Publications
SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism. 2024 BioRxiv Avrami Aharonoff, Jun Kim, Aaliyah Washington, Sevinc Ercan Twittorial here
Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos. 2024 BioRxiv. Laura Breimann, Ella Bahry, Marwan Zouinkhi, Klim Kolyvanov, Lena Annika Street, Stephan Preibisch and Sevinç Ercan Twittorial here.
Cohesin mediated loop extrusion from active enhancers form chromatin jets in C. elegans. 2023 BioRxiv Jun Kim, Haoyu Wang, Sevinç Ercan Twittorial here.
Topoisomerases I and II facilitate condensin DC translocation to organize and repress X chromosomes in C. elegans Morao AK, Jun Kim, Daniel Obaji, Siyu Sun, Sevinç Ercan BioRxiv (2021) Twittorial here Mol Cell 2022 Nov 17;82(22):4202-4217.e5. doi: 10.1016/j.molcel.2022.10.002. PMID: 36302374
Data from this study is available at GEO: GSE188851
Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans Jun Kim*, David Sebastian Jimenez*, Bhavana Ragipani, Bo Zhang, Lena Annika Street1 Maxwell Kramer, Sarah E Albritton, Lara Winterkorn, Ana Morao, Sevinç Ercan BioRxiv (2022) * Equal contribution Elife 2022 https://doi.org/10.7554/eLife.68745
Data from this study is available at GEO: GSE168803
Increased gene dosage and mRNA expression from chromosomal duplications in C. elegans. Ragipani B, Albritton SE, Morao AK, Mesquita D, Kramer M, Ercan S BioRxiv (2022) Twittorial here G3 2022 Jul 29;12(8):jkac151. doi: 10.1093/g3journal/jkac151 PMID: 35731207 PMCID: PMC9339279
This preprint has been highlighted by preLights! Data from this study is available at GEO: GSE198682
Hatched and starved: Two chromatin compaction mechanisms join forces to silence germ cell genome. Morao AK, Ercan S. J Cell Biol. (2021) Sep 6;220(9):e202107026. doi: 10.1083/jcb.202107026. Epub 2021 Aug 12. A spotlight on this article.
An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system in Caenorhabditis elegans Kelly Hills-Muckey, Michael A. Q. Martinez, Natalia Stec, Shilpa Hebbar, Joanne Saldanha, Taylor N. Medwig-Kinney, Frances E. Q. Moore, Mariia Ivanova, Ana Morao, Jordan D. Ward, Eric G. Moss, Sevinc Ercan, Anna Y. Zinovyeva, David Q. Matus, Christopher M. Hammell BioRxiv (2021) Genetics. 2021 Oct 12;iyab174. doi: 10.1093/genetics/iyab174
A noncatalytic activity of the H4K20 demethylase DPY-21 regulates condensin DC binding. Laura Breimann*, Ana Karina Morao*, Jun Kim, David Sebastian Jimenez, Nina Maryn, Krishna Bikkasani, Michael J Carrozza, Sarah E Albritton, Maxwell Kramer, Lena Annika Street, Kustrim Cerimi, Vic-Fabienne Schumann, Ella Bahry2, Stephan Preibisch, Andrew Woehler, Sevinç Ercan BioRxiv (2022) J Cell Sci (2022) 135 (2): jcs258818. PMID: 34918745 PMCID: PMC8917352 DOI: 10.1242/jcs.258818
Data from this study is available at GEO: GSE169458
FRAP protocol is available at protocols.io: Fluorescence Recovery after Photobleaching (FRAP) in adult C. elegans nuclei
Identification and prediction of developmental enhancers in sea urchin embryos César Arenas-Mena, Sofija Miljovska, Edward J. Rice, Justin Gurges, Tanvi Shashikant, Sevinç Ercan, Charles G. Danko BioRxiv (2021) Published at BMC Genomics. 2021 Oct 19;22(1):751. doi: 10.1186/s12864-021-07936-0
