bims-cebooc 2024-11-10 papers

Issue of 2024–11–10
five papers selected by
Gabriele Zaffagnini, Universität zu Köln

Nat Commun. 2024 Nov 01. 15(1): 9463

Increased DNA damage in full-grown oocytes is correlated with diminished autophagy activation.

Fei Sun, Nourhan Nashat Ali, Daniela Londoño-Vásquez, Constantine A Simintiras, Huanyu Qiao, M Sofia Ortega, Yuksel Agca, Masashi Takahashi, Rocío M Rivera, Andrew M Kelleher, Peter Sutovsky, Amanda L Patterson, Ahmed Z Balboula.

Unlike mild DNA damage exposure, DNA damage repair (DDR) is reported to be ineffective in full-grown mammalian oocytes exposed to moderate or severe DNA damage. The underlying mechanisms of this weakened DDR are unknown. Here, we show that moderate DNA damage in full-grown oocytes leads to aneuploidy. Our data reveal that DNA-damaged oocytes have an altered, closed, chromatin state, and suggest that the failure to repair damaged DNA could be due to the inability of DDR proteins to access damaged loci. Our data also demonstrate that, unlike somatic cells, mouse and porcine oocytes fail to activate autophagy in response to DNA double-strand break-inducing treatment, which we suggest may be the cause of the altered chromatin conformation and inefficient DDR. Importantly, autophagy activity is further reduced in maternally aged oocytes (which harbor severe DNA damage), and its induction is correlated with reduced DNA damage in maternally aged oocytes. Our findings provide evidence that reduced autophagy activation contributes to weakened DDR in oocytes, especially in those from aged females, offering new possibilities to improve assisted reproductive therapy in women with compromised oocyte quality.

DOI: https://doi.org/10.1038/s41467-024-53559-w

Genesis. 2024 Oct;62(5): e23616

Generation and Characterization of a TRIM21 Overexpressing Mouse Line.

Lisa M Mehlmann, Tracy F Uliasz, Siu-Pok Yee, Deborah Kaback, Katie M Lowther.

Specific removal of a protein is a key to understanding its function. "Trim-Away" utilizes TRIM21, an antibody receptor and ubiquitin ligase, for acute and specific reduction of proteins. When TRIM21 is expressed in cells, introduction of a specific antibody causes rapid degradation of the targeted protein; however, TRIM21 is endogenously expressed in few cell types. We have generated a mouse line using CRISPR to insert a conditional overexpression cassette of TRIM21 into the safe harbor site, Rosa26. These conditionally-expressing mice can be bred to a wide variety of Cre mice to target cell-specific TRIM21 overexpression in different tissues. Zp3Cre mice expressed TRIM21 protein specifically in oocytes, whereas HprtCre mice expressed the protein globally. When TRIM21-overexpressing oocytes were microinjected with specific antibodies targeting either the IP3 receptor or SNAP23, these proteins were effectively degraded. In addition, cortical neural cells from globally-overexpressing TRIM21 mice showed a dramatic reduction in IP3 receptor protein within hours after electroporation of a specific antibody. These experiments confirm the effectiveness of the Trim-Away method for protein reduction. These mice should make a valuable addition to the broader research community, as a wide range of proteins and cell types can be studied using this method.

Keywords: TRIM21; Trim‐Away; mouse; oocyte; protein degradation

DOI: https://doi.org/10.1002/dvg.23616

G3 (Bethesda). 2024 Nov 04. pii: jkae252. [Epub ahead of print]

Female germline expression of OVO transcription factor bridges Drosophila generations.

Leif Benner, Savannah Muron, Charli L Wingfield, Brian Oliver.

