
Differential Etv2 threshold requirement for endothelial and erythropoietic development.
Tanvi Sinha, Kelly Lammerts van Bueren, Diane E Dickel, Ivana Zlatanova, Reuben Thomas, Carlos O Lizama, Shan-Mei Xu, Ann C Zovein, Kohta Ikegami, Ivan P Moskowitz, Katherine S Pollard, Len A Pennacchio, Brian L Black
Cell Reports (2022) PMID: 35649376

Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development
Scott A Rankin , Jeffrey D Steimle, Xinan H Yang, Ariel B Rydeen, Kunal Agarwal, Praneet Chaturvedi, Kohta Ikegami, Michael J Herriges, Ivan P Moskowitz, Aaron M Zorn

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