Award Date

8-1-2020

Degree Type

Thesis

Degree Name

Master of Science (MS)

Department

Life Sciences

First Committee Member

Mira Han

Second Committee Member

Philippos Tsourkas

Third Committee Member

Jeffery Shen

Fourth Committee Member

Edwin Oh

Number of Pages

57

Abstract

Transposable elements (TEs) are genetic sequences which are mobile within the genome, including DNA transposons and retrotransposons. Though the vast majority are no longer able to move or duplicate in humans, they still are actively transcribed in both germline and somatic cells, particularly in early human development. TEs are expressed in an extremely cell-type and stage specific pattern during embryogenesis, suggesting that they may either have a regulatory role in the cell or be transcribed along with cell-specific genes. However, earlier studies have focused on hESC models or early embryos up to day 6, with differing patterns of TE expression.

Here, I investigate the pattern of differentially expressed TEs in single-cell RNA- seq data obtained from human embryos ranging in age from day 6 to day 14 post fertilization. The high resolution of this dataset lays bare the expression pattern of specific retrotransposons known as human endogenous retroviruses, specifically of subfamily H (HERVH), found exclusively in epiblasts. I confirm that TE expression is cell-type specific and does not rely entirely on proximity to cell-type specific genes. Additionally, HERVHs have a similar pattern of expression to stem cell and pluripotency regulation genes according to network analysis. Functionally, HERVH elements contain open reading frames which could have coding potential. Lastly, HERVHs associated with epiblasts are enriched for developmental transcription factor binding sites, suggesting that they may be candidate enhancers. This work demonstrates that HERVH expression is epiblast cell specific up to 14 days post fertilization, and provides a starting point for further analysis on the functional potential of these HERVs as promoters, enhancers or possibly as coding proteins.

Keywords

Single-Cell RNA Seq; Transposable Elements

Disciplines

Bioinformatics | Genetics

File Format

pdf

File Size

9600 KB

Degree Grantor

University of Nevada, Las Vegas

Language

English

Rights

IN COPYRIGHT. For more information about this rights statement, please visit http://rightsstatements.org/vocab/InC/1.0/

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