OVO is required for female germ cell viability but has no known function in the male germline in Drosophila. ovo is autoregulated by two antagonistic isoforms, OVO-A and OVO-B. All ovo- alleles were created as partial revertants of the antimorphic ovoD1 allele. Creation of new targeted alleles in an ovo+ background indicated that disrupting the germline-specific exon extension of ovo-B leads to an arrested egg chamber phenotype, rather than germ cell death. RNA-seq analysis, including >1K full length cDNAs, indicates that ovo has several unannotated splice variations in the extended exon and a minor population of ovo-B transcripts have an alternative splice. This indicates that classical ovo alleles such as ovoD1rv23, are not truly null for ovo, and are likely to be weak antimorphs. To generate bonafide nulls, we deleted the ovo-A and ovo-B promoters showing that only ovo-B is required for female germ cell viability and there is an early and continual developmental requirement for ovo-B in the female germline. To visualize OVO expression and localization, we endogenously tagged ovo and found nuclear OVO in all differentiating female germ cells throughout oogenesis in adults. We also found that OVO is maternally deposited into the embryo, where it showed nuclear localization in newly formed pole cells. Maternal OVO persisted in embryonic germ cells until zygotic OVO expression was detectable, suggesting that there is continuous nuclear OVO expression in the female germline in the transition from one generation to the next.

Keywords: Drosophila melanogaster ; ovo ; embryogenesis; germ cell; oogenesis; pole cell; zinc-finger

DOI: https://doi.org/10.1093/g3journal/jkae252

Cell Rep. 2024 Oct 31. pii: S2211-1247(24)01239-7. [Epub ahead of print]43(11): 114888

Transcriptomic profiling of day 3 human embryos of poor quality reveals molecular links to divergent developmental trajectories.

Yan Li, Wencheng Zhu, Yuchen Qian, Haiyan Yang, Yonggen Wu, Juan Meng, Xuefeng Huang, Zhen Liu, Liangshan Mu.

Poor-quality (PQ) embryos are commonly formed in assisted reproduction and often discarded, but emerging evidence suggests that some can develop into healthy children. Here, we performed single-embryo transcriptome profiling of day 3 human embryos of both good quality (GQ) and PQ. Our analyses revealed that day 3 PQ embryos can be categorized into two distinct subgroups: genuine PQ (gPQ) and morphological PQ (mPQ) embryos. This was further supported by additional transcriptomic data of GQ and PQ embryos donated by the same individuals. gPQ embryos showed greater impairments in both RNA decay and zygotic genome activation (ZGA) compared to mPQ embryos. Blastocysts that emerged from PQ embryos, more likely from mPQ embryos, demonstrated transcriptomic similarity to normal blastocysts. We also identified genes highly upregulated in day 3 gPQ embryos. These molecular insights may improve embryo selection and offer valuable clues for enhancing embryo quality in the future.

Keywords: CP: Developmental biology

DOI: https://doi.org/10.1016/j.celrep.2024.114888

Nucleic Acids Res. 2024 Nov 04. pii: gkae941. [Epub ahead of print]

The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes.

Alla Krasikova, Tatiana Kulikova, Mikhail Schelkunov, Nadezhda Makarova, Anna Fedotova, Vladimir Plotnikov, Valeria Berngardt, Antonina Maslova, Anton Fedorov.

Lampbrush chromosomes, with their unusually high rate of nascent RNA synthesis, provide a valuable model for studying mechanisms of global transcriptome up-regulation. Here, we obtained a whole-genomic profile of transcription along the entire length of all lampbrush chromosomes in the chicken karyotype. With nuclear RNA-seq, we obtained information about a wider set of transcripts, including long non-coding RNAs retained in the nucleus and stable intronic sequence RNAs. For a number of protein-coding genes, we visualized their nascent transcripts on the lateral loops of lampbrush chromosomes by RNA-FISH. The set of genes transcribed on the lampbrush chromosomes is required for basic cellular processes and is characterized by a broad expression pattern. We also present the first high-throughput transcriptome characterization of miRNAs and piRNAs in chicken oocytes at the lampbrush chromosome stage. Major targets of predicted piRNAs include CR1 and long terminal repeat (LTR) containing retrotransposable elements. Transcription of tandem repeat arrays was demonstrated by alignment against the whole telomere-to-telomere chromosome assemblies. We show that transcription of telomere-derived RNAs is initiated at adjacent LTR elements. We conclude that hypertranscription on the lateral loops of giant lampbrush chromosomes is required for synthesizing large amounts of transferred to the embryo maternal RNA for thousands of genes.

DOI: https://doi.org/10.1093/nar/gkae941