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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
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Updated: May 26, 2025

High-throughput Purification of Affinity-tagged Recombinant Proteins
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Master transcription factor binding sites constitute the core of early replication control elements.

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    Early Replication Control Elements (ERCEs) are key to genome replication timing and cell fate. These elements, composed of subERCEs, act as enhancers and structural organizers, driving epigenomic changes during cell transitions.

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    Area of Science:

    • Genomics
    • Epigenetics
    • Developmental Biology

    Background:

    • Eukaryotic genomes follow a replication timing (RT) program, crucial for development.
    • Mechanisms controlling RT and its role in cell fate transitions are not fully understood.
    • Early Replication Control Elements (ERCEs) were previously linked to early RT, transcription, and chromatin organization.

    Purpose of the Study:

    • To dissect the functional components of ERCEs.
    • To elucidate the mechanisms by which ERCEs regulate replication timing and transcription.
    • To understand the role of ERCEs in chromatin organization and cell fate transitions.

    Main Methods:

    • CRISPR-based deletion of subERCEs and transcription start sites in mouse embryonic stem cells (mESCs).
    • Analysis of replication timing (RT) profiles.
    • Assessment of genome-wide transcription levels.
    • Evaluation of 3D chromatin architecture and compartmentalization.

    Main Results:

    • ERCEs are compound elements (subERCEs) driven by master transcription factor binding and long-range interactions.
    • Deletion of subERCEs significantly impacted both transcription and RT.
    • Deletion of transcription start sites abolished transcription with moderate effects on RT.
    • SubERCEs function as both transcription enhancers and structural chromatin organizers supporting early RT.

    Conclusions:

    • SubERCEs are critical regulatory units within ERCEs.
    • A model is proposed where subERCEs integrate transcription factor signals to orchestrate transcription, chromatin structure, and early replication timing.
    • This mechanism may provide a feed-forward loop for robust epigenomic changes during cell fate transitions.