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Open Access Publications from the University of California

Scholarly Works (3 results)

  • Thesis
  • Peer Reviewed
UC Santa Barbara Electronic Theses and Dissertations (2023)

The deceased of Ancient China were sometimes accompanied into the afterlife with a list of various types of funerary and offering goods. However, the subject remains less developed than those in other ancient civilizations due to its intricate nature. Funerary inventories of ancient China also stand out for their constantly changing ritual nature over a long period of history, which is most abundantly evident in burials from the Warring States period (475-221 BCE) to the Tang Dynasty (618-907 CE).This dissertation presents the physical, textual, material, and ritual development of funerary inventories of ancient China from the Warring States period to the Wei-Jin period. It examines the changes in the items on the inventories under the framework of “rites of passage” and illustrates how Chinese in different times adopted funerary inventories as a tool to negotiate the social identities of the living during the funeral and reestablish the social identities of the dead in the netherworld. This dissertation also argues against the stereotypical understanding in current scholarship, which sees the funerary inventory as a static and unifunctional text. It analyzes the physical form, textual features, and functions of funerary inventories to comprehensively study the evolution of mortuary inventories and related funerary practices in ancient China. It has been argued that itemized burial goods, as well as their archaeological and ritual contexts, indicate a change in the focus of funerary inventories from the living to the deceased. From the Warring States period to the early Western Han dynasty, funerary inventories gradually shifted to a focus on creating an underground afterlife for the deceased. And the evolution of funerary inventories in the Han-Jin period is arguably driven by changing understanding of death and the afterlife which led to a variety of ways to separate the dead from the living.

    Cover page: From the Living to the Afterlife: Funerary Inventories of Ancient China
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2010)
    Next-generation sequencing is revolutionizing the identification of transcription factor binding sites throughout the human genome. However, the bioinformatics analysis of large datasets collected using chromatin immunoprecipitation and high-throughput sequencing is often a roadblock that impedes researchers in their attempts to gain biological insights from their experiments. We have developed integrated peak-calling and analysis software (Sole-Search) which is available through a user-friendly interface and (i) converts raw data into a format for visualization on a genome browser, (ii) outputs ranked peak locations using a statistically based method that overcomes the significant problem of false positives, (iii) identifies the gene nearest to each peak, (iv) classifies the location of each peak relative to gene structure, (v) provides information such as the number of binding sites per chromosome and per gene and (vi) allows the user to determine overlap between two different experiments. In addition, the program performs an analysis of amplified and deleted regions of the input genome. This software is web-based and automated, allowing easy and immediate access to all investigators. We demonstrate the utility of our software by collecting, analyzing and comparing ChIP-seq data for six different human transcription factors/cell line combinations.
      Cover page: Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2011)
      The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither bioinformatic nor experimental approaches support the hypothesis that the 3' exons of ZNFs are promoters. We further characterized the histone modifications at the 3' ZNF exons and found that these regions also contain H3K36me3, a mark of transcriptional elongation. A genome-wide analysis of ChIP-seq data revealed that ZNFs constitute the majority of genes that have high levels of both H3K9me3 and H3K36me3. These results suggested the possibility that the ZNF genes may be imprinted, with one allele transcribed and one allele repressed. To test the hypothesis that the contradictory modifications are due to imprinting, we used a SNP analysis of RNA-seq data to demonstrate that both alleles of certain ZNF genes having H3K9me3 and H3K36me3 are transcribed. We next analyzed isolated ZNF 3' exons using stably integrated episomes. We found that although the H3K36me3 mark was lost when the 3' ZNF exon was removed from its natural genomic location, the isolated ZNF 3' exons retained the H3K9me3 mark. Thus, the H3K9me3 mark at ZNF 3' exons does not impede transcription and it is regulated independently of the H3K36me3 mark. Finally, we demonstrate a strong relationship between the number of tandemly repeated domains in the 3' exons and the H3K9me3 mark. We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription.
        Cover page: Characterization of the Contradictory Chromatin Signatures at the 3′ Exons of Zinc Finger Genes
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