{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/121365"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/121365","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Single cell RNA-seq analysis uncovers transcription regulation mechanisms in mouse germline cells","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-08-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-08-01","abstract_has_math":false,"creators":["Peng, Yiheng"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"VMS - Comparative Biosciences","degree_department":null,"school":null,"contributors":["Qiao, Joe","Yang, Jing","Bagchi, Indrani C.","Kalsotra, Auinash"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-08","date_published":"2023-08","updated_at":"2026-07-22T22:24:57Z","subjects":["Meiosis","Scrna-seq","Sex Body","Transcription","Phase Seperation"],"languages":["en","eng"],"rights":["Copyright 2023 Yiheng Peng"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/121365","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Qiao, Joe","Yang, Jing","Bagchi, Indrani C.","Kalsotra, Auinash"]},{"key":"dc:creator","label":"Author","values":["Peng, Yiheng"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2023-08","2023-07-14"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["VMS - Comparative Biosciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Meiosis","Scrna-seq","Sex Body","Transcription","Phase Seperation"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2023 Yiheng Peng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/121365"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-08-01","The student, Yiheng Peng, accepted the attached license on 2023-07-13 at 13:19.","The student, Yiheng Peng, submitted this Dissertation for approval on 2023-07-13 at 13:29.","This Dissertation was approved for publication on 2023-07-14 at 14:20.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19678 on 2023-12-04 at 17:18:40","Meiosis, a specialized cellular division process, forms the basis of sexual reproduction through the generation of gametes. At the core of meiosis lie complex events, such as synapsis and homologous recombination, disruption of which can culminate in infertility and aneuploidy. This thesis presents a holistic investigation of these intricate events, facilitated by advancements in transcriptomic studies, and leveraging the fine-resolution capabilities of single-cell RNA sequencing (scRNA-seq) technologies. Our research underscores the advantages of scRNA-seq in effectively discerning the heterogeneities and subtle variations between cell types and stages, as opposed to conventional bulk RNA-seq and RT-qPCR. Particular emphasis is laid on the strengths and limitations of two widely adopted scRNA-seq platforms, Smart-seq2 and Drop-seq, contextualized to meiosis studies. Building upon these analytical capabilities, we report new findings on the transcriptional landscape of mammalian meiosis and introduce a novel technique, digital chromosome banding, that enables accurate measurement of transcription levels within chromosomal regions of oocytes and spermatocytes. Innovatively applying scRNA-seq to the investigation of meiotic silencing of unsynapsed chromatin (MSUC) and meiotic sex chromosome inactivation (MSCI) events, our research uncovers the fundamental distinctions between these processes and the inherent inability of certain structures to induce effective chromosomal silencing. These discoveries prompt a fresh understanding of meiotic silencing and emphasize the importance of phase separation in this context. Subsequently, we employ scRNA-seq to dissect the transcriptomic profile of mouse spermatocytes during the critical Prophase I stage of meiosis. Our data reveal novel gene markers that delineate the early, mid, and late substages of pachytene, and provide insights into the temporal dynamics of synapsis and double-strand breaks repair checkpoints. We further unearth evidence of multiple checkpoint layers safeguarding meiosis, ensuring the process's fidelity even in the face of aberrations. Altogether, our findings pave the way towards an unprecedented understanding of the meiotic process and its regulatory mechanisms. The techniques and insights put forth in this research constitute valuable tools and knowledge base for future inquiries into reproductive biology and related disorders, heralding new frontiers in our comprehension of meiosis."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Single cell RNA-seq analysis uncovers transcription regulation mechanisms in mouse germline cells"]}]}],"canonical_facts":{"dc:contributor":["Qiao, Joe","Yang, Jing","Bagchi, Indrani C.","Kalsotra, Auinash"],"dc:creator":["Peng, Yiheng"],"dc:date":["2023-08","2023-07-14"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-08-01","The student, Yiheng Peng, accepted the attached license on 2023-07-13 at 13:19.","The student, Yiheng Peng, submitted this Dissertation for approval on 2023-07-13 at 13:29.","This Dissertation was approved for publication on 2023-07-14 at 14:20.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19678 on 2023-12-04 at 17:18:40","Meiosis, a specialized cellular division process, forms the basis of sexual reproduction through the generation of gametes. At the core of meiosis lie complex events, such as synapsis and homologous recombination, disruption of which can culminate in infertility and aneuploidy. This thesis presents a holistic investigation of these intricate events, facilitated by advancements in transcriptomic studies, and leveraging the fine-resolution capabilities of single-cell RNA sequencing (scRNA-seq) technologies. Our research underscores the advantages of scRNA-seq in effectively discerning the heterogeneities and subtle variations between cell types and stages, as opposed to conventional bulk RNA-seq and RT-qPCR. Particular emphasis is laid on the strengths and limitations of two widely adopted scRNA-seq platforms, Smart-seq2 and Drop-seq, contextualized to meiosis studies. Building upon these analytical capabilities, we report new findings on the transcriptional landscape of mammalian meiosis and introduce a novel technique, digital chromosome banding, that enables accurate measurement of transcription levels within chromosomal regions of oocytes and spermatocytes. Innovatively applying scRNA-seq to the investigation of meiotic silencing of unsynapsed chromatin (MSUC) and meiotic sex chromosome inactivation (MSCI) events, our research uncovers the fundamental distinctions between these processes and the inherent inability of certain structures to induce effective chromosomal silencing. These discoveries prompt a fresh understanding of meiotic silencing and emphasize the importance of phase separation in this context. Subsequently, we employ scRNA-seq to dissect the transcriptomic profile of mouse spermatocytes during the critical Prophase I stage of meiosis. Our data reveal novel gene markers that delineate the early, mid, and late substages of pachytene, and provide insights into the temporal dynamics of synapsis and double-strand breaks repair checkpoints. We further unearth evidence of multiple checkpoint layers safeguarding meiosis, ensuring the process's fidelity even in the face of aberrations. Altogether, our findings pave the way towards an unprecedented understanding of the meiotic process and its regulatory mechanisms. The techniques and insights put forth in this research constitute valuable tools and knowledge base for future inquiries into reproductive biology and related disorders, heralding new frontiers in our comprehension of meiosis."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/121365"],"dc:language":["en","eng"],"dc:rights":["Copyright 2023 Yiheng Peng"],"dc:subject":["Meiosis","Scrna-seq","Sex Body","Transcription","Phase Seperation"],"dc:title":["Single cell RNA-seq analysis uncovers transcription regulation mechanisms in mouse germline cells"],"dc:type":["text"],"thesis:degree_discipline":["VMS - Comparative Biosciences"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:57Z"}