Cesar Arenas-Mena

Associate Professor

My lab is interested in the mechanisms that control developmental gene regulation and the crucial transformations that enabled the evolution of complex multicellularity.  Our research combines molecular, developmental, genomic and evolutionary approaches.  We currently study genome-wide quantitative DNA accessibility and transcription at regulatory elements during sea urchin development.  This is helping to map the precise location and activity of proximal and distal gene regulatory elements at the same time that we identify specific mechanisms that set developmental potency in early embryos and stem cells.  We are also performing genomic and developmental reprogramming experiments to functionally test the relationships among DNA, nucleosomes and transcription factors that modulate transcriptional potency.  In collaboration with researchers at Cornell University, Ithaca, and the Institute of Evolutionary Biology in Barcelona, we are further exploring which regulatory mechanisms facilitated the evolution of metazoan developmental gene regulatory networks.     


BS. Universitat de Barcelona

Ph.D. CID/CSIC and Universitat de Barcelona

Postdoctoral research at Caltech

Scholarship and Publications

Full List of publications at:

Selected publications

Arenas-Mena, Cesar, and Serhat Akin. 2023. “Widespread Priming of Transcriptional Regulatory Elements by Incipient Accessibility or RNA Polymerase II Pause in Early Embryos of the Sea Urchin Strongylocentrotus Purpuratus.” Genetics, August, 2023, iyad145. https://doi.org/10.1093/genetics/iyad145

Alexandra G. Chivu, Abderhman Abuhashem, Gilad Barshad, Edward J. Rice, Michelle M. Leger, Albert C. Vill, Wilfred Wong, Rebecca Brady, Jeramiah J. Smith, Athula H. Wikramanayake, César Arenas-Mena, Ilana L. Brito, Iñaki Ruiz-Trillo, Anna-Katerina Hadjantonakis, John T. Lis, James J. Lewis, Charles G. Danko. (Submitted). Evolution of promoter-proximal pausing enabled a new layer of transcription control. bioRxiv 2023.02.19.529146; doi: https://doi.org/10.1101/2023.02.19.529146

Arenas-Mena, C., Miljovska, S., Rice, E. J., Gurges, J., Shashikant, T., Wang, Z., Ercan, S., & Danko, C. G. (2021). Identification and prediction of developmental enhancers in sea urchin embryos. BMC Genomics, 22(1), 751. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07936-0

Arenas-Mena, C. (2017). The origins of developmental gene regulation. Evolution & Development, 19(2), 96–107. https://doi.org/10.1111/ede.12217

Hajdu, M., Calle, J., Puno, A., Haruna, A., & Arenas-Mena, C. (2016). Transcriptional and post-transcriptional regulation of histone variant H2A.Z during sea urchin development. Development, Growth & Differentiation, 9(3), 231–243. https://doi.org/10.1111/dgd.12329

Wong, K. S.-Y., & Arenas-Mena, C. (2016). Expression of GATA and POU transcription factors during the development of the planktotrophic trochophore of the polychaete serpulid Hydroides elegans. Evolution & Development, 254–266. https://doi.org/10.1111/ede.12196

Arenas-Mena, C., & Coffman, J. A. (2015). Developmental control of transcriptional and proliferative potency during the evolutionary emergence of animals. Developmental Dynamics, 244(10), 11093–11201. https://doi.org/10.1002/dvdy.24305

Arenas-Mena, C., & Li, A. (2014). Development of a feeding trochophore in the polychaete Hydroides elegans. The International Journal of Developmental Biology, 58, 575–583. https://doi.org/10.1387/ijdb.140100ca

Arenas-Mena, C. (2010). Indirect development, transdifferentiation and the macroregulatory evolution of metazoans. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1540), 653–669. https://doi.org/10.1098/rstb.2009.0253

Arenas-Mena, C. (2007). Developmental transcriptional-competence model for a histone variant and a unicellular origin scenario for transcriptional-multipotency mechanisms. Evolution & Development, 9(3), 208–211. https://doi.org/10.1111/j.1525-142X.2007.00156.x

Arenas-Mena, C., Wong, K. S.-Y., & Arandi-Foroshani, N. R. (2007). Histone H2A. Z expression in two indirectly developing marine invertebrates correlates with undifferentiated and multipotent cells. Evolution & Development, 9(3), 231–243. https://doi.org/10.1111/j.1525-142X.2007.00155.x

Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C.-H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Brown, C. T., Livi, C. B., Revilla, R., Rust, A. G., Pan, Z., Schilstra, M. J., Clarke, P. J. C., Arnone, M. I., Rowen, L., … Bolouri, H. (2002). A Genomic Regulatory Network for Development. Science, 295(5560), 1669–1678. https://doi.org/10.1126/science.1069883


• Genome-wide characterization of transcriptional regulatory elements
We are performing genome-wide analysis of sea urchin transcriptional regulatory elements during development. We use ATAC-seq, PRO-seq to identify and functionally characterize the enhancers and promoters that control sea urchin development (Arenas-Mena and Akin, 2023; Arenas-Mena et at., 2021).  The research questions relate to transcriptional networks and the unicellular origins of developmental gene regulation (Arenas-Mena, 2017).  In particular, we are interested in the unicellular precursors of distal enhancers.

Genome-Wide data set including ATAC-seq, PolII Chip-seq, PRO-seq at the H2A.Z locus

• Developmental control of transcriptional and proliferative potency
My original hypothesis of a histone variant H2A.Z role in developmental potency (Arenas-Mena, 2007; Arenas-Mena et al., 2007) has been validated experimentally (Arenas-Mena and Coffman, 2015).  H2A.Z is associated with transcriptional regulatory DNA, where it promotes an open chromatin state accessible to sequence-specific transcription factors.  We study of the cis-regulatory machinery that controls the developmental expression of H2A.Z (Hajdu et al., 2016).   In addition, we have elaborated a method of developmental reprogramming Doxycycline-inducible expression , and we are testing how H2A.Z maintains  transcriptional potency during development.

Outline of cis-regulatory analysis of H2A.Z including ATAC-seq data, major BAC recombineering construct and its GFP expression


• A new polychaete system relevant to bilaterian body plan evolution
We have spearheaded the implementation of methods and resources in the annelid Hydroides elegans, an indirectly developing polychaete with feeding trochophore relevant to bilaterian body plan evolution (Arenas-Mena and Li, 2014). We are currently undertaking transgenic and genomics approaches in this new model.

Current Lab Members

Serhat Akin, PhD student, MCD program.

Syeda Batool. Master's Student

Former Lab Members


Mihai Hajdu


Basimah Sibawe
Maria Graham
Jasmine Calle
Andrea Puno
Aminat Haruna    
Justin Gurges
Krystal Baird
Winnie Darius
Navid Arandi
Tia Leung
Fedan Avrumova
Crystal Lucas
Merlin Raj
Jose Alvarenga
Leila Lager
Alfonso Clemente    
Andrew Fischler    
Ashley Woods    
Joseph Deas    
Kasey Mobley    
Moriel Khaykin    
Rossana Cruciata    
Charisse White    
Dimitri Mazidis     
Jacob Maddela
Lisa Lamanna    
Mark Montano    
Monique Brewton     
Natalie Birkin    
Ojeh Agnes    


Zihe Wang
Kimberly Suk-Ying Wong    
Ava Li,    
Shona Shonghai    
Nayomi Fernando    
Dasari Srividya    
Triveni Golagani    

Strongylocentrotus purpuratus 

Research in sea urchins has lead the experimental characterization of developmental gene regulatory networks thanks to their experimental and biological.  Genomic resouces are available at EchinoBase. Cover from (Arenas-Mena et al., 2000). 

Cover of Development 2000 including sea urchin blastula, larva, metamorphosing lava and  juvenile.

Arenas-Mena et. al, 2000


Adult Sea Urchin


Hydroides elegans

Arenas-Mena et. al, 2006

Hydroides elegans

We have lead efforts to develop a polychaete model system with spiral cleavage and feeding trochophore that has great evolutionary and developmental relevance (Arenas-Mena and Li, 2014).  Cover from (Arenas-Mena, 2013). 

Cover of The International Journal of Developmental Biology. Stages of Hydroides elegans including adult in tube, embryo, and larva

Arenas-Mena, 2013

Nasa logo

NASA Exobiology



NIH logo


Charles Danko, Cornell University

CUNY Graduate Center 

Developmental Biology 


Genomics Laboratory
Developmental Biology
Gene Regulatory Systems
Cell Biology
Evolution of Development
Invertebrate zoology
General Biology


Cesar Arenas-Mena

Contact Information

Office: Building 6S Room 140
Usually after each class or by appointment

Research opportunities

I am currently recruiting Ph.D. students from the graduate programs in

I am also accepting highly motivated Master's and undergraduate students.