Biology subjects

Babarinde, I. A.

Publications and source records attributed to Babarinde, I. A..

8 recordsLinked to original sources

bioRxiv2026

A candidate HNRNPU-CHD2 RNA-processing axis in neurodevelopmental disease

Heterozygous loss-of-function variants in HNRNPU, which encodes a nuclear RNA-binding scaffold protein, cause a neurodevelopmental disorder with epilepsy, intellectual disability and brain malformations, but the programs that link HNRNPU dosage to neuronal dysfunction remain poorly defined. We depleted HNRNPU in Human embryonic kidney 293T (HEK293T) cells, profiled gene expression and alternative splicing, intersected the two datasets, and asked which of the resulting genes already carried a neurodevelopmental annotation. Knockdown produced 5,643 differentially expressed genes and 21,728 high-confidence splicing events; 1,222 genes changed at both levels, and two pre-specified neurodevelopmental panel genes were among them: CHD2 and DYRK1A. In K562 eCLIP experiments, 107 reproducible HNRNPU peaks were detected across the CHD2 gene body, and three of the four regulated exons introduce a reading-frame shift whose premature termination codon lies far upstream of the final exon junction, predicting nonsense-mediated decay. Public K562 knockdown data reproduced the rise in CHD2 mRNA and the same skipped-exon change, and CHD2 depletion in the neural line SH-SY5Y altered cell-cycle, DNA-repair and neural gene programs. HNRNPU therefore constrains a frameshift-prone splicing switch in CHD2, a candidate route from HNRNPU haploinsufficiency to loss of functional CHD2 if these transcripts are degraded.

cell biology↗

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

Modulating the epigenetic state promotes the reprogramming of transformed cells to pluripotency in a line-specific manner

Somatic cell reprogramming and oncogenic transformation share surprisingly similar features, yet transformed cells are highly resistant to reprogramming. There must be barriers that block transformed cells from reprogramming, but the nature of those barriers is unclear. In this study, we generated a systematic panel of transformed mouse embryonic fibroblasts (MEFs) using a variety of oncogenic transgenes, and discovered transformed cell lines that remain compatible with reprogramming when transfected with Oct4/Sox2/Klf4/Myc. By comparing the reprogramming-capable and incapable transformed lines we identified multiple stages of failure in the reprogramming process. Some transformed lines failed very early, whilst other lines seemed to progress through a normal-looking reprogramming process. Finally, we show that MEK inhibition overcomes one critical reprogramming barrier by indirectly suppressing a hyperactive epigenetic state in some of the transformed cells. This study reveals that the barriers underlying resistance to reprogramming vary between the different transformation methods. Key findingsO_LISomatic cell reprogramming of transformed cells is context-specific C_LIO_LIInhibition of MEK converts some cell lines to reprogramming-capable C_LIO_LITransformed cell lines are characterized by a hyperactive chromatin state C_LIO_LIMEK inhibition indirectly affects chromatin to enable reprogramming C_LI

cell biology↗

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↗

bioRxiv2020

Transposable Element-Gene Splicing Modulates the Transcriptional Landscape of Human Pluripotent Stem Cells

Transposable elements (TEs) occupy nearly 50% of mammalian genomes and are both potential dangers to genome stability and functional genetic elements. TEs can be expressed and exonised as part of a transcript, however, their full contribution to the transcript splicing remains unresolved. Here, guided by long and short read sequencing of RNAs, we show that 26% of coding and 65% of non-coding transcripts of human pluripotent stem cells (hPSCs) contain TEs. Different TE families have unique integration patterns with diverse consequences on RNA expression and function. We identify hPSC-specific splicing of endogenous retroviruses (ERVs) as well as LINE L1 elements into protein coding genes that generate TE-derived peptides. Finally, single cell RNA-seq reveals that proliferating hPSCs are dominated by ERV-containing transcripts, and subpopulations express SINE or LINE-containing transcripts. Overall, we demonstrate that TE splicing modulates the pluripotency transcriptome by enhancing and impairing transcript expression and generating novel transcripts and peptides.

genomics↗

bioRxiv2020

Unveiling transposable element expression heterogeneity in cell fate regulation at the single-cell level

Transposable elements (TEs) make up a majority of a typical eukaryotes genome, and contribute to cell heterogeneity and fate in unclear ways. Single cell-sequencing technologies are powerful tools to explore cells, however analysis is typically gene-centric and TE activity has not been addressed. Here, we developed a single-cell TE processing pipeline, scTE, and report the activity of TEs in single cells in a range of biological contexts. Specific TE types were expressed in subpopulations of embryonic stem cells and were dynamically regulated during pluripotency reprogramming, differentiation, and embryogenesis. Unexpectedly, TEs were expressed in somatic cells, including human disease-specific TEs that are undetectable in bulk analyses. Finally, we applied scTE to single cell ATAC-seq data, and demonstrate that scTE can discriminate cell type using chromatin accessibly of TEs alone. Overall, our results reveal the dynamic patterns of TEs in single cells and their contributions to cell fate and heterogeneity.

bioinformatics↗