Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells DOI Creative Commons
Isaac A. Babarinde, Gang Ma, Yuhao Li

et al.

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 49(16), P. 9132 - 9153

Published: Aug. 3, 2021

Transposable elements (TEs) occupy nearly 40% of mammalian genomes and, whilst most are fragmentary and no longer capable transposition, they can nevertheless contribute to cell function. TEs within genes transcribed by RNA polymerase II be copied as parts primary transcripts; however, their full contribution mature transcript sequences remains unresolved. Here, using long short read (LR SR) sequencing data, we show that 26% coding 65% noncoding transcripts in human pluripotent stem cells (hPSCs) contain TE-derived sequences. Different TE families incorporated into RNAs unique patterns, with consequences structure The presence a is correlated TE-type specific changes its subcellular distribution, alterations steady-state levels half-life, differential association Binding Proteins (RBPs). We identify hPSC-specific incorporation endogenous retroviruses (ERVs) LINE:L1 protein-coding mRNAs, which generate sequence-derived peptides. Finally, single RNA-seq reveals hPSCs express ERV-containing transcripts, differentiating subpopulations lack ERVs SINE LINE-containing transcripts. Overall, our comprehensive analysis demonstrates the more widespread has greater impact than previously appreciated.

Language: Английский

Nucleosomes in mammalian sperm: conveying paternal epigenetic inheritance or subject to reprogramming between generations? DOI Creative Commons
Laura Gaspa-Toneu, Antoine H.F.M. Peters

Current Opinion in Genetics & Development, Journal Year: 2023, Volume and Issue: 79, P. 102034 - 102034

Published: March 7, 2023

The genome of mammalian sperm is largely packaged by sperm-specific proteins termed protamines. presence some residual nucleosomes has, however, emerged as a potential source paternal epigenetic inheritance between generations. Sperm bear important regulatory histone marks and locate at gene-regulatory regions, functional elements, intergenic regions. It unclear whether are retained specific genomic locations in deterministic manner or randomly preserved due to inefficient exchange histones Recent studies indicate heterogeneity chromatin packaging within populations an extensive reprogramming post fertilization. Obtaining single-sperm nucleosome distributions fundamental estimating the sperm-borne instructing embryonic development transmission acquired phenotypes.

Language: Английский

Citations

22
A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome DOI Creative Commons
Catherine Wilson, John H. Postlethwait

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(5)

Published: March 11, 2024

Wild zebrafish (Danio rerio) have a ZZ/ZW chromosomal sex-determination system with the major sex locus on right arm of chromosome-4 (Chr4R) near largest heterochromatic block in genome, suggesting that Chr4R transcriptomics might differ from rest genome. To test this hypothesis, we conducted an RNA-seq analysis adult ZW ovaries and ZZ testes Nadia strain identified 4 regions Chr4 different gene expression profiles. Unique protein-coding genes 41.7 Mb section (Region-2) were expressed testis but silent ovary. The AB lab strain, which lacks chromosomes, verified result, showing testis-biased Region-2 depends gonad biology, not sex-determining mechanism. analyses female male brains livers validated reduced transcripts somatic cells, without specificity. corresponds to portion its content repetitive elements distinguishes it human orthologs; has zinc finger early zygotic genome activation; maternal 5S rRNA genes, spliceosome concentration tRNA distinct set elements. colocalization (1) silenced are (2) embryos briefly at onset (3) maternal-specific for translation machinery; (4) components; (5) adjacent encoding miR-430, mediates transcript degradation, suggest is maternal-to-zygotic-transition regulatory block.

Language: Английский

Citations

6
Regulation and Roles of the Nucleolus in Embryonic Stem Cells: From Ribosome Biogenesis to Genome Organization DOI Creative Commons
Shivani Gupta, Raffaella Santoro

Stem Cell Reports, Journal Year: 2020, Volume and Issue: 15(6), P. 1206 - 1219

Published: Sept. 24, 2020

The nucleolus is the largest compartment of eukaryotic cell's nucleus. It acts as a ribosome factory, thereby sustaining translation machinery. also subnuclear with highest transcriptional activity in cell, where hundreds ribosomal RNA (rRNA) genes transcribe overwhelming majority RNAs. structure and composition change according to developmental state. For instance, embryonic stem cells (ESCs), rRNA display hyperactive state open chromatin compared differentiated cells. Increasing evidence indicates that role might go beyond control biogenesis. One such linked genome architecture, since repressive domains are often located close nucleolus. This review highlights recent findings describing how regulated ESCs its regulating biogenesis organization for maintenance cell identity.

Language: Английский

Citations

47
Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate Transitions DOI Creative Commons
Li Sun,

Xiuling Fu,

Gang Ma

et al.

Frontiers in Cell and Developmental Biology, Journal Year: 2021, Volume and Issue: 9

Published: Feb. 18, 2021

A major event in embryonic development is the rearrangement of epigenetic information as somatic genome reprogrammed for a new round organismal development. Epigenetic data are held chemical modifications on DNA and histones, there dramatic dynamic changes these marks during embryogenesis. However, mechanisms behind this intricate process how it regulating responding to remain unclear. As embryos develop from totipotency pluripotency, they pass through several distinct stages that can be captured permanently or transiently vitro . Pluripotent naïve cells resemble early epiblast, primed late blastomere-like have been isolated, although fully totipotent elusive. Experiments using model systems led insights into chromatin development, which has informed exploration pre-implantation embryos. Intriguingly, human mouse rely different signaling pathways, remains mystery why variation exists. In review, we will summarize rearrangements drawing genomic cell lines,

Language: Английский

Citations

37
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells DOI Creative Commons
Isaac A. Babarinde, Gang Ma, Yuhao Li

et al.

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 49(16), P. 9132 - 9153

Published: Aug. 3, 2021

Transposable elements (TEs) occupy nearly 40% of mammalian genomes and, whilst most are fragmentary and no longer capable transposition, they can nevertheless contribute to cell function. TEs within genes transcribed by RNA polymerase II be copied as parts primary transcripts; however, their full contribution mature transcript sequences remains unresolved. Here, using long short read (LR SR) sequencing data, we show that 26% coding 65% noncoding transcripts in human pluripotent stem cells (hPSCs) contain TE-derived sequences. Different TE families incorporated into RNAs unique patterns, with consequences structure The presence a is correlated TE-type specific changes its subcellular distribution, alterations steady-state levels half-life, differential association Binding Proteins (RBPs). We identify hPSC-specific incorporation endogenous retroviruses (ERVs) LINE:L1 protein-coding mRNAs, which generate sequence-derived peptides. Finally, single RNA-seq reveals hPSCs express ERV-containing transcripts, differentiating subpopulations lack ERVs SINE LINE-containing transcripts. Overall, our comprehensive analysis demonstrates the more widespread has greater impact than previously appreciated.

Language: Английский

Citations

35