methods (2011); Muers M: the modENCODE guide to the genome. Nature Reviews Genetics (2011)

Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2

Ikegami K, Egelhofer TA, Strome S, Lieb JD

Genome Biology (2010) PMID: 21176223

Nucleoporins and transcription: new connections, new questions

Ikegami K, Lieb JD 

PLoS Genetics (2010) commentary PMID: 20195517

Commented on: Vaquerizas JM, Suyama R, Kind J, Miura K, Luscombe NM, Akhtar A. (2010) Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome.PLoS Genet 6, e1000846

Interplay between DNA methylation, histone modification and chromatin remodeling in stem cells and during development

International Journal of Developmental Biology (2009) review PMID: 19412882

Ikegami K, Ohgane J, Tanaka S, Yagi S, Shiota K

Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells

Ikegami K, Iwatani M, Suzuki M, Tachibana M, Shinkai Y, Tanaka S, Greally JM, Yagi S, Hattori N, Shiota K

Genes to Cells (2007) PMID: 17212651

Dimethyl sulfoxide has an impact on epigenetic profile in mouse embryoid body 

Iwatani M, Ikegami K, Kremenska Y, Hattori N, Tanaka S, Yagi S, Shiota K 

Stem Cells (2006) PMID: 16840553