My research interests are focused on how gene regulatory traits are encoded in DNA sequence. Most of my work has been done in the context of animal embryos. Using whole-genome sequences from related organisms, I am interested in identifying and parsing this regulatory logic for entire genomic sets of regulatory modules underlying either key phylogenetic transitions or important developmental mechanisms, such as morphogen gradient systems. My interests span the gamut of eukaryotic gene regulation (evolution, biochemistry, molecular genetics, genomics). My motivation is both in learning about these systems and in extracting principles on the nature of organismal evolution. My work is currently funded by the National Science Foundation. I am currently seeking graduate students and post-docs with similar interests.
Listed below are recent publications, organized by topic.
(1) Identifying the regulatory logic and evolution of morphogen concentration threshold-specific responses
Crocker, J., Potter, N. and Erives, A. (2010) Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers. Nature Communications 1:99 doi: 10.1038/ncomms1102.
Crocker, J. and Erives, A. (2008) A closer look at the eve stripe 2 enhancers of Drosophila and Themira. PLoS Genetics 4(11):e1000276
Crocker, J., Tamori, Y. and Erives, A. (2008) Evolution acts on enhancer organization to fine-tune gradient threshold readouts. PLoS Biology 6(11):e263.
Erives, A., Levine, M. (2004) Coordinate enhancers share common organizational features in the Drosophila genome. Proc. Nat. Acad. Sci. U.S.A. 101:3851-6.
Markstein, M., Zinzen, R., Markstein, P., Yee, K., Erives, A., Stathopoulos, A., Levine, M. (2004) A regulatory code for neurogenic gene expression in the Drosophila embryo. Development 131: 2387-94.
Stathopoulos, A., Van Drenth, M., Erives, A., Markstein, M. and Levine, M. (2002) Whole-Genome Analysis of Dorso- Ventral Patterning in the Drosophila Embryo. Cell 111: 687-701.
(2) Identifying the regulatory logic of the B4.1 lineage-specific enhancers of the ascidian, Ciona intestinalis
Kugler, J.E., Gazdoiu, S., Oda-Ishii, I., Passamaneck, Y.J., Erives, A.J. and Di Gregorio, A. (2010) Temporal regulation of the muscle gene cascade by Macho1 and Tbx6 transcription factors in Ciona intestinalis. J Cell Science 123:2453-2463.
Erives, A. (2009) Non-homologous structured CRMs from the Ciona genome. J Comp Biology 16:369-77.
Erives, A., Levine, M. (2001) Cis-regulation of ascidian tail muscle genes. Proceedings of the First International Symposium on the Biology of Ascidians. Springer-Verlag, Tokyo 2001.
Erives, A. and Levine, M. (2000) Characterization of a maternal T-box gene in Ciona intestinalis. Developmental Biology 225: 169-178.
Erives, A., Corbo, J.C., Levine, M. (1998) Lineage-specific regulation of the Ciona snail gene in the embryonic mesoderm and neuroectoderm. Developmental Biology 194: 213-225.
(3) Identifying the regulatory logic, evolutionary origin and ancestral role of the Myc:Max regulon
Brown, S., Cole, M. and Erives, A.J. (2008) Evolution of the holozoan ribosome biogenesis regulon. BMC Genomics 9:442.
(4) Developmental regulatory biology of chordate features in Ciona intestinalis
Hotta, K., Takahashi, H., Erives, A., Levine, M. and Satoh, N. (1999) Temporal expression patterns of 39 Brachyury-downstream genes associated with notochord formation in the Ciona intestinalis embryo. Development Growth & Differentiation 41: 657-664.
Takahashi, H., Hotta, K., Erives, A., Di Gregorio, A., Zeller, R.W., Levine, M. and Satoh, N. (1999) Brachyury downstream notochord differentiation in the ascidian embryo. Genes & Development 13: 1519-1523.
Corbo, J.C., Erives, A., Di Gregorio, A., Chang, A. and Levine, M. (1997) Dorsoventral patterning of the vertebrate neural tube is conserved in a protochordate. Development 124: 2335-2344.
(5) How a journal club paper on identifying tRNA genes in archaeal genomes led to a specific stereochemical model for the combined evolutionary origin of (i) the proteinogenic amino acids, (ii) amino acid homochirality, (iii) ribose sugar homochirality, and (iv) the genetic code via anti-codon cradles, in an ancient aminoacylated RNA world (a primordial world in which RNAs and amino acids co-existed)
Erives, A. (2011). A model of proto-anti-codon RNAs requiring L-amino acid homochirality. J. Molecular Evolution doi 10.1007/s00239-011-9453-4.