An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output during C. elegans Development Natalia Stec, Katja Doerfel, Kelly Hills-Muckey, Victoria M Ettorre, Sevinc Ercan, Wolfgang Keil, Christopher M Hammell. Curr Biol. (2020) Dec 17;S0960-9822(20)31773-5. doi: 10.1016/j.cub.2020.11.060
An X-specific condensin binds to gene regulatory elements and reduces histone modifications associated with active transcription in C. elegans. Street LA, Winterkorn LH, Jiao C, Albritton SE, Sadic M, Kramer M, Ercan S. Genetics (2019) Jul;212(3):729-742. doi: 10.1534/genetics.119.302254 Also in BioRxiv
Condensin action and compaction Paul MR, Hochwagen A and Ercan S (2018) Current Genetics doi:10.1007/s00294-018-0899-4 Available to read at https://rdcu.be/baaZu
Condensin depletion causes genome decompaction without altering the level of global gene expression in Saccharomyces cerevisiae Paul MR, Markowitz TE, Hochwagen A and Ercan S in BioRxiv (2018) Genetics Sep;210(1):331-344. doi: 10.1534/genetics.118.301217
Caenorhabditis elegans Dosage Compensation: Insights into Condensin-Mediated Gene Regulation Albritton SE and Ercan S. (2017) Trends in Genetics https://doi.org/10.1016/j.tig.2017.09.010
Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation. Albritton SE, Kranz AL, Winterkorn LH, Street LA, Ercan S. (2017) Elife. May 30;6. pii: e23645. doi: 10.7554/eLife.23645. Data from this study is available at GEO: GSE87741
Untangling the contributions of sex-specific gene regulation and X-chromosome dosage to sex-biased gene expression in C. elegans. Kramer M, Rao P, Ercan S. (2016) Genetics. Sep;204(1):355-69. doi: 10.1534/genetics.116.190298. Epub 2016 Jun 29.
Data from this study is available at GEO: GSE77794
Developmental dynamics of X-chromosome dosage compensation by the DCC and H4K20me1 in C. elegans. Kramer M, Kranz AL, Su A, Winterkorn L, Albritton SE, Ercan S. (2015) PLoS Genetics Dec 7;11(12):e1005698 doi: 10.1371/journal.pgen.1005698
Data from this study is available at GEO: GSE67650
Mechanisms of X Chromosome Dosage Compensation. Ercan S. (2015) J Genomics ; 3:1-19. doi:10.7150/jgen.10404.
Comparative analysis of metazoan chromatin organization. Ho JW et al., (2014) Nature. Aug 28;512(7515):449-52. doi: 10.1038/nature13415. PMID:25164756
Data from this study is organized at: https://www.encodeproject.org/comparative/
Sex-Biased Gene Expression and Evolution of the X Chromosome in Nematodes. Albritton SE, Kranz AL, Rao P, Kramer M, Dieterich C, Ercan S. (2014) Genetics. May 2. [Epub ahead of print] PMID:24793291
Data from this study is available at GEO: GSE53144
Modern techniques for the analysis of chromatin and nuclear organization in C. elegans. WormBook. Askjaer P, Ercan S, Meister P. (2014) Apr 2:1-35. doi: 10.1895/wormbook.1.169.1.PMID:24706462
Regulation of the X Chromosomes in Caenorhabditis elegans. Strome S, Kelly WG, Ercan S, Lieb JD. (2014) Cold Spring Harb Perspect Biol. Mar 1;6(3). pii: a018366. doi: 10.1101/cshperspect.a018366.
