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Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

Transcription Factors

JoVE 10983

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of certain tissues or body parts without affecting the entire organism. An additional layer of complexity is added by transcription factors in eukaryotes exerting combinatorial control. That means input provided by several transcription factors synchronously regulate the expression of a single gene. The combination of several transcriptional activators and repressors enables a gene to be differentially regulated and adapt to a variety of environmental changes without the need for additional genes.

 Core: Biology

Transcription

JoVE 10794

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. In eukaryotes, the DNA is first transcribed into a primary RNA, or pre-mRNA, that can be further processed into a mature mRNA to serve as a template for the synthesis of proteins. In prokaryotes such as bacteria, however, translation of RNA into polypeptides can begin while the transcription is still ongoing, as RNA can be quickly degraded. Transcription can also produce different kinds RNA molecules that do not code for protein, such as microRNAs, transfer RNA (tRNA), and ribosