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In eukaryotic organisms chromatin plays a key role in the highly efficient regulation of gene expression. The genome is organized into discrete structural and functional chromatin domains with different potentials for gene expression. Our major goal is to understand the mechanisms underlying the establishment and maintenance of genomic domains in the highly tractably yeast model system by addressing the following questions.
How do silencers initiate the formation of transcriptionally silent chromatin?
Silencers are small regulatory sequences flanking HML and HMR in yeast that are responsible for the initiation of formation of a special silent chromatin across these loci. An outstanding question concerning silencer function is whether they act in an orientation-dependent or –independent fashion. We have recently demonstrated that a silencer is intrinsically unidirectional but its genomic context can regulate its directionality. We are examining cis-acting DNA elements and trans-acting protein factors that contribute to the determination of the directionality of silencers.
How do barriers block the propagation of silent chromatin?
The Sir complex is an integral part of silent chromatin. It is recruited to the silencers during the initiation of formation of silent chromatin. Sir complexes have the ability to spread along the chromatin fiber in a step-by-step fashion thereby encroaching upon transcriptionally active chromatin. This poses the question of how an active chromatin domain is protected from adjacent silent chromatin. We and others have identified various special sequences referred to as barrier elements that could block the spread of silent chromatin. Barriers exist near the silent HM loci but the mechanisms of their functions have not been resolved. We are investigating how these elements restrict silent chromatin to limited domains.
How does silent chromatin repress gene expression?
Silent chromatin in yeast is equivalent to the condensed heterochromatin in higher organisms. Compared to active chromatin (euchromatin), silent chromatin has a more compact structure, is associated with reduced histone acetylation, and is covered by the Sir silencing complexes. It is generally believed that the compactness of silent chromatin hinders the initiation and/or elongation of transcription by RNA polymerases. However, this contention is challenged by our recent findings. We are currently testing the hypothesis that it is histone hypoacetylation, not the special chromatin structure that is mainly responsible for the repression of genes residing in silent loci.
How does a chromatin-associated histone acetyl transferase (HAT) acetylate nucleosomes at a distance?
Histone acetylation by HATs is intimately linked to gene expression, as transcriptionally active chromatin domains are usually hyperacetylated. HATs are recruited to gene enhancers/promoters by transcriptional activators. We have recently shown that a targeted HAT could acetylate at least eight consecutive nucleosomes on either side. We are examining the mechanism(s) underlying how a targeted HAT “reaches” and acetylates nucleosomes at a distance.
- Siler, J., Xia, B., Wong, C., Kath, M., Bi, X. 2017 Cell cycle-dependent positive and negative functions of Fun30 chromatin remodeler in DNA damage response. DNA Repair (Amst). 50: 61-70.
- Bi., X., Ren, Y., Kath, M. 2016 Proliferating cell nuclear antigen (PCNA) contributes to the high-order structure and stability of heterochromatin in Saccharomyces cerevisiae. Chromosome Res DOI 10.1007/s10577-016-9540-x.
- Bi, X. 2015 Mechanism of DNA damage tolerance. World J Biol Chem. 6: 48-56.
- Bi, X., Yu, Q., Siler, J., Li, C., Khan, A. 2015 Functions of Fun30 chromatin remodeler in regulating cellular resistance to genotoxic stress. PLOS ONE 10(3):e0121341.
- Bi, X. (2014) Heterochromatin structure: lessons from the budding yeast. IUBMB Life. 66: 657-666. (Review)
- Zhang, L., Chen, H., Bi, X., and Gong, F. 2013 Detection of an altered heterochromatin structure in the absence of the nucleotide excision repair protein Rad4 in Saccharomyces cerevisiae. Cell Cycle 12:15, 2435-2442.
- Bi, X. 2012 Functions of chromatin remodeling factors in heterochromatin formation and maintenance. Sci. China – Life Sci. 55, 89-96 (Review)
- 2012Functions of Protosilencers in the Formation and Maintenance of Heterochromatin in Saccharomyces cerevisiae.PLoS One7(5):e37092.
- 2011Differential contributions of histone H3 and H4 residues to heterochromatin structure.Genetics188: 291-308.
- 2011Roles of chromatin remodeling factors in the formation and maintenance of heterochromatin structure.J Biol Chem.286:14659-14669.
