Biology subjects

Zeng, T.-B.

Publications and source records attributed to Zeng, T.-B..

4 recordsLinked to original sources

bioRxiv2025

Maternal SETDB1 enables development beyond cleavage stages by extinguishing the MERVL-driven 2-cell totipotency transcriptional program in the mouse embryo

Loss of maternal SETDB1, a histone H3K9 methyltransferase, leads to developmental arrest prior to implantation, with very few mouse embryos advancing beyond the 8-cell stage, which is currently unexplained. We genetically investigate SETDB1s role in the epigenetic control of the transition from totipotency to pluripotency--a process demanding precise timing and forward directionality. Through single-embryo total RNA sequencing of 2-cell and 8-cell embryos, we find that Setdb1mat-/+ embryos fail to extinguish 1-cell and 2-cell transient genes--alongside persistent expression of MERVL retroelements and MERVL-driven chimeric transcripts that define the totipotent state in mouse 2-cell embryos. Comparative bioinformatics reveals that SETDB1 acts at MT2 LTRs and MERVL-driven chimeric transcripts, which normally acquire H3K9me3 during early development. The dysregulated targets substantially overlap with DUXBL-responsive genes, indicating a shared regulatory pathway for silencing the 2-cell transcriptional program. We establish maternal SETDB1 as a critical chromatin regulator required to extinguish retroelement-driven totipotency networks and ensure successful preimplantation development.

genetics↗

bioRxiv2025

Advanced eTAM-seq enables high-fidelity, low-input N6-methyladenosine profiling in human cells and embryonic mouse tissues

Functional dissection of N6-methyladenosine (m6A), the most abundant internal messenger RNA modification in mammals, demands quantitative, scalable detection technology. We previously reported eTAM-seq, which supports transcriptome-wide quantification of m6A by enzyme-assisted adenosine deamination. While effective, TadA8.20--the enzyme used in our first-generation technology--is sensitive not only to m6A but also to RNA structure, making accurate detection dependent on the inclusion of control transcriptomes. Here, we introduce eTAM-seq-v2, in which we replace TadA8.20 with TadA8r, a further evolved adenosine deaminase with superior catalytic efficiency. eTAM-seq-v2 supports control-free m6A calling with high fidelity. Because enzyme treatment preserves RNA integrity, eTAM-seq surveys >51% of A sites in all expressed genes with moderate sequencing depth (60 million uniquely mapped reads) and delivers robust performance with as little as 10 ng of total RNA ([~]500 cells). With eTAM-seq-v2, we delineate the m6A landscape across six human cell lines and seven embryonic mouse tissues. While uncovering broadly conserved m6A patterns, we reveal that most neighboring m6A sites are independently deposited at the single-molecule level. Moving forward, we envision that eTAM-seq-v2 will enable researchers to survey m6A in diverse biological contexts and uncover new insights into its regulatory roles.

molecular biology↗

bioRxiv2021

H3K9 methyltransferase EHMT2/G9a controls ERVK-driven non-canonical imprinted genes

Unlike regular imprinted genes, non-canonical imprinted genes are known to not depend on gamete-specific DNA methylation difference. Instead, the paternal allele-specific expression of these genes in the extra-embryonic lineages depends on an H3K27me3-based imprint in the oocyte, but this marking is not maintained beyond pre-implantation development. The maintenance of non-canonical imprinting corresponds to maternal allele-specific DNA methylation and paternal allele-specific H3K4me3 at their somatic DMRs, which occur at ERVK repeats. We hypothesized that EHMT2, the main euchromatic H3K9 methyltransferase, also has a role in this process. Using reciprocal mouse crosses and allele-specific RNA-seq analysis, we found that the maternal allele of each known non-canonical imprinted gene was derepressed from its ERVK promoter in the Ehmt2-/- ectoplacental cone of somite-matched 8.5 dpc embryos. In the Ehmt2-/- embryos, loss of DNA methylation accompanied the derepression of both parental alleles of those ERVK promoters. Our study identifies EHMT2 as an essential player that maintains the repressed chromosomal state in non-canonical imprinting.

genetics↗

bioRxiv2021

EHMT2 Controls Transcriptional Noise and the Developmental Switch after Gastrulation in the Mouse Embryo

Embryos that carry zygotic or parental mutations in Ehmt2, the gene encoding the main euchromatic histone H3K9 methyltransferase, EHMT2, exhibit variable developmental delay. We asked the question whether the delayed embryo is different transcriptionally from the normally developing embryo when they reach the same developmental stage. We collected embryos carrying a series of genetic deficiencies in the Ehmt2 gene and performed total RNA sequencing of somite stage-matched individual embryos. We applied novel four-way comparisons to detect differences between normal versus deficient embryos, and between 12-somite and 6-somite embryos. Importantly, we also identified developmental changes in transcription that only occur during the development of the normal embryo. We found that at the 6-somite stage, gastrulation-specific genes were not precisely turned off in the Ehmt2-/- embryos, and genes involved in organ growth, connective tissue development, striated muscle development, muscle differentiation, and cartilage development were not precisely switched on in the Ehmt2-/- embryos. Zygotic EHMT2 reduced transcriptional variation of developmental switch genes and at some repeat elements at the six-somite stage embryos. Maternal EHMT2-mutant embryos also displayed great transcriptional variation consistent with their variable survival, but transcription was normal in developmentally delayed parental haploinsufficient embryos, consistent with their good prospects. Global profiling of transposable elements in the embryo revealed that specific repeat classes responded to EHMT2. DNA methylation was specifically targeted by EHMT2 to LTR repeats, mostly ERVKs. Long noncoding transcripts initiated from those misregulated driver repeats in Ehmt2-/- embryos, and extended to several hundred kilobases, encompassing a multitude of additional, similarly misexpressed passenger repeats. These findings establish EHMT2 as an important regulator of the transition between gastrulation programs and organ specification programs and of variability.

developmental biology↗