Biology subjects

Merzouk, S.

Publications and source records attributed to Merzouk, S..

7 recordsLinked to original sources

bioRxiv2026

Optimized parameters for Cas9 CRISPR interference library design

CRISPR interference (CRISPRi) is a powerful technology for studying loss-of-function phenotypes, enabling transient and reversible control of gene expression without the introduction of double-stranded DNA breaks. The cost of conducting large-scale CRISPR screens necessitates the selection of effective and specific sgRNAs for the design of compact libraries. While several genome-wide Cas9 CRISPRi libraries have been created, updates to transcript annotations, the generation of higher-resolution chromatin accessibility datasets and the development of newer on-target prediction models motivate an updated CRISPRi library design approach. Here, we generate large CRISPRi datasets tiling essential and nonessential genes. We compare the performance of multiple KRAB domain systems, develop an updated CRISPRi-specific on-target scoring scheme, and quantitatively characterize off-target effects associated with seed sequence patterns. We leverage these findings to design an optimized Cas9 CRISPRi library, Katsano, and validate its performance with genome-wide viability screens.

bioengineering↗

bioRxiv2025

HCFC1 and YY1 mediate recruitment of COMPASS and Integrator to initiate X chromosome inactivation.

The evolution of mammalian sex chromosomes has driven the emergence of mechanisms that balance X-linked gene dosage between male (XY) and female (XX) cells. In females, dosage compensation is achieved through X chromosome inactivation (XCI), initiated by upregulation of the long non-coding RNA Xist, which spreads in cis, recruiting chromatin modifiers to silence gene expression on one X chromosome. Here, we conducted a forward genetic screen and identified X-encoded Host Cell Factor 1 (HCFC1), a member of the COMPASS H3K4 methyltransferase complex, as a dose-dependent XCI-activator. HCFC1 loss results in genome-wide reduction of H3K4me3 at specific regulatory elements and downregulation of nearby genes, including Xist. We show that HCFC1 and YY1 are co-recruited genome-wide to gene regulatory elements. Mass spectrometry analysis confirmed an interaction of HCFC1 and YY1 and uncovered the Integrator complex as another prominent YY1 partner. YY1 depletion results in genome-wide loss of Integrator recruitment at gene regulatory elements and reduced expression of nearby genes, including Xist cis-regulatory genes Jpx and Ftx. These results highlight a co-regulatory role for HCFC1 in COMPASS recruitment and Xist activation, alongside YY1-mediated recruitment of Integrator to Xist regulatory elements and genes to activate female-exclusive XCI.

molecular biology↗

bioRxiv2025

Balancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library design

The continued development of high-dimensional CRISPR screen readouts, such as single-cell RNA sequencing and high-content imaging, necessitates compact libraries to enable functional interrogation at genome scale. Improved genome annotations yield library deprecation over time, further motivating an updated genome-wide design effort. Recently, we have developed an enhanced model, Rule Set 3, which leveraged an expansive training set and feature space to predict guide efficacy. However, the benefit of such advances to library design is limited by current approaches to balance predictions of on-target activity with off-target considerations. Here we present a guide selection strategy that identifies guides with sufficient off-target activity to justify omission from the library, thus avoiding the unnecessary exclusion of active guides. We pair this model with strategic design choices to create Jacquere, an updated, optimized, and validated Cas9 CRISPR knockout (CRISPRko) genome-wide library for the human genome.

genomics↗

bioRxiv2025

X-chromosome upregulation operates on a gene-by-gene basis at RNA and protein levels

Gene dosage compensation mechanisms are crucial for mammalian development. In mice, recent findings show that cells can sense the number of X chromosomes. Loss or inactivation of one of the two X chromosomes is compensated by upregulating the remaining active X chromosome, a process termed X-chromosome upregulation (XCU). However, how cells sense X-chromosome dosage and induce XCU remains unclear. Here, we show that heterozygous X chromosome fragment deletions in mouse pluripotent stem cells induces XCU in trans, and that compensation takes place at the mRNA and protein level. Furthermore, we found that inducing gene silencing in cis on autosomes induces gene dosage compensation in trans. This work provides significant insights into the molecular foundations of mammalian gene dosage compensation.

developmental biology↗

bioRxiv2024

Decoding primitive endoderm - epiblast interactions using mouse ICM embryoids

Stem cell-based embryo models are promising alternatives for investigating early embryogenesis. We introduce two distinct models to replicate the dynamics between extra-embryonic endoderm and epiblast during mouse embryonic development. Inducible Gata6 (iGata6) embryoid bodies (EBs), exclusively derived from iGata6 embryonic stem (ES) cells, are valuable for modeling the position-dependent development of the primitive endoderm. Inner cell mass (ICM) embryoids, conversely, efficiently formed by aggregating wild-type and iGata6 ES cells, accurately and at a comparable pace simulate in vivo development from E3.5 to E7.5. Notably, ICM embryoids model cell sorting and through a rosette-like stage, the transition of the epiblast from naive to primed pluripotency. Furthermore, the absence of extra-embryonic ectoderm-like cells in this model, directs both the epiblast and visceral endoderm towards an anterior developmental fate. As such, iGata6 EBs and ICM embryoids are powerful tools for advancing our understanding of cell fate decisions during early embryonic development in mice.

developmental biology↗

bioRxiv2020

SPEN is Required for Xist Upregulation during Initiation of X Chromosome Inactivation

At initiation of X chromosome inactivation (XCI), Xist is monoallelically upregulated from the future inactive X (Xi) chromosome, overcoming repression by its antisense transcript Tsix. Xist recruits various chromatin remodelers, amongst them SPEN, which are involved in silencing of X-linked genes in cis and establishment of the Xi. Here, we show that SPEN plays an important role in the initiation of XCI. Spen null female mouse embryonic stem cells (ESCs) are defective in Xist upregulation upon differentiation. We find that Xist-mediated SPEN recruitment to the Xi chromosome happens very early in XCI, and that SPEN-mediated silencing of the Tsix promoter is required for Xist upregulation. Accordingly, failed Xist upregulation in Spen-/- ESCs can be rescued by concomitant removal of Tsix. These findings indicate that SPEN is not only required for the establishment of the Xi, but is also crucial in the initiation of the XCI process.

developmental biology↗

bioRxiv2017

BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes

Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand-sequencing (Strand-seq) to map the genomic locations of SCEs at a resolution that is orders of magnitude better than was previously possible. Our results show that, in the absence of BLM, sister chromatid exchanges in human and murine cells do not occur randomly throughout the genome but are strikingly enriched at coding regions, specifically at sites of putative guanine quadruplex (G4) motifs in transcribed genes. We propose that BLM protects against genome instability by suppressing recombination at sites of G4 structures, particularly in transcribed regions of the genome.

cell biology↗