Isoform-resolved transcriptome of the human preimplantation embryo

Denis Torre, Nancy J. Francoeur, Yael Kalma, Ilana Gross Carmel, Betsaida S. Melo, Gintaras Deikus, Kimaada Allette, Ron Flohr, Maya Fridrikh, Konstantinos Vlachos, Kent Madrid, Hardik Shah, Ying-Chih Wang, Shwetha H. Sridhar, Melissa L. Smith, Efrat Eliyahu, Foad Azem, Hadar Amir, Yoav Mayshar, Ivan Marazzi, Ernesto Guccione, Eric Schadt, Dalit Ben-Yosef () and Robert Sebra ()
Additional contact information
Denis Torre: Icahn School of Medicine at Mount Sinai
Nancy J. Francoeur: Pacific Biosciences, Inc.
Yael Kalma: Affiliated to Tel Aviv University
Ilana Gross Carmel: Affiliated to Tel Aviv University
Betsaida S. Melo: Icahn School of Medicine at Mount Sinai
Gintaras Deikus: Icahn School of Medicine at Mount Sinai
Kimaada Allette: Icahn School of Medicine at Mount Sinai
Ron Flohr: Tel-Aviv University
Maya Fridrikh: Icahn School of Medicine at Mount Sinai
Konstantinos Vlachos: Immunai Inc.
Kent Madrid: Icahn School of Medicine at Mount Sinai
Hardik Shah: Icahn School of Medicine at Mount Sinai
Ying-Chih Wang: Icahn School of Medicine at Mount Sinai
Shwetha H. Sridhar: Icahn School of Medicine at Mount Sinai
Melissa L. Smith: University of Louisville
Efrat Eliyahu: Icahn School of Medicine at Mount Sinai
Foad Azem: Affiliated to Tel Aviv University
Hadar Amir: Affiliated to Tel Aviv University
Yoav Mayshar: Weizmann Institute of Science
Ivan Marazzi: University of California
Ernesto Guccione: Icahn School of Medicine at Mount Sinai
Eric Schadt: Icahn School of Medicine at Mount Sinai
Dalit Ben-Yosef: Affiliated to Tel Aviv University
Robert Sebra: Icahn School of Medicine at Mount Sinai

Nature Communications, 2023, vol. 14, issue 1, 1-23

Abstract: Abstract Human preimplantation development involves extensive remodeling of RNA expression and splicing. However, its transcriptome has been compiled using short-read sequencing data, which fails to capture most full-length mRNAs. Here, we generate an isoform-resolved transcriptome of early human development by performing long- and short-read RNA sequencing on 73 embryos spanning the zygote to blastocyst stages. We identify 110,212 unannotated isoforms transcribed from known genes, including highly conserved protein-coding loci and key developmental regulators. We further identify 17,964 isoforms from 5,239 unannotated genes, which are largely non-coding, primate-specific, and highly associated with transposable elements. These isoforms are widely supported by the integration of published multi-omics datasets, including single-cell 8CLC and blastoid studies. Alternative splicing and gene co-expression network analyses further reveal that embryonic genome activation is associated with splicing disruption and transient upregulation of gene modules. Together, these findings show that the human embryo transcriptome is far more complex than currently known, and will act as a valuable resource to empower future studies exploring development.

Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-023-42558-y Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42558-y

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-023-42558-y

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().