東華大學圖書館 |

Unraveling Heterogeneity in X Chromosome Regulation and Transcriptional Heterogeneity in Naive Human Pluripotent Stem Cells.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Unraveling Heterogeneity in X Chromosome Regulation and Transcriptional Heterogeneity in Naive Human Pluripotent Stem Cells./
作者:	Patterson, Benjamin Daniel.
出版者:	Ann Arbor : ProQuest Dissertations & Theses, : 2021,
面頁冊數:	151 p.
附註:	Source: Dissertations Abstracts International, Volume: 83-02, Section: B.
Contained By:	Dissertations Abstracts International83-02B.
標題:	Developmental biology. -
電子資源:	https://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28322142
ISBN:	9798522974145

Unraveling Heterogeneity in X Chromosome Regulation and Transcriptional Heterogeneity in Naive Human Pluripotent Stem Cells.
Patterson, Benjamin Daniel.

Unraveling Heterogeneity in X Chromosome Regulation and Transcriptional Heterogeneity in Naive Human Pluripotent Stem Cells. - Ann Arbor : ProQuest Dissertations & Theses, 2021 - 151 p.

Source: Dissertations Abstracts International, Volume: 83-02, Section: B.

Thesis (Ph.D.)--Yale University, 2021.

This item must not be sold to any third party vendors.

In the works described below, I investigate and describe heterogeneity in naive human pluripotent stem cells (hPSCs)-both the heterogeneity exhibited in XCI status and the nearly unexplored transcriptional heterogeneity in these cells. Stem cells are a highly desirable model for studying XCI, as both pluripotency and XCI play out during peri-implantation. By comparing female naive and primed stem cells, I elucidate the functional differences in their XCI state. Recent studies incorporating single-cell RNA sequencing (scRNA-seq) have demonstrated that transcript-based technologies are insufficiently developed to unequivocally resolve these questions in a human system (Kaur et al., 2020; Mandal et al., 2020; Moreira de Mello et al., 2017; Petropoulos et al., 2016a; Reinius and Sandberg, 2019; Sahakyan et al., 2017). Further studies have instead shown that 3D genomics holds immense promise for studying XCI by interrogating changes to the X chromosomes' 3D states (Darrow et al., 2016; Giorgetti et al., 2016; Wang et al., 2016b). As such, I have collaborated with the Wang lab to characterize the 3D state of the X chromosome in naive and primed human pluripotent stem cells. Using a combination of Hi-C and DNA FISH, we analyzed 40 TADs across the X chromosome in multiple naive and primed hPSC lines. From this, we determined that naive cells typically exhibit the 3D conformation of active X chromosomes. Naive X chromosomes generally compartmentalize around the centromere and appear more dispersed than primed X chromosomes on average, which further suggests that naive X chromosomes exist in the active state. The addition of FGF does not seem to have a major effect on the X chromosome conformation in the naive state either.In naive hPSCs, transcriptional heterogeneity is an almost completely open question regarding its variation across cell lines, mechanism(s), cultural conditions, and even its effects. However, multiple studies using primed cells, including those published by my lab, have shown that some degree of heterogeneity is present in this culture system. Because naive cells are a fairly recent discovery-and transgene-free naive hPSCs are an even more recent innovation-there is ample space in this undeveloped field to leverage single-cell RNA sequencing to conduct a basal characterization of transcriptional heterogeneity in these cells. From this, we found that the cells clustered into two distinct populations, independently of the scRNA-seq method used. We also leveraged previously published scRNA-seq data from the same cell line (performed by another group in a different cultural context) in order to correlate our findings; their data also contained these two populations.Based on the research described here, my colleagues and I have made novel advancements within the field of stem cell biology, implementing novel experimental approaches. Critically, we have found that naive X chromosomes are not explicitly heterogeneous, finding no evidence of X chromosome inactivation in female naive hPSCs. From a transcriptional perspective, we conclude that naive cells demonstrate discrete heterogeneity and form developmentally and functionally distinct populations. This body of work represents one of the first efforts in the field to characterize the heterogeneity of naive hPSCs at single-cell resolution, both in a 3D genomics and transcriptional context.

