Epigenomic Regulation of Stem Cell Maintenance and Differentiation
1. Pattison JM, Melo SP, Piekos SN, Torkelson JL, Bashkirova E, Mumbach MR, Rajasingh C, Zhen HH, Li L, Liaw E, Alber D, Rubin AJ, Shankar G, Bao X, Chang HY, Khavari PA, Oro AE. Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. Nat Genet. 2018 Dec;50(12):1658-1665.
2. Bao X*, Siprashvili Z, Shenoy R, Rios E, Zarnegar B, Natalie N, Qu K, Mah A, Webster D, Wozniak G, Rubin A, Tao S, Wysocka J, Khavari PA. CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-renewing Somatic Tissue. Dev Cell. 2017 Oct 23;43(2):227-239.
[* Co-corresponding author]
3. Bao X*, Rubin A, Qu K, Zhang J, Giresi P, Chang HY and Khavari PA*. A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biology. 2015 Dec 18;16(1):284. [*Co-corresponding Author]
4. Bao X, Tang J, Lopez-Pajares V, Tao S, Qu K, Crabtree GR and Khavari PA. ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4. Cell Stem Cell. 2013 Feb 7;12(2):193-203.
This work characterized the role of ACTL6a/BAF53a as a key regulator that maintains the progenitor state by suppressing differentiation. Mechanistically, this work identified KLF4 as a key down stream transcription factor that is repressed by ACTL6a in progenitor state to inhibit differentiation. This work further demonstrated that ACTL6a suppresses differentiation by preventing the genomic targeting of the SWI/SNF chromatin remodeling complex to differentiation genes.
* Previewed by Cell Stem Cell.
* Recommended by F1000 Prime.
5. Cai W, Wang C, Li Y, Yao C, Shen L, Liu S, Bao X, Schnable PS, Girton J, Johansen J, Johansen KM. Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 kinase mediated histone H3S10 phosphorylation in Drosophila. Nucleic Acid Res. 2014; 42(9):5456-67.
6. Wang C, Li Y, Cai W, Bao X, Girton J, Johansen J, Johansen KM. Histone H3S10 phosphorylation by the JIL-1 kinase in pericentric heterochromatin and on the 4th chromosome creates a composite H3S10phK9mes epigenetic mark. Chromosoma. 2014 Jun; 123(3):273-80.
7. Wang C, Yao C, Li Y, Cai W, Bao X, Girton J, Johansen J, Johansen KM. Evidence against a role for the JIL-1 kinase in H3S28 phosphorylation and 14-3-3 recruitment to active genes in Drosophila. PLoS One. 2013 Apr 30;8(4):e62484.
8. Li Y, Cai W, Wang C, Yao C, Bao X, Deng H, Girton J, Johansen J, Johansen KM. Domain requirements of the JIL-1 tandem kinase for histone H3 serine 10 phosphorylation and chromatin remodeling in vivo. J Biol Chem. 2013 Jul 5;288(27):19441-9.
9. Wang C, Cai W, Li Y, Deng H, Bao X, Girton J, Johansen J, Johansen KM. The epigenetic H3S10 phosphorylation mark is required for counteracting heterochromatic spreading and gene silencing in Drosophila melanogaster. J Cell Sci. 2011 Dec 15;124(Pt 24):4309-17.
10. Johansen KM, Cai W, Deng H, Bao X, Zhang W, Girton J, Johansen J. Polytene chromosome squash methods for study transcription and epigenetic chromatin modification in Drosophila using antibodies. Methods. 2009 Aug;48(4):387-97.
11. Bao X, Cai W, Deng H, Zhang W, Krencik R, Girton J, Johansen J, Johansen KM. The COOH-terminal domain of the JIL-1 H3S10 kinase interacts with histone H3 and is required for correct targeting to chromatin. The Journal of Biological Chemistry. 2008 Nov 21;283(47):32741-50.
This work highlighted the importance of the C-terminal non-kinase domain both in targeting the JIL-1 kinase to chromatin via direct binding to histone H3, as well as the in maintaining the higher-order chromatin structure of Drosophila.