- Yu, Q., Kuzmiak, H., Olsen, L., Kulkarni, A., Fink, E., Zou, Y., and X. Bi. 2010. Saccharomyces cerevisiae Esc2p Interacts with Sir2p through a Small Ubiquitin-like Modifier (SUMO)-binding Motif and Regulates Transcriptionally Silent Chromatin in a Locus-dependent Manner. J. Biol. Chem. 285: 7525-7536.
- Yu, Q., Kuzmiak, H., Zou, Y., Olsen, L., Defossez, P.-A., and X. Bi. 2009. Saccharomyces cerevisiae linker histone Hho1p functionally interacts with core histone H4 and negatively regulates the establishment of transcriptionally silent chromatin. J. Biol. Chem. 284:740-750.
- Zou, Y., and X. Bi. 2008. Positive roles of SAS2 in DNA replication and transcriptional silencing in yeast. Nucleic Acids Res. 36: 5189-5200.
- 2006. Asymmetric positioning of nucleosomes and directional establishment of transcriptionally silent chromatin by Saccharomyces cerevisiae silencers.Mol. Cell Biol26: 7806-7819.
- 2006. Position effect on the directionality of silencer function in Saccharomyces cerevisiae.Genetics174: 203-213.
- 2006. Histone H1 of Saccharomyces cerevisiae inhibits transcriptional silencing.Genetics173: 579-587.
- 2006. Structural analyses of Sum1-1p-dependent transcriptionally silent chromatin in Saccharomyces cerevisiae.J. Mol. Biol356: 1082-1092.
- 2006. Mechanism of the long range anti-silencing function of targeted histone acetyltransferases in yeast.J. Biol. Chem281: 3980-3988.
- 2005. Mutations in the nucleosome core enhance transcriptional silencing.Mol. Cell Biol25: 1846-1859.
- 2004. Regulation of transcriptional silencing in yeast by growth temperature.J. Mol. Biol344: 893-905.
- 2004. Formation of boundaries of transcriptionally silent chromatin by nucleosome-excluding structures.Mol. Cell Biol24: 2118-2131.
- 2003. A targeted histone acetyltransferase can create a sizable region of hyperacetylated chromatin and counteract the propagation of transcriptionally silent chromatin.Genetics165: 115-125.
- 2003. Rap1p and other transcriptional regulators can function in defining distinct domains of gene expression.Nucl. Acids Res31: 1224-1233.
- 2002. Domains of gene silencing near the left end of chromosome III in S. cerevisiae.Genetics160: 1401-1407.
- 2001. Chromosomal boundaries in S. cerevisiae.Curr. Opin. Genet. Dev11: 199-204.
- 1999. UASrpg can function as a heterochromatin boundary element in yeast.Genes Dev13: 1089-1101.
- 1999. Cell type determination in yeast.Development: Genetics, Epigenetics and Environmental Regulation, ed. N. Russo, D. Cove, L. Edgar, F. Jarenisch and F. SalaminiSpringer-Verlag, Heidelberg, Germany: 49-65.
- 1999. The yeast HML I silencer defines a heterochromatin domain boundary by directional establishment of silencing.Proc. Natl. Acad. Sci. USA96: 11934-11939.
- 1997. DNA within transcriptionally silenced chromatin assumes a distinct topology that is sensitive to cell cycle progression.Mol. Cell Biol17: 7077-7087.
- 1996. DNA rearrangement mediated by inverted repeats.Proc. Natl. Acad. Sci. USA93: 819-823.
- 1996. A replicational model for DNA recombination between direct repeats.J. Mol. Biol256: 849-858.
- 1996. recA-independent DNA recombination between repetitive sequences: mechanisms and implications.Prog. Nucl. Acid Res. and Mol. Biol54: 253-292.
- 1995. Specific stimulation of recA-independent plasmid recombination by a DNA sequence at a distance.J. Mol. Biol247: 890-902.
- 1994. recA-independent and recA-dependent intramolecular plasmid: differential homology requirement and distance effect.J. Mol. Biol235: 414-423.
- 1994. Hypernegative supercoiling of the DNA template during transcription elongation in vitro.J. Biol. Chem269: 2068-2074.