@misc{sikes_mcmillan_bradshaw_2010, title={The Center of Accessibility: D beta Control of V(D)J Recombination}, volume={58}, ISSN={["0004-069X"]}, DOI={10.1007/s00005-010-0101-2}, abstractNote={Developmental patterning of antigen receptor gene assembly in lymphocyte precursors correlates with decondensation of the chromatin surrounding individual gene segments. Ongoing V(D)J recombination is associated with hyperacetylation of histones H3 and H4 and the expression of sterile germline transcripts across the region of recombinational accessibility. Likewise, histone acetyltransferase and SWI/SNF chromatin remodeling complexes each appear to be required for recombination, and the PHD-finger of RAG-2 preferentially associates with recombination signal sequence (RSS) chromatin that contains H3 trimethylated on lysine 4. However, the regulatory mechanisms that direct chromatin alteration and rearrangement have proven elusive, due in large part to the interdependency of individual stages in gene activation, our limited understanding of functional significance of changes to the histone code, and the difficulty of modeling recombinational accessibility in existing experimental systems. Examining Tcrb assembly in developing thymocytes, we review the central roles of RSS elements and germline promoters as foci for epigenetic reorganization of recombinationally accessible gene segments in light of recent findings and persistent questions.}, number={6}, journal={ARCHIVUM IMMUNOLOGIAE ET THERAPIAE EXPERIMENTALIS}, author={Sikes, Michael L. and McMillan, Ruth E. and Bradshaw, Justin M.}, year={2010}, month={Dec}, pages={427–433} }
 @article{sikes_bradshaw_ivory_lunsford_mcmillan_morrison_2009, title={A streamlined method for rapid and sensitive chromatin immunoprecipitation}, volume={344}, ISSN={["0022-1759"]}, DOI={10.1016/j.jim.2009.03.007}, abstractNote={We report a streamlined procedure to efficiently carry samples from chromatin to qPCR-compatible DNA in as little as 4 h. We use this streamlined ChIP to quantify histone H3 modifications at active (cad) and repressed (T early alpha) promoters in a Rag1-deficient pro-T cell line after 1–2 h IP. We further show that the protocol readily quantified histone modifications in chromatin from 104 Rag-deficient DN thymocytes. Taken together, these data outline a simple, cost-effective procedure for efficient ChIP analysis.}, number={1}, journal={JOURNAL OF IMMUNOLOGICAL METHODS}, author={Sikes, Michael L. and Bradshaw, Justin M. and Ivory, Wendell T. and Lunsford, Jessica L. and McMillan, Ruth E. and Morrison, Clayton R.}, year={2009}, month={May}, pages={58–63} }
 @article{mcmillan_sikes_2009, title={Promoter activity 5 ' of D beta 2 is coordinated by E47, Runx1, and GATA-3}, volume={46}, ISSN={["0161-5890"]}, DOI={10.1016/j.molimm.2009.06.013}, abstractNote={V(D)J recombination involves the stepwise assembly of B and T cell receptor genes as lymphocytes progress through the early stages of development. While the mechanisms that restrict each step in recombination to its appropriate developmental stage are largely unknown, they share many of the components that regulate transcription. For example, enhancer-dependent modifications in histone acetylation and methylation are essential for both germline transcription and rearrangement of antigen receptor genes. Promoters positioned proximal to individual D and J gene segments in Tcra, Tcrb, Tcrd, IgH, and Igk also contribute to antigen receptor gene assembly, though their effects appear more localized than those of enhancers. Tcrb assembly initiates with D-to-J joining at each of the two D-J-C gene segment clusters in DN1/2 thymocytes. DJ joints are fused with Vbeta elements to complete Tcrb recombination in DN3 cells. We have previously shown that Dbeta2 is flanked by upstream and downstream promoters, with the 5' promoter being held inactive until D-to-J recombination deletes the NFkappaB-dependent 3' promoter. We now report that activity of the 5' promoter reflects a complex interplay among Runx1, GATA-3, and E47 transcription factors. In particular, while multiple E47 and Runx1 binding sites clustered near the Dbeta2 5'RS and overlapping inr elements define the core 5'PDbeta2, they act in concert with an array of upstream GATA-3 sites to overcome the inhibitory effects of a 110bp distal polypurine.polypyrimidine (R.Y) tract. The dependence of 5'PDbeta2 on E47 is consistent with the reported role of E proteins in post-DN1 thymocyte development and V-to-DJbeta recombination.}, number={15}, journal={MOLECULAR IMMUNOLOGY}, author={McMillan, Ruth E. and Sikes, Michael L.}, year={2009}, month={Sep}, pages={3009–3017} }
 @article{mcmillan_sikes_2008, title={Differential activation of dual promoters alters D beta 2 germline transcription during thymocyte development}, volume={180}, ISSN={["0022-1767"]}, DOI={10.4049/jimmunol.180.5.3218}, abstractNote={Abstract}, number={5}, journal={JOURNAL OF IMMUNOLOGY}, author={McMillan, Ruth E. and Sikes, Michael L.}, year={2008}, month={Mar}, pages={3218–3228} }