Biology subjects

Jauch, R.

Publications and source records attributed to Jauch, R..

5 recordsLinked to original sources

bioRxiv2025

A scalable screening platform for discovering predominant miRNA target genes and druggable siRNA sequences

Programmable RNA-targeting systems, including RNA interference (RNAi) and CRISPR-Cas13, are transformative tools for research and therapeutics. However, a lack of high-resolution comparative data obscures whether these mechanistically distinct platforms share fundamental rules for target-site selection. To address this, we developed shRNAone, an engineered scaffold that eliminates processing heterogeneity to guarantee guide biogenesis at single-nucleotide precision. Deploying this platform to systematically decouple microRNA pairing rules in cellulo, we demonstrate that while seed pairing drives primary target recognition, 3'-supplementary pairing is strictly essential for specific transcript repression. Furthermore, single-nucleotide shRNAone tiling screens accurately predict siRNA efficacy and reveal clustered, highly permissive silencing hotspots localized within 3' UTRs. By mapping CasRx and PspCas13b silencing landscapes across the identical mRNA, we show that these hotspots represent intrinsic structural vulnerabilities governed by local RNA accessibility. However, while shRNAone and CasRx activity is largely restricted to the 3' UTR, PspCas13b efficiently targets the coding sequence, highlighting its unique capacity to overcome ribosome occupancy. Together, these high-resolution profiles define the shared and distinct structural barriers governing diverse RNA-targeting systems and provide a rationally designed, transcriptome-wide guide resource for PspCas13b applications.

molecular biology↗

bioRxiv2024

BRD8 guards the pluripotent state by sensing and maintaining histone acetylation

Epigenetic control of cell fates is a critical determinant to maintain cell type stability and permissive differentiation. However, the epigenetic control mechanisms are not well understood. Here, we show that the histone acetyltransferase reader protein BRD8 impairs the conversion of primed mouse EpiSCs (epiblast stem cells) to naive mouse ESCs (embryonic stem cells). BRD8 works by maintaining histone acetylation on promoters and transcribed gene bodies. BRD8 is responsible for maintaining open chromatin at somatic genes, and histone acetylation at naive-specific genes. When Brd8 expression was reduced, chromatin accessibility was unchanged, but histone acetylation at primed-specific genes was reduced. Conversely, naive-specific genes had reduced repressive chromatin marks, and acquired accessible chromatin more rapidly during the cell type conversion. We show that this process requires active histone deacetylation to promote the conversion of primed to naive. Our data supports a model for BRD8 reading histone acetylation to accurately localize the genome-wide binding of the histone acetyltransferase KAT5. Overall, this study shows how the reading of the histone acetylation state by BRD8 maintains cell type stability. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/585857v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@199139forg.highwire.dtl.DTLVardef@d735c6org.highwire.dtl.DTLVardef@10b6e15org.highwire.dtl.DTLVardef@16863cf_HPS_FORMAT_FIGEXP M_FIG C_FIG Key findingsO_LIBRD8 blocks the primed-to-naive transition. C_LIO_LIReduced Brd8 promoted the suppression of somatic and primed genes through reduced chromatin repression. C_LIO_LIReduced Brd8 enabled the accelerated activation of naive-specific genes by opening chromatin. C_LIO_LIBRD8 anchors the histone acetyltransferase KAT5 to acetylated genomic loci. C_LI

cell biology↗

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

Enhancing Sox/Oct cooperativity induces higher-grade developmental reset

The discovery of induced pluripotent stem cell (iPSC) technology by Shinya Yamanaka has truly enabled the stem cell field. After 16 years of intense research, the delivery methods and culture media have improved but the original factors--Oct4, Sox2, Klf4, and Myc (OSKM)--remain central for driving reprogramming. Here we define structural elements in chimeric Sox2/Sox17 transcription factors that rescued the ability of nonfunctional Oct factors to induce pluripotency. Most importantly, we discovered a single amino acid swap in the DNA-binding domain of Sox2, A61V, that stabilizes the Sox/Oct heterodimer on DNA through hydrophobic interaction with Oct. The highly cooperative Sox2AV mutant enables iPSC generation with Oct4 orthologs, such as Oct2 and Oct6, as well as rescues otherwise detrimental Oct4 mutants and domain deletions. Sox2AV has a dramatic effect on the cell fate reset, significantly improving the developmental potential of OSKM iPSCs. Moreover, by swapping multiple beneficial elements of Sox17 into Sox2 we have built a chimeric super-SOX factor--Sox2-17--that delivers unprecedented reprogramming efficiency and kinetics in five tested species. Sox2-17 enhances five-, four-, and three-factor reprogramming up to hundreds of times, enables two-factor generation of human iPSCs, and allows integration-free reprogramming of otherwise non-permissive aged human, non-human primate, and cattle fibroblasts. Our study demonstrates that a complete developmental reset requires both robust activation of regulatory elements controlled by the canonical SoxOct motif and limiting cellular proliferation driven by Oct4 and Myc. A high level of Sox2 expression and Sox2/Oct4 heterodimerization emerge as the key determinants of high-grade pluripotency that fades along the naive-to-primed continuum. Transient expression of SK cocktail can restore the naivety, providing a powerful technology to induce more complete developmental reset in pluripotent cells across species.

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↗