Bao Lab         

Gene Regulation of Adult Stem Cell Maintenance & Human Tissue Regeneration

Key Contributions to the field of Epidermal Gene Regulation:

1. CDK9 kinase activity switch underlies the earliest events of epidermal differentiation

   Combining chemical inhibitors together with RNAi, RNA-seq and ChIP-seq, we identified that the AFF1 scaffold of the super-elongation complex cooperates with HEXIM1 to hold CDK9 in an inactive state in epidermal progenitors. Activation of CDK9 triggers rapid activation of their direct targets within a couple of hours, and to subsequently upregulate several differentiation-activating transcription factors such as ZNF750, OVOL1 and GRHL3. 

2. Epidermal differentiation is influenced by transcription termination in the INTRONS

    We applied 3'READS+ for the first time in epithelial tissue, and identified 373 genes that are differentially regulated by premature transcription termination in the introns, comparing the progenitor-state versus terminally differentiated keratinocytes. This phenomenon is also known as intronic polyadenylation (IpA). 

    We identified that the genes regulated by IpA in epidermal differentiation include GRHL3, a transcriptional factor essential for activating terminal differentiation. Using CRISPR KO, we confirmed that IpA is essential for suppressing GRHL3 function in progenitor-state keratinocytes. Using a combination of protein complex purification and targeted RNAi screen, we discovered that GRHL3 IPA is controlled through the cooperation between the transcription termination regulator CPSF and the splicing regulator HNRNPA3. 

2. Epidermal progenitor maintenance requires the intact function of protein arginine methyltransferase 1 (PRMT1)

    Using both human and mouse models, we found that the depletion of PRMT1 abolished the epidermal progenitor function. Using tandem affinity purification, we discovered that PRMT1 interacts with a number of transcription regulators, RNA-binding proteins, and kinases. We further elucidated that PRMT1 is phosphorylated by the casein kinase CSNK1a1, and this phosphorylation controls PRMT1's chromatin binding. 

4. Development of the on-plate ATAC-seq and identification of BAF-p63 cooperation

    We discovered that the loss of the catalytic subunits of the BAF complex, BRG1 and BRM, selectively leads to decreased chromatin accessibility at the p63 binding sites with p63 motif. Using ChIP-seq, we further demonstrated that p63 and BAF cooperatively bind to maintain open chromatin landscape. 

5. The actin-like subunit of the BAF complex BAF53a is essential for epidermal progenitor Maintenance

    The actin-like subunit ACTL6A/BAF53A is highly enriched in the progenitor state, and it is downregulated during epidermal differentiation. Using both mouse and human epidermal tissue models, we found that ACTL6a depletion induced premature differentiation of epidermal cells in the progenitor compartment. We further identified the transcription activator KLF4 as a key downstream factor repressed by ACTL6a. 

TOTAL List of Publications

Lloyd SM, Leon DB, Brady MO, Rodriguez D, McReynolds MP, Kweon J, Neely AE, Blumensaadt LA, Ho PJ, Bao X.CDK9 activity switch associated with AFF1 and HEXIM1 controls differentiation initiation from epidermal progenitors. Nature Communications, 2022 July 29; 13, 4408

Godsel LM, Roth-Carter QR, Koetsier JL, Tsoi L, Huffine AL, Broussard JA, Fitz GN, Lloyd SM, Kweon J, Burks HE, Hegazy M, Amagi S, Harms PW, Xing X, KirmaJ, Johnson JL, Urciuoli G, Doglio LT, Swindell WR, Awatramain R, Sprecher E, Bao X, Cohen-Barak, Missero C, Gudjonsson JE, Green KJ. Translational Implications of Th17-skewed Inflammation Due to Genetic Deficiency of a Cadherin Stress Sensor. J. Clin Invest. 2021 Dec 14; e144363. 

Dong A, Bao X. GPSmatch: An R package for comparing genomic-binding profile similarity among transcriptional regulators using customizable databases. Bioinformatics. 2021 Oct 21; 38(3): 853-855. 

Droll S, Bao X. Oh, the Mutations You’ll acquire! A systematic overview of cutaneous squamous cell carcinoma. Cell Physiol Biochem, 2021 Sep 22;55(S2):89-119. 

Chen X, Lloyd SM, Kweon J, Gamalong G, Bao X. Epidermal Progenitors Suppress GRHL3-mediated Differentiation through Intronic Polyadenylation by CPSF-HNRNPA3 Collaboration. Nature Communications, 2021 Jan 19;12(1):448. 
     News coverage by “Northwestern Now”, “EurekAlert!”, “infosurhoy”, “ScienMag”, “The Medical News”, “EOSWetenschap”, “MedicalXpress”. 

Hua ZY, Hansen JN, He M, Dai SK, Choi Y, Fulton MD, Lloyd SM, Szemes M, Sen J, Ding HF, Angelastro JM, Fei X, Li HP, Wu CR, Yang SY, Malik K, Bao X, George Zheng Y, Liu CM, Schor NF, Li ZJ, Li XG. PRMT1 promotes neuroblastoma cell survival through ATF5. Oncogenesis. 2020 May 15;9(5):50.

Ho PJ, Lloyd SM, Bao X. Unwinding chromatin at the right places: how BAF is targeted to specific genomic locations during development. Development. 2019 Sep 30;146(19). 

Neely AE and Bao X. Nuclei Isolation Staining (NIS) Method for Imaging Chromatin-Associated Proteins in Difficult Cell Types. Current Protocols in Cell Biology. 2019. 

Lloyd SM and Bao X. Pinpointing the Genomic Localizations of Chromatin-Associated Proteins: The Yesterday, Today, and Tomorrow of ChIP-seq. Current Protocols in Cell Biology. 2019 Sep;84(1):e89. 

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. Nature Genetics. 2018 Dec;50(12):1658-1665. 

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 Oct23;43(2)227-239. [* Co-corresponding author]

Bao X*, Rubin AJ, Qu K, Zhang J, Giresi PG, 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 Biol. 2015 Dec 18;16(1):284. [* Co-corresponding author]

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. 
     Previewed by Cell Stem Cell. 
     Recommended by F1000 Prime.

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. 

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. 

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.

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. 

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.

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.

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. 

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.

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. 

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)

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.  
Selected as “issue highlights” by Genetics journal. 

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.

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.

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.

 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.

 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.

 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.
            ¶ 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.

 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.