ISBN: 9798522974145Subjects--Topical Terms:

592588
Developmental biology.
Subjects--Index Terms:

3D genomics

Unraveling Heterogeneity in X Chromosome Regulation and Transcriptional Heterogeneity in Naive Human Pluripotent Stem Cells.
LDR:04702nmm a2200397 4500 001 2282923
005 20211022115800.5
008 220723s2021 ||||||||||||||||| ||eng d
020 $a 9798522974145
035 $a (MiAaPQ)AAI28322142
035 $a AAI28322142
040 $a MiAaPQ $c MiAaPQ
100 1 $a Patterson, Benjamin Daniel. $3 3561797
245 1 0 $a Unraveling Heterogeneity in X Chromosome Regulation and Transcriptional Heterogeneity in Naive Human Pluripotent Stem Cells.
260 1 $a Ann Arbor : $b ProQuest Dissertations & Theses, $c 2021
300 $a 151 p.
500 $a Source: Dissertations Abstracts International, Volume: 83-02, Section: B.
500 $a Advisor: Park, In-Hyun;Reinke, Valerie.
502 $a Thesis (Ph.D.)--Yale University, 2021.
506 $a This item must not be sold to any third party vendors.
520 $a In the works described below, I investigate and describe heterogeneity in naive human pluripotent stem cells (hPSCs)-both the heterogeneity exhibited in XCI status and the nearly unexplored transcriptional heterogeneity in these cells. Stem cells are a highly desirable model for studying XCI, as both pluripotency and XCI play out during peri-implantation. By comparing female naive and primed stem cells, I elucidate the functional differences in their XCI state. Recent studies incorporating single-cell RNA sequencing (scRNA-seq) have demonstrated that transcript-based technologies are insufficiently developed to unequivocally resolve these questions in a human system (Kaur et al., 2020; Mandal et al., 2020; Moreira de Mello et al., 2017; Petropoulos et al., 2016a; Reinius and Sandberg, 2019; Sahakyan et al., 2017). Further studies have instead shown that 3D genomics holds immense promise for studying XCI by interrogating changes to the X chromosomes' 3D states (Darrow et al., 2016; Giorgetti et al., 2016; Wang et al., 2016b). As such, I have collaborated with the Wang lab to characterize the 3D state of the X chromosome in naive and primed human pluripotent stem cells. Using a combination of Hi-C and DNA FISH, we analyzed 40 TADs across the X chromosome in multiple naive and primed hPSC lines. From this, we determined that naive cells typically exhibit the 3D conformation of active X chromosomes. Naive X chromosomes generally compartmentalize around the centromere and appear more dispersed than primed X chromosomes on average, which further suggests that naive X chromosomes exist in the active state. The addition of FGF does not seem to have a major effect on the X chromosome conformation in the naive state either.In naive hPSCs, transcriptional heterogeneity is an almost completely open question regarding its variation across cell lines, mechanism(s), cultural conditions, and even its effects. However, multiple studies using primed cells, including those published by my lab, have shown that some degree of heterogeneity is present in this culture system. Because naive cells are a fairly recent discovery-and transgene-free naive hPSCs are an even more recent innovation-there is ample space in this undeveloped field to leverage single-cell RNA sequencing to conduct a basal characterization of transcriptional heterogeneity in these cells. From this, we found that the cells clustered into two distinct populations, independently of the scRNA-seq method used. We also leveraged previously published scRNA-seq data from the same cell line (performed by another group in a different cultural context) in order to correlate our findings; their data also contained these two populations.Based on the research described here, my colleagues and I have made novel advancements within the field of stem cell biology, implementing novel experimental approaches. Critically, we have found that naive X chromosomes are not explicitly heterogeneous, finding no evidence of X chromosome inactivation in female naive hPSCs. From a transcriptional perspective, we conclude that naive cells demonstrate discrete heterogeneity and form developmentally and functionally distinct populations. This body of work represents one of the first efforts in the field to characterize the heterogeneity of naive hPSCs at single-cell resolution, both in a 3D genomics and transcriptional context.
590 $a School code: 0265.
650 4 $a Developmental biology. $3 592588
650 4 $a Genetics. $3 530508
650 4 $a Cellular biology. $3 3172791
650 4 $a Embryos. $3 2152917
650 4 $a Mammals. $3 531989
650 4 $a Gene expression. $3 643979
650 4 $a Experiments. $3 525909
650 4 $a Mutation. $3 837917
650 4 $a DNA damage. $3 916185
650 4 $a Medical research. $2 bicssc $3 1556686
650 4 $a Hybridization. $3 1615790
650 4 $a Researchers. $3 3560729
650 4 $a Ligands. $3 686413
650 4 $a Biology. $3 522710
650 4 $a Epigenetics. $3 1568224
650 4 $a Localization. $3 3560711
650 4 $a Stem cells. $3 767761
650 4 $a Cell cycle. $3 766119
650 4 $a X chromosomes. $3 3561798
650 4 $a Proteins. $3 558769
653 $a 3D genomics
653 $a hESC
653 $a Naive Human Pluripotent Stem Cells
653 $a X Chromosome Inactivation
653 $a Transcriptional heterogeneity
653 $a Genetic sequencing
690 $a 0758
690 $a 0369
690 $a 0379
690 $a 0306
710 2 $a Yale University. $b Genetics. $3 2101672
773 0 $t Dissertations Abstracts International $g 83-02B.
790 $a 0265
791 $a Ph.D.
792 $a 2021
793 $a English
856 4 0 $u https://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28322142