Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naïve Pluripotency

N, Mor; Rais, Yoach; Peles, Shani; Sheban, Daoud; Aguilera-Castrejon, Alejandro; Zviran, Asaf; Elinger, Dalia; Viukov, Sergey; Geula, Shay; Krupalnik,; Zerbib, Mirie; Chomsky, Elad; Lasman, Lior; Shani, Tom; Bayerl, Jonathan; Gafni, Ohad; Hanna, Suhair; Buenrostro, JD; Hagai, Tzachi; Masika, Hagit; Bergman, Yehudit; Wj, Greenleaf; Esteban, M. Ángeles; Levin, Yishai; Massarwa, Rada; Merbl, Yifat; Novershtern, Noa; Jh, Hanna

doi:10.1101/192781

Cited by 4 publications

(2 citation statements)

References 90 publications

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“…The NuRD complex plays a crucial function in embryonic stem cell biology and development, and cancer [1][2][3]. The NuRD complex consists of seven core subunits, namely MTA, HDAC, RBBP, MBD, GATAD2, CDK2AP1, and CHD, with each subunit interchangeable with its paralogous family members: MTA1, MTA2 and MTA3; HDAC1 and HDAC2; RBBP4 and RBBP7; MBD3 and MBD2; GATAD2A and GATAD2B; CHD3, CHD4 and CHD5 [4][5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Unique protein interaction networks define the chromatin remodelling module of the NuRD complex

et al. 2021

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The combination of four proteins and their paralogues including MBD2/3, GATAD2A/B, CDK2AP1, and CHD3/4/5, which we refer to as the MGCC module, form the chromatin remodeling module of the Nucleosome Remodeling and Deacetylase (NuRD) complex. To date, mechanisms by which the MGCC module acquires paralogue-specific function and specificity have not been addressed. Understanding the protein-protein interaction (PPI) network of the MGCC subunits is essential in defining underlying mechanisms of gene regulation. Therefore, using pulldown followed by mass spectrometry analysis (PD-MS) we report a proteome-wide interaction network of the MGCC module in a paralogue-specific manner. Our data also demonstrate that the disordered C-terminal region of CHD3/4/5 is a gateway to incorporate remodeling activity into both the ChAHP (CHD4, ADNP, HP1γ) and NuRD complexes in a mutually exclusive manner.We define a short aggregation prone region (APR) within the C-terminal segment of GATAD2B that is essential for the interaction of CHD4 and CDK2AP1 with the NuRD complex. Finally, we also report an association of CDK2AP1 with the Nuclear Receptor Co-Repressor (NCOR) complex. Overall, this study provides insight into the possible mechanisms through which the MGCC module can achieve specificity and diverse biological functions.

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Section: Introductionmentioning

confidence: 99%

Unique protein interaction networks define the chromatin remodelling module of the NuRD complex

et al. 2021

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“…ChIP-seq analysis -CTCF and Max-Myc. Myc ChIP-seq datasets (79)(80)(81) were merged. Reads of ChIP-seq data (CTCF ChIP data (10) and merged Myc ChIP-seq data) at a 500 bp window surrounding unique CTCF or Max-Myc binding sites were counted using the qCount function from the R package QuasR (58).…”

Section: Smf -State Frequencies and Fraction Methylation Tfbsmentioning

confidence: 99%

Single molecule multi-omics reveals context-dependent regulation of enhancers by DNA methylation

Kreibich

Kleinendorst²,

Barzaghi

et al. 2022

Preprint

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Enhancers are cis-regulatory elements that control the establishment of cell identities during development. In mammals, enhancer activation is tightly coupled with local DNA de-methylation. Yet, whether this epigenetic remodelling is necessary for enhancer activation is unknown. Here, we developed a single molecule multi-omics approach to measure chromatin accessibility and transcription factor binding as a function of the presence of methylation on the same DNA molecules. We leveraged natural epigenetic heterogeneity at active enhancers to test the impact of DNA methylation on their activity in multiple cell lineages. While reduction of DNA methylation appears dispensable for the activity of most enhancers, we identify a class of cell-type-specific enhancers where presence of DNA methylation antagonises the binding of transcription factors. Genetic perturbations reveal that chromatin accessibility and transcription factor binding are a direct function of active demethylation at these loci. Thus, in addition to safeguarding the genome from spurious activation, DNA methylation directly controls transcription factor occupancy at cell-type-specific active enhancers.

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High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency

Zviran

Mor

Rais

et al. 2017

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The ability to reprogram somatic cells into induced pluripotent stem cells (iPSCs) with four transcription factors Oct4, Sox2, Klf4 and cMyc (abbreviated as OSKM) 1 has provoked interest to define the molecular characteristics of this process 2-7 . Despite important progress, the dynamics of epigenetic reprogramming at high resolution in correctly reprogrammed iPSCs and throughout the entire process remain largely undefined. This gap in understanding results from the inefficiency of conventional reprogramming methods coupled with the difficulty of prospectively isolating the rare cells that eventually correctly reprogram into iPSCs. Here we characterize cell fate conversion from fibroblast to iPSC using a highly efficient deterministic murine reprogramming system engineered through optimized inhibition of Gatad2a-Mbd3/NuRD repressive sub-complex. This comprehensive characterization provides single-day resolution of dynamic changes in levels of gene expression, chromatin modifications, TF binding, DNA accessibility and DNA methylation. The integrative analysis identified two transcriptional modules that dominate successful reprogramming. One consists of genes whose transcription is regulated by on/off epigenetic switching of modifications in their promoters (abbreviated as ESPGs), and the second consists of genes with promoters in a constitutively active chromatin state, but a dynamic expression pattern (abbreviated as CAPGs). ESPGs are mainly regulated by OSK, rather than Myc, and are enriched for cell fate determinants and pluripotency factors. CAPGs are predominantly regulated by Myc, and are enriched for cell biosynthetic regulatory functions. We used the ESPG module to study the identity and temporal occurrence of activating and repressing epigenetic switching during reprogramming. Removal of repressive chromatin modifications precedes chromatin opening and binding of RNA polymerase II at enhancers and promoters, and the opposite dynamics occur during repression of enhancers and promoters. Genome wide DNA methylation analysis demonstrated that de novo DNA methylation is not required for highly efficient conducive iPSC reprogramming, and identified a group of super-enhancers targeted by OSK, whose early demethylation marks commitment to a successful reprogramming trajectory also in inefficient conventional reprogramming systems. CAPGs are distinctively regulated by multiple synergystic ways: 1) Myc activity, delivered either endogenously or exogenously, dominates CAPG expression changes and is indispensable for induction of pluripotency in somatic cells; 2) A change in tRNA codon usage which is specific to CAPGs, but not ESPGs, and favors their translation. In summary, our unbiased high-resolution mapping of epigenetic changes on somatic cells that are committed to undergo successful reprogramming reveals interleaved epigenetic and biosynthetic reconfigurations that rapidly commission and propel conducive reprogramming toward naïve pluripotency. correlation above 0.5 between consecutive samples ( Extended Data...

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Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naïve Pluripotency

Cited by 4 publications

References 90 publications

Unique protein interaction networks define the chromatin remodelling module of the NuRD complex

Unique protein interaction networks define the chromatin remodelling module of the NuRD complex

Single molecule multi-omics reveals context-dependent regulation of enhancers by DNA methylation

High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency

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