Biology subjects

Hutchins, A. P.

Publications and source records attributed to Hutchins, A. P..

8 recordsLinked to original sources

bioRxiv2026

SALL2 constrains TEAD4 by maintaining repressive chromatin to restrict trophectoderm identity

Embryonic development is marked by the successive restriction of developmental potential and the specification of embryonic and extraembryonic lineages. Yet, how these lineage decisions are established, and how the epigenome is remodelled to promote and restrict cell fate transitions, remains poorly understood. Here, we demonstrate that SALL2 knockdown in primed human pluripotent stem cells (hPSCs) triggers a trophectoderm (TE)-like phenotype, characterized by palisade-like morphology and the up-regulation of TE-associated genes. Mechanistically, SALL2 physically interacts with the key TE driver TEAD4 and maintains bivalent, repressive chromatin (H3K4me3/H3K27me3) at TE-specific loci. Reduced SALL2 led to enhanced TEAD4 occupancy and disrupted H3K27me3 and increased active chromatin marks at TE genes. Importantly, depletion of TEAD4 abolished the TE-like phenotype induced by SALL2 knockdown, demonstrating that TEAD4 is required for the downstream effects of SALL2 loss. In support of this, blastoid-like aggregates can be generated from primed hPSCs with SALL2 knocked down. Together, our findings identify SALL2 as a key epigenetic barrier that restrains TE lineage commitment by limiting TEAD4-dependent activation of the trophoblast transcriptional program. Key findingsO_LISALL2 acts as a molecular barrier to trophectoderm differentiation. C_LIO_LISALL2 suppresses the trophectoderm by maintaining bivalent repressive chromatin at TEAD4-bound loci. C_LIO_LIBlastoid-like structures can be generated from primed-state media when SALL2 was knocked down. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/737659v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@42cafaorg.highwire.dtl.DTLVardef@11c040borg.highwire.dtl.DTLVardef@4d9ffborg.highwire.dtl.DTLVardef@42546a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗

bioRxiv2024

Dissecting the Contribution of Transposable Elements to Interphase Chromosome Structure

Transposable elements (TEs) occupy nearly half of the human genome and play diverse biological roles. Despite their abundance, the extent to which TEs contribute to three-dimensional (3D) genome structure remains unclear. To investigate this, we developed te_hic, a computational pipeline that integrates genomic data with chromatin interactions. Our analysis reveals that TE sequences are responsible for 3D genome structure in interphase nuclei. This phenomenon is mediated by the recruitment of specific transcription factors to TEs, which enables both the formation and disruption of chromatin contacts. We computationally identified known contact-forming proteins (CTCF, RAD21, SMC3) and breaking proteins (RNF2), as well as novel candidate contact-formers (SMARCA4, MAFK). Knockdown of the predicted contact-formers SMARCA4 and MAFK decreased contacts and loops at and between TEs. Notably, SMARCA4 knockdown selectively reduced short-range contacts, highlighting its role in maintaining 3D genome structure mediated by TE binding. Overall, our findings demonstrate that TEs are crucial determinants of 3D genome organization in mammalian cells. Key findingsO_LITEs determine 48% of the 3D genome structure alone, and 70% of heterotypic contacts. C_LIO_LIA/B compartments, TADs, and loop signatures can be retrieved using TE-mapped reads only. C_LIO_LITFs can be divided into contact formers and breakers at TEs. C_LIO_LISMARCA4 and MAFK build chromatin contacts between TE sequences. C_LI

cell biology↗

bioRxiv2024

Transposable Element Expression and Sub-cellular Dynamics During hPSC Differentiation to Endoderm, Mesoderm, and Ectoderm Lineages

Transposable elements (TEs) are genomic elements that are found in multiple copies in mammalian genomes. TEs were previously thought to have little functional relevance but recent studies have reported TE roles in multiple biological processes, particularly in embryonic development. To investigate the expression dynamics of TEs during human early development, we used long-read sequence data generated from in vitro differentiation of human pluripotent stem cells (hPSCs) to endoderm, mesoderm, and ectoderm lineages to construct lineage-specific transcriptome assemblies and accurately place TE sequences in their transcript context. Our analysis revealed that specific TE types, such as LINEs and LTRs, exhibit distinct expression patterns across different lineages. Notably, an expression outburst was observed in the ectoderm lineage, with multiple TE types showing dynamic expression trajectories. Additionally, certain LTRs, including HERVH and LTR7Y, were highly expressed in hPSCs and endodermal cells, but these HERVH and LTR7Y sequences originated from completely different transcripts. Interestingly, TE-containing transcripts exhibit distinct levels of transcript stability and subcellular localization across different lineages. Moreover, we showed a consistent trend of increased chromatin association of TE-containing transcripts in germ lineage cells compared to hPSCs. This study suggests that TEs contribute to human embryonic development through dynamic chromatin interactions. Key findingsO_LIDifferent loci of the same TEs are independently regulated in different cell states C_LIO_LIEctoderm has the highest frequency of TE-containing transcripts C_LIO_LIThe presence of TEs dynamically drives transcripts to different sub-cellular compartments in different cell states C_LIO_LIhPSCs have the least stable TE transcripts with the weakest TE chromatin association, highlighting loose hPSC chromatin and potential roles in cell differentiation C_LI

