Smith, S.T. and Jaynes, J.B.  (1996). A conserved region of engrailed, shared among all en-, gsc‑, Nk1-, Nk2-, and msh-class homeoproteins, mediates active transcriptional repression in vivo, Development 122, 3141-3150.

Here, the conserved repressor domain of Engrailed was defined and characterized.  This domain has been used by many laboratories to convert other transcription factors into repressors, helping to reveal their target genes and their modes of action in vivo.

Fujioka, M., Emi-Sarker, Y., Yusibova, G.L., Goto, T., and Jaynes, J.B.  (1999). Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients, Development 126, 2527-2538.

Here it is shown that the complex spatial and temporal pattern of expression of the even skipped gene can be dissected into an array of discrete enhancers, one for each major pattern element.  This serves as a textbook example of how genes are regulated in higher eukaryotic organisms, including humans.

Miki Fujioka, Galina L. Yusibova, Jian Zhou, and James B. Jaynes  (2008). The DNA binding Polycomb-group protein Pleiohomeotic maintains both active and repressed transcriptional states through a single site;  Development 135: 4131-4139.  Cited by 12.  http://dev.biologists.org/cgi/content/full/135/24/4131

This paper describes the discovery of the bifunctional role of one of the DNA-binding Polycomb-group proteins, Pleiohomeotic (Pho), which is required to maintain either the active or the repressed state of a gene in an epigenetic fashion, depending on whether the gene was activated or repressed earlier in development.

Fujioka, M., Sun, G., and Jaynes, J.B.  (2013). The Drosophila eve Insulator Homie Promotes eve Expression and Protects the Adjacent Gene from Repression by Polycomb Spreading.  PLoS-Genetics 9(10): e1003883.  doi:10.1371/journal.pgen.1003883.  http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003883

This work showed that chromatin insulators block Polycomb-mediated repression from spreading along a chromosome, preventing the repression 

Miki Fujioka, Hemlata Mistry, Paul Schedl, and James B. Jaynes  (2016).  Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans. PLoS Genet 12(2): e1005889.   doi:10.1371/journal.pgen.1005889
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005889

Here, the modes of action of the even skipped chromatin insulators homie and nhomie are analyzed using long-range gene regulation in cis and in trans, along with chromosome conformation capture, to show how directional pairing of insulators dictates which enhancers interact with which promoters, thereby orchestrating genome function.

D. Chetverina, M. Fujioka, M. Erokhin, P. Georgiev, J. B. Jaynes, and P. Schedl (2017). Boundaries of loop domains (insulators): Determinants of chromosome form and function in multicellular eukaryotes. Bioessays 38: 1600233, DOI 10.1002/bies.201600233

This paper reviews recent insights into the interplay between gene regulation and chromosome architecture in 3 dimensions.

Jacob Peacock, James B. Jaynes (2017)  Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands, Biochimica et Biophysica Acta (BBA) - General Subjects, ISSN 0304-4165, doi:10.1016/j.bbagen.2017.07.024
http://www.sciencedirect.com/search?qs=&authors=jaynes&pub=Biochimica%20et%20Biophysica%20Acta%20%28BBA%29%20-%20General%20Subjects&volume=&issue=&page=&origin=journal&zone=qSearch&publicationTitles=271022&withinJournalBook=true

This work describes novel methods for analyzing cooperativity in sequence-specific DNA binding by transcription factors in eukaryotic organisms.