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Related Concept Videos

Reproductive Cloning01:27

Reproductive Cloning

32.8K
Reproductive cloning is the process of producing a genetically identical copy—a clone—of an entire organism. While clones can be produced by splitting an early embryo—similar to what happens naturally with identical twins—cloning of adult animals is usually done by a process called somatic cell nuclear transfer (SCNT).
Somatic Cell Nuclear Transfer
In SCNT, an egg cell is taken from an animal and its nucleus is removed, creating an enucleated egg. Then a somatic...
32.8K
Transcription01:10

Transcription

156.8K
Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
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Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

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Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a...
11.0K
Master Transcription Regulators02:23

Master Transcription Regulators

7.8K
Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
7.8K
Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

12.8K
Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These...
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Related Experiment Video

Updated: Feb 7, 2026

Reprogramming Mouse Embryonic Fibroblasts with Transcription Factors to Induce a Hemogenic Program
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Reprogramming Mouse Embryonic Fibroblasts with Transcription Factors to Induce a Hemogenic Program

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Reconstructing clone-resolved transcriptional programs from bulk tumor sequencing.

Jiaying Lai, Yi Yang, Kathleen Noller

    Biorxiv : the Preprint Server for Biology
    |February 6, 2026
    PubMed
    Summary
    This summary is machine-generated.

    PICTographPlus reconstructs clone-specific gene expression from bulk RNA sequencing data by integrating DNA-inferred tumor evolution. This method maps transcriptional programs to specific evolutionary transitions, revealing cancer clone dynamics.

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    Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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    Standardized Modular Assembly of Polycistronic Operons with Modular Cloning (MoClo) using the In-Cloning toolkit
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    Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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    Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

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    Area of Science:

    • Genomics
    • Computational Biology
    • Cancer Research

    Background:

    • Tumors consist of related clones with obscured evolutionary structures and clone-specific transcriptional programs in bulk sequencing data.
    • Inferring clonal architecture from bulk DNA sequencing is possible, but recovering clone-resolved transcriptional programs from bulk RNA-seq remains challenging.

    Purpose of the Study:

    • To develop a computational framework, PICTographPlus, for reconstructing clone-resolved transcriptomes by integrating DNA-inferred clonal phylogenies with bulk RNA-seq.
    • To enable inference of clone-specific gene expression and localization of pathway gains and losses to specific evolutionary transitions.

    Main Methods:

    • Developed PICTographPlus, a probabilistic framework utilizing a phylogeny-regularized mixture model.
    • Integrated DNA-inferred clonal phylogenies with bulk RNA-seq data.
    • Validated using single-cell derived clone structures and simulated bulk mixtures across varying tumor purities and sampling densities.

    Main Results:

    • Demonstrated robust recovery of clone-level gene set regulation.
    • Applied to lung and pancreatic cancer cohorts, revealing clone-restricted transcriptional programs.
    • Identified associations between transcriptional programs, tumor suppressor loss, and metastatic progression.

    Conclusions:

    • PICTographPlus transforms bulk assays into evolutionary, clone-resolved transcriptional maps.
    • Enables retrospective and cohort-scale analyses of tumor evolution and transcriptional programs without specialized experimental data.
    • Provides a powerful tool for understanding cancer heterogeneity and progression.