Reconstitution of MSL2 binding in vtiro
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA715747 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14009300_1.fastq.gz | Fastqsanger.gz | |||
| SRR14009300_2.fastq.gz | Fastqsanger.gz | |||
| SRR14009301_1.fastq.gz | Fastqsanger.gz | |||
| SRR14009301_2.fastq.gz | Fastqsanger.gz | |||
| SRR14009302_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcription factors distinguish functional response elements from a large excess of similar sequences in metazoan genomes. Faithful discrimination relies on DNA sequence and shape, but how shape is modulated by chromatin organisation is unclear. We explored binding site selection principles by blending unique biological and experimental systems. First, we assemble Drosophila genomes into physiological embryonic chromatin as a substrate for genome-wide binding assays. Secondly, we monitor binding site selection of a protein, MSL2, for which all functional elements reside on the X chromosome. We observe direct and nucleosome-mediated cooperativity between MSL2 and two other transcription factors and discover an extended DNA shape signature of functional elements that is read out in chromatin. Strikingly, the physiological binding profile is not achieved through intrinsic properties of MSL2 but is sculpted by an unrelated transcription factor, GAF, that occludes non-functional sites. Our results reveal novel aspects of target selection in a complex chromatin environment.
2021-06-10 | GSE169222 | GEO
Project description:MSL2, the DNA-binding subunit of the Drosophila dosage compensation complex, cooperates with the ubiquitous protein CLAMP to bind MSL recognition elements (MREs) on the X chromosome. We explore the nature of the cooperative binding to these GA-rich, composite sequence elements in reconstituted naïve embryonic chromatin. We found that the cooperativity requires physical interaction between both proteins. Remarkably, disruption of this interaction does not lead to indirect, nucleosome-mediated cooperativity as expected, but to competition. The protein interaction apparently not only increases the affinity for composite binding sites, but also locks both proteins in a defined dimeric state that prevents competition. High Affinity Sites of MSL2 on the X chromosome contain variable numbers of MREs. We find that the cooperation between MSL2/CLAMP is not influenced by MRE clustering or arrangement, but happens largely at the level of individual MREs. The sites where MSL2/CLAMP bind strongly in vitro locate to all chromosomes and show little overlap to an expanded set of X-chromosomal MSL2 in vivo binding sites generated by CUT&RUN. Apparently, the intrinsic MSL2/CLAMP cooperativity is limited to a small selection of potential sites in vivo. This restriction must be due to components missing in our reconstitution, such as roX2 lncRNA.
2023-07-27 | GSE228935 | GEO
Project description:We used H83M2 P element to ectopically expressed MSL2 protein in females to test if the novel formed MSL complex is the directly reason of dosage compensation Compare the MSL2 females with normal females and normal males; MSL2 males also included.
2012-10-16 | E-GEOD-41570 | biostudies-arrayexpress
Project description:Biallelic expression is important to ensure adequate mRNA levels as well as protect cells from deleterious heterozygous mutations. However, the factors determining biallelic expression at individual gene loci are unknown. Deletion of the MSL complex component MSL2 in hybrid mouse NPCs uncovers an unprecedented function for MSL2 in allelic regulation. While biallelically expressed in wildtype NPCs, a class of MSL2 targets switches from bi to monoallelic expression upon MSL2 loss. The silenced allele loses nascent transcription, accompanied by dramatic changes in local chromatin landscape such as monoallelic gain of H3K27me3 and DNA methylation. Meanwhile, active histone modifications, RNA POL II, BRD4 and KANSL3 are retained on the active allele. MSL2 targets include several sex-biased genes on autosomes as well as X-chromosomal genes that escape X inactivation. Together, the allele-specific resolution allowed us to unravel an MSL2 mediated safeguarding mechanism to promote biallelic gene expression of sexually dimorphic and dosage-sensitive genes in mammals.
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Project description:Biallelic expression is important to ensure adequate mRNA levels as well as protect cells from deleterious heterozygous mutations. However, the factors determining biallelic expression at individual gene loci are unknown. Deletion of the MSL complex component MSL2 in hybrid mouse NPCs uncovers an unprecedented function for MSL2 in allelic regulation. While biallelically expressed in wildtype NPCs, a class of MSL2 targets switches from bi to monoallelic expression upon MSL2 loss. The silenced allele loses nascent transcription, accompanied by dramatic changes in local chromatin landscape such as monoallelic gain of H3K27me3 and DNA methylation. Meanwhile, active histone modifications, RNA POL II, BRD4 and KANSL3 are retained on the active allele. MSL2 targets include several sex-biased genes on autosomes as well as X-chromosomal genes that escape X inactivation. Together, the allele-specific resolution allowed us to unravel an MSL2 mediated safeguarding mechanism to promote biallelic gene expression of sexually dimorphic and dosage-sensitive genes in mammals.
