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 studied the expression of Hox cluster genes during embryonic and postembryonic development and contributed to the characterization of the gene regulatory network that controls endomesoderm specification. 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 during development, metazoan evolution and transcriptional multipotency.
BS. Universitat de Barcelona
Ph.D. CID/CSIC and Universitat de Barcelona
Postdoctoral research at Caltech
Full List of publications at:
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. (2013). Brachyury, Tbx2/3 and sall expression during embryogenesis of the indirectly developing polychaete Hydroides elegans. The International Journal of Developmental Biology, 57(1), 73–83. https://doi.org/10.1387/ijdb.120056ca
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 Experimental Zoology Part B: Molecular and Developmental Evolution, 310B(7), 567–576. https://doi.org/10.1002/jez.b.21225
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
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, PRO-seq to identify and functionally characterize the enhancers and promoters that control sea urchin development (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 mechanisms that determine enhancer-promoter specificity and the unicellular precursors of distal enhancers.
• 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.
• 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.
Former Lab Members
Kimberly Suk-Ying Wong
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).
Arenas-Mena et. al, 2000
Arenas-Mena et. al, 2006
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).
Funding and Collaborators
CUNY Graduate Center
Gene Regulatory Systems
Evolution of Development