genomics↗

bioRxiv2022

The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome

BackgroundInvestigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts. The heterogeneity of the assembled transcript sets might be partially explained by sequencing depth. ResultsHere, we used real and simulated short-read sequencing data as well as long-read data to systematically investigate the impact of sequencing depths on the accuracy of assembled transcripts. We assembled and analyzed transcripts from 671 human short-read data sets and four long-read data sets. At the first level, there is a positive correlation between the number of reads and the number of recovered transcripts. However, the effect of the sequencing depth varied based on cell or tissue type, the type of read considered and the nature and expression levels of the transcripts. The detection of coding transcripts saturated rapidly for both short-read and long-reads, however, there was no sign of saturation for noncoding transcripts at any sequencing depth. Increasing long-read sequencing depth specifically benefited transcripts containing transposable elements. Finally, we show how single-cell RNA-seq can be guided by transcripts assembled from bulk long-read samples, and demonstrate that noncoding transcripts are expressed at similar levels to coding transcripts but are expressed in fewer cells. ConclusionsThis study shows the impact of sequencing depth on transcript assembly. Sequencing read depth has a relatively minor impact on coding transcript assembly, but a major effect on the assembly of noncoding transcripts. This study highlights important factors to consider when deciding the sequencing read depths to be used for transcript assembly.

bioinformatics↗

bioRxiv2021

Human embryos arrest in a quiescent-like state characterized by metabolic and zygotic genome activation problems

Around 60% of in vitro fertilized (IVF) human embryos irreversibly arrest before compaction between the 3-8-cell stage, posing a significant clinical problem. The mechanisms behind this arrest are unclear. Here, we show that the arrested embryos enter a quiescent-like state, marked by cell cycle arrest, the downregulation of ribosomes and histones and downregulation of MYC and p53 activity. Mechanistically, the arrested embryos can be divided into three types. Type I embryos fail to complete the maternal-zygotic transition, and type II/III embryos have erroneously low levels of glycolysis and variable levels of oxidative phosphorylation. Treatment with resveratrol or nicotinamide riboside (NR) can partially rescue the arrested phenotype. The mechanism of reactivation involves the upregulation of SIRT1, and activation of glycolysis and fatty acid oxidation which forces the embryos out of a quiescent state. Overall, our data reveal how human embryo arrest can be overcome by modulating metabolic pathways.

developmental biology↗

bioRxiv2021

A programmable system to methylate and demethylate m6A on specific mRNAs

RNA N6-Methyladenosine (m6A) is the most abundant mRNA modification, and forms part of an epitranscriptomic system that modulates RNA function. RNA modifications can be reversibly catalyzed by several specific enzymes, and those modifications can be recognized by RNA binding proteins that in turn regulate biological processes. Although there are many reports demonstrating m6A participation in critical biological functions, this exploration has mainly been conducted through the global knockout or knockdown of the writers, erasers, or readers of m6A. Consequently, there is a lack of information about the role of m6A on single transcripts in biological processes, posing a challenge in understanding the biological functions of m6A. Here, we demonstrate a CRISPR/dCas13a-based RNA m6A-editor which can target mRNAs using single crRNA or multiple crRNAs array to methylate or demethylate m6A. We systematically assay its capabilities to enable the targeted rewriting of m6A dynamics, including modulation of circular RNA translation and transcript half-life. Finally, we demonstrate the utility of the system by specifically modulating XIST m6A levels, which can control X chromosome silencing and activation. Based on our editors, m6A on single and multiple transcripts can be modified to allow the exploration of the role of m6A on in biological processes.

cell biology↗

bioRxiv2017

Resolution of Reprogramming Transition States by Single Cell RNA-Sequencing

The Yamanaka factors convert mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs) through a highly heterogeneous process. Here we profile single cells undergoing an optimized 7-day reprogramming process and show that cells start reprogramming relatively in sync, but diverge into two branches around day 2. The first branch of cells expressing Cd34/Fxyd5/Psca become nonpluripotent. The second one contains cells that are first Oct4+, then Dppa5a+ and pluripotent. We show that IFN-{gamma} blocks this late transition. Our results reveal the heterogeneous nature of somatic cell reprogramming, identify Dppa5a as a marker for pluripotent and innate immunity as a potential barrier for reprogramming.\n\nOne Sentence SummarySingle cell RNA sequencing reveals a continuum of cell fates from somatic to pluripotent and Dppa5a as a marker for chimera-competent iPSCs.

cell biology↗