Dr. Arenas-Mena initiated his research career at the CSIC, Barcelona, studying the transcriptional regulation of water stress genes in plants. During his postdoctoral research at Caltech, Pasadena, he contributed to the characterization of the gene regulatory network that controls the specification of the endomesoderm in sea urchin embryos, and he also studied the expression of Hox cluster genes during embryonic and postembryonic development. At San Diego State University he studied trascriptional multipotency mechanisms in a polychaete model system that has feeding trochophore larva. Ongoing projects relate to the genome-wide characterization transcriptional regulatory mechanisms.


BS. Universitat de Barcelona

Ph.D. CID/CSIC and Universitat de Barcelona

Postdoctoral research at Caltech

Scholarship / Publications

Full List of publications at:

Seleted publications

*Arenas-Mena C. (2017). The Origins of Developmental Gene Regulation.Evolution & Development. 19 (2): 96-107.

Hajdu M., Calle J., Haruna A., Puno A. and *Arenas-Mena C.  (2016). Transcriptional and Post-Transcriptional Regulation of H2A.Z Expression in the Sea Urchin Strongylocentrotus purpuratus.  Development Growth & Differentiation. 58: 727-740. 

Suk-Ying Wong K. and *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. 18 (4):254-266.

*Arenas-Mena C. and Coffman J. (2015). Developmental control of transcriptional and proliferative potency during the evolution of complex multicellularity.  Developmental ­­Dynamics.  244(10): 11093-1201.

*Arenas-Mena C. and Li, A. (2014).  The feeding trochophore of the polychaete Hydroides elegans and the evolution of indirect development. International Journal of Developmental Biology. 58: 575-583  

*Arenas-Mena, C. (2013). The transcription factors Brachyury, Sal, Tbx2/3, Gata1/3, Gata4/6, Brain and Snail, and their roles in gastrulation, endodermal, mesodermal and neural precursors of Hydroides elegans embryos. International Journal of Developmental Biology. 2013;57(1):73-83

*Arenas-Mena, C. (2010). Indirect development, transdifferentiation and the macroregulatory evolution metazoans. Philosophical Transactions of the Royal Society B: Biological Sciences. 365, 653-669.

*Arenas-Mena, C. (2008). The transcription factors HeBlimp and HeT-Brain of an indirectly developing polychaete suggest ancestral endodermal, gastrulation and sensory cell type specification roles. Journal of Experimemtal Zoology. Part B: Molecular and Developmental Evolution. 310B, 567-576.

*Arenas-Mena, C., Wong, K. S-Y and Arandi, N. (2007). Histone H2A.Z expression in two indirectly developing marine invertebrates correlates with undifferentiated and multipotent cells. Evolution and development.  May-Jun; 9(3):231-43.

*Arenas-Mena, C. (2007). Developmental transcriptional-competence model for a histone variant and a unicellular origin scenario for transcriptional-multipotency mechanisms. Evolution and Development. May-Jun; 9(3):208-11.

*Arenas-Mena C, Cameron RA, Davidson EH. (2006). Hindgut specification and cell-adhesion functions of Sphox11/13b in the endoderm of the sea urchin embryo. Development Growth and Differentiation. Sep: 48(7): 463-72.

*Davidson, E. H., et. al. (2002). A genomic Regulatory Network for Development. Science. 295 (5560): 1669-1678 MAR 1.



We study developmental gene regulatory mechanisms and their evolution.  We use sea urchins and a new polychaete model system.  The emphasis is on transcriptional gene regulatory networks (GRNs) (Peter and Davidson, 2015) and we combine gene-targeted and genome-wide approaches.
• Genome-wide characterization of transcriptional regulatory elements
In collaboration with the laboratory of Dr. Charles Danko at Cornell University, we are performing genome-wide analysis of sea urchin transcriptional regulatory elements during development.  We use ATAC-seq (Buenrostro et al., 2013), PRO-seq (Mahat et al., 2016), HiChip (Mumbach et al., 2016) in combination with genome-wide and gene-targeted functional analyses (Arnold et al., 2013; Hajdu et al., 2016) to identify and functionally characterize the enhancers and promoters that control sea urchin development.  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 mechanisms that determine enhancer-promoter specificity and 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) and extended this approach to CylinD, which controls metazoan cell proliferation (Arenas-Mena and Coffman, 2015).   In addition, we have elaborated a method of developmental reprogramming by inducible expression of regulatory genes, 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

• Characterization of in vivo DNA-protein interactions
In collaboration with Dr. Sebastien Poget (CSI) and Dr. Rinat Abzalinov (ASRC-CUNY), we are characterizing the biochemical interactions between transcription factors and regulatory DNA sequences in vivo.  The project involves advanced MS/MS methods.

• 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.


Arenas-Mena, C. (2007). Developmental transcriptional-competence model for a histone variant and a unicellular origin scenario for transcriptional-multipotency mechanisms. Evolution & development 9, 208–211.

Arenas-Mena, C. (2013). Brachyury, Tbx2/3 and sall expression during embryogenesis of the indirectly developing polychaete Hydroides elegans. The International Journal of Developmental Biology 57, 73–83.

Arenas-Mena, C. (2017). The origins of developmental gene regulation. Evolution & Development 19, 96–107.

Arenas-Mena, C. and Coffman, J. A. (2015). Developmental control of transcriptional and proliferative potency during the evolutionary emergence of animals. Developmental Dynamics 244, 11093–1201.

Arenas-Mena, C. and Li, A. (2014). Development of a feeding trochophore in the polychaete Hydroides elegans. Int. J. Dev. Biol 58, 575–583.

Arenas-Mena, C., Cameron, A. R. and Davidson, E. H. (2000). Spatial expression of Hox cluster genes in the ontogeny of a sea urchin. Development 127, 4631–4643.

Arenas-Mena, C., Cameron, R. A. and Davidson, E. H. (2006). Hindgut specification and cell-adhesion functions of Sphox11/13b in the endoderm of the sea urchin embryo. Development, Growth and Differentiation 48, 463–472.

Arenas-Mena, C., Wong, K. S.-Y. and Arandi-Foroshani, N. R. (2007). Histone H2A. Z expression in two indirectly developing marine invertebrates correlates with undifferentiated and multipotent cells. Evolution & development 9, 231–243.

Arnold, C. D., Gerlach, D., stelzer, C., Boryń, Ł. M., Rath, M. and Stark, A. (2013). Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq. Science 339, 1074–1077.

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. and Greenleaf, W. J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods 10, 1213–1218.

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

Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., Waters, C. T., Munson, K., Core, L. J. and Lis, J. T. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat. Protocols 11, 1455–1476.

Mumbach, M. R., Rubin, A. J., Flynn, R. A., Dai, C., Khavari, P. A., Greenleaf, W. J. and Chang, H. Y. (2016). HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nature Methods 13, 919–922.

Peter, I. S. and Davidson, E. H. (2015). Genomic Control Process: development and evolution. San Diego: Academic Press.


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

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

Funding and Collaborators


Nasa logo

NASA Exobiology




NIH logo


Charles Danko, Cornell University

Sevinc Ercan, NYU

Bluma Lesch, Yale University