2023-08-10 | GSE183765 | GEO
Project description:Biallelic expression is important to ensure adequate mRNA levels as well as protect cells from deleterious heterozygous mutations. However, the factors determining biallelic expression at individual gene loci are unknown. Deletion of the MSL complex component MSL2 in hybrid mouse NPCs uncovers an unprecedented function for MSL2 in allelic regulation. While biallelically expressed in wildtype NPCs, a class of MSL2 targets switches from bi to monoallelic expression upon MSL2 loss. The silenced allele loses nascent transcription, accompanied by dramatic changes in local chromatin landscape such as monoallelic gain of H3K27me3 and DNA methylation. Meanwhile, active histone modifications, RNA POL II, BRD4 and KANSL3 are retained on the active allele. MSL2 targets include several sex-biased genes on autosomes as well as X-chromosomal genes that escape X inactivation. Together, the allele-specific resolution allowed us to unravel an MSL2 mediated safeguarding mechanism to promote biallelic gene expression of sexually dimorphic and dosage-sensitive genes in mammals.
2023-08-10 | GSE183764 | GEO
Project description:Allele-specific gene expression have been observed in genomic imprinting, X chromosome inactivation, allelic exclusion of immunoglobulin loci and non-canonical random monoallelic expression. Here we show that MSL2 can regulate allele specific gene expression and we elucidate its mechanism of action. MSL2 is known to regulate gene dosage up to two fold in drosophila and mammals. In addition to its canonical role as a milder modulator, we found that the loss of MSL2 switches off gene expression completely in an allele specific way and results in biallelic to monoallelic gene expression, which will be ignored as classical down regulated genes without applying the mouse hybrid F1 system. It indicates that MSL2 can activate the expression of the allele which is otherwise inactive intrinsically. We further found this is achieved by the interplay between MSL and KANSL complex. MSL2 acts as a methylation-insensitive factor, which can prevent DNA methylation of the inactive allele, thus facilitating occupancy of methylation-sensitive factor KANSL3 and activating the gene expression. The novel mechanism of MSL2 provides a safeguarding system to warrant biallelic gene expression of intrinsically monoallelic expressed genes including X-inactivated and imprinting genes. These genes are further discovered as sex bias genes such as X-inactivation escaped genes (escapees) are expressed higher in females. Furthermore, the biallelic expression of MSL2 regulated escapees may protect females from single loss of function mutation and contribute to male severer or predominance neurodevelopmental diseases.
2023-08-10 | GSE227741 | GEO
Project description:Allele-specific gene expression have been observed in genomic imprinting, X chromosome inactivation, allelic exclusion of immunoglobulin loci and non-canonical random monoallelic expression. Here we show that MSL2 can regulate allele specific gene expression and we elucidate its mechanism of action. MSL2 is known to regulate gene dosage up to two fold in drosophila and mammals. In addition to its canonical role as a milder modulator, we found that the loss of MSL2 switches off gene expression completely in an allele specific way and results in biallelic to monoallelic gene expression, which will be ignored as classical down regulated genes without applying the mouse hybrid F1 system. It indicates that MSL2 can activate the expression of the allele which is otherwise inactive intrinsically. We further found this is achieved by the interplay between MSL and KANSL complex. MSL2 acts as a methylation-insensitive factor, which can prevent DNA methylation of the inactive allele, thus facilitating occupancy of methylation-sensitive factor KANSL3 and activating the gene expression. The novel mechanism of MSL2 provides a safeguarding system to warrant biallelic gene expression of intrinsically monoallelic expressed genes including X-inactivated and imprinting genes. These genes are further discovered as sex bias genes such as X-inactivation escaped genes (escapees) are expressed higher in females. Furthermore, the biallelic expression of MSL2 regulated escapees may protect females from single loss of function mutation and contribute to male severer or predominance neurodevelopmental diseases.
2023-08-10 | GSE231588 | GEO
Project description:We have studied the regulatory potential of MYST1-(MOF)-containing MSL and NSL complexes in mouse embryonic stem cells (ESCs) and neuronal progenitors. We find that both complexes influence transcription by binding to promoters as well as TSS-distal enhancer regions. In contrast to flies, the MSL complex is not enriched on the X chromosome yet it is crucial for mammalian X chromosome regulation as it specifically regulates Tsix ncRNA, the major repressor of Xist lncRNA. MSL depletion leads to severely decreased Tsix expression, reduced REX1 recruitment, and consequently accumulation of Xist RNA in ESCs. The NSL complex provides additional, Tsix-independent repression of Xist by maintaining pluripotency. MSL and NSL complexes therefore act synergistically by using distinct pathways to ensure a fail-safe mechanism for the repression of X inactivation in ESCs. We have performed ChIP-seq of KANSL3, MCRS1, MOF, MSL1 and MSL2 in mouse ESCs, and KANSL3, MOF and MSL2 in NPCs, in duplicate and normalised against their inputs. We have also performed RNA-seq following knockdown of Kansl3, Mof, Msl1 and Msl2 mouse embryonic stem cells in triplicate. NB: Kansl3 and Mof knockdown-RNAseq are analyzed against their own scrambled controls, and Msl1 and Msl2 against another scrambled control triplicate.
2014-06-03 | E-GEOD-57698 | biostudies-arrayexpress
Project description:Transcription factors have to distinguish proper targets from a large pool of potential binding sites. Here we explore how MSL2 and CLAMP cooperate to bind their specific targets. Using an in vitro chromatin reconstitution system and by mutating the interaction domain of CLAMP we show how direct and indirect cooperation of TF binding influence binding specificity.
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