12. Cai W, Bao X, Deng H, Girton J, Johansen J, Johansen KM. Pol II mediated transcription at active loci does not require H3S10 phosphorylation in Drosophila. Development. 2008 Sep;135(17):2917-25.
13. Deng H, Bao X, Cai W, Blacketer MJ, Belmont AS, Girton J, Johansen J, Johansen KM. Ectopic histone H3S10 phosphorylation causes chromatin structure remodeling in Drosophila. Development. 2008 Feb;135(4):699-705.
14. Deng H*, Bao X*, Zhang W, Girton J, Johansen J, Johansen KM. Reduced Levels of Su(var)3-9 but not Su(var)2-5(HP1) Counteract the Effects on Chromatin Structure and Viability in Loss-of-Function Mutants of the JIL-1 Histone HS310 Kinase. Genetics. 2007 Sep;177(1):79-87.(* These authors contributed equally to this work)
The findings indicate that while Su(var)3-9 histone methyltransferase activity is a major factor in the lethality and chromatin structure perturbations associated with loss of the JIL-1 histone H3S10 kinase, these effects are likely to be uncoupled from HP1.
15. Bao X, Deng H, Johansen J, Girton J, Johansen KM. Loss-of-Function Alleles of the JIL-1 Histone H3S10 Kinase Enhance Position-Effect Variegation at Pericentric Sites in Drosophila Heterochromatin. Genetics. 2007 Jun;176(2):1355-8.
This work supports a functional role for JIL-1 in maintaining euchromatic chromatin and counteracting heterochromatic spreading and gene silencing.
* Selected as “issue highlights” by Genetics journal.
16. Bao X, Girton J, Johansen J, Johansen KM. The lamin Dm0 allele Ari3 acts as an enhancer of position effect variegation of the wm4 allele in Drosophila. Genetica. 2007 Mar;129(3):339-42.
The results indicate that lamins may be involved in regulating gene silencing and heterochromatin spreading.
17. Rath U, Ding Y, Deng H, Qi H, Bao X, Zhang W, Girton J, Johansen J, Johansen KM. The chromodomain protein, Chromator, interacts with JIL-1 kinase and regulates the structure of Drosophila polytene chromosomes. Journal of Cell Science. 2006 Jun 1;119(Pt 11):2332-41.
18. Lerach S, Zhang W, Bao X, Deng H, Girton J, Johansen J, Johansen KM. Loss-of-function alleles of the JIL-1 kinase are strong suppressors of position effect variegation of the wm4 allele in Drosophila. Genetics. 2006 Aug;173(4):2403-6.
19. Zhang W, Deng H, Bao X, Lerach S, Girton J, Johansen J, Johansen KM. The JIL-1 histone H3S10 kinase regulates dimethyl H3K9 modifications and heterochromatic spreading in Drosophila. Development. 2006 Jan;133(2):229-35.
20. Lerach S, Zhang W, Deng H, Bao X, Girton J, Johansen J, Johansen KM. JIL-1 kinase, a member of the male-specific lethal (MSL) complex, is necessary for proper dosage compensation of eye pigmentation in Drosophila. Genesis. 2005 Dec;43(4):213-5.
21. Bao X, Zhang W, Krencik R, Deng H, Wang Y, Girton J, Johansen J, Johansen KM. The JIL-1 kinase interacts with lamin Dm0 and regulates nuclear lamina morphology of Drosophila nurse cells. Journal of Cell Science. 2005 Nov 1;118(21):5079-87.
This paper provides the first direct evidence that the interactions between chromatin and the nuclear lamina are critical for the gene expression programs that regulate development.
* Designated as a Faculty of 1000 paper.
* Selected as “editor’s pick” by Journal of Cell Science.
* Chosen as the cover paper for the issue of November 2005 by Journal of Cell Science.
22. Deng H, Zhang W, Bao X, Martin JN, Girton J, Johansen J, Johansen KM. The JIL-1 kinase regulates the structure of Drosophila polytene chromosomes. Chromosoma. 2005 Aug;114(3):173-82.