Genome-wide analysis of condensin binding in Caenorhabditis elegans. Kranz AL, Jiao CY, Winterkorn LH, Albritton SE, Kramer M, Ercan S. (2013) Genome Biol. Oct 14;14(10):R112. PMID: 24125077
Data from this study is available at GEO: GSE45678
H4K20me1 Contributes to Downregulation of X-Linked Genes for C. elegans Dosage Compensation. Vielle A, Lang J, Dong Y, Ercan S, Kotwaliwale C, Rechtsteiner A, Appert A, Chen QB, Dose A, Egelhofer T, Stempor P, Dernburg A, Lieb JD, Strome S, Ahringer J. (2012) PLoS Genet 8(9): e1002933. doi:10.1371/journal.pgen.1002933
An inverse relationship to germline transcription defines centromeric chromatin in C. elegans. Gassmann R, Rechtsteiner A, Yuen KW, Muroyama A, Egelhofer T, Gaydos L, Barron F, Maddox P, Essex A, Monen J, Ercan S, Lieb JD, Oegema K, Strome S, Desai A. (2012) Nature. Apr 8;484(7395):534-7. doi: 10.1038/nature10973
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, Disteche CM. (2011) Nat Genet. Oct 23;43(12):1179-85. doi: 10.1038/ng.948. PMID:22019781
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Ercan S, Lubling Y, Segal E, Lieb JD. (2010) Genome Res. Dec 22.
Data from this study is available at GEO GSE20136
Broad chromosomal domains of histone modification patterns in C. elegans. Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung MS, Ercan S, Ikegami K, Jensen M, Kolasinska-Zwierz P, Rosenbaum H, Shin H, Taing S, Takasaki T, Iniguez AL, Desai A, Dernburg AF, Lieb JD, Ahringer J, Strome S, Liu XS. (2010) Genome Res. Feb;21(2):227-36. doi: 10.1101/gr.115519.110.
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, et al. (2010) Science. Dec 24;330(6012):1775-87. Epub 2010 Dec 22.PMID: 21177976 [PubMed - in process]
The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. Rechtsteiner A., Ercan S., Takasaki T., Phippen TM, Egelhofer TA, Wang W, Kimura H, Lieb JD and Strome S. (2010). PLoS Genet. Sep 2;6(9). pii: e1001091.
The C. elegans dosage compensation complex propagates dynamically and independently of X-chromosome sequence. Ercan S., Dick L.L., Lieb J.D. (2009). Curr Biol. Nov 17;19(21):1777-87. PMCID: PMC2783177 Data from this study is available at GEO GSE16621
C. elegans dosage compensation: A window into mechanisms of domain-scale gene regulation. Ercan S., Lieb, J.D. (2009). Chromosome Res. 17(2):215-27.
The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis.
Whittle C.M., McClinic K.N., Ercan S., Zhang X., Green R.D., Kelly W.G., Lieb J.D. (2008). PLoS Genetics. 4(9):e1000187. PMCID: PMC2522285
Chromatin proteins do double duty. Ercan S., Lieb, J.D. (2008). Cell. 133(5):763-5.
Histone Variants and Nucleosome Occupancy. Ercan S., Carrozza M.J. (2008). In Epigenetics, J. Tost, ed. (Wymondham, UK: Horizon Scientific Press), Chapter 5
X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation. Ercan S., Giresi P.G., Whittle C.M., Zhang X., Green R.D., Lieb, J.D. 2007. Nature Genetics. 39(3):403-8 Data from this study is available at GEO GSE6739
New evidence that DNA encodes its packaging. Ercan S., Lieb, J.D. 2006. Nature Genetics. 38(10):1104-5
Yeast recombination enhancer is stimulated by transcription activation. Ercan S., Reese J.C., Workman, J.L., Simpson, R.T. 2005. Molecular and Cellular Biology 25(18):7976-87
Global Nucleosome Distribution and the Regulation of Transcription in Yeast. Ercan S., Carrozza M.J., Workman, J.L. 2004. Genome Biology. 5(10):243
Global chromatin structure of 45,000 base pairs of chromosome III in a- and alpha-cell yeast and during mating-type switching. Ercan S., Simpson R.T. 2004. Molecular and Cellular Biology. 24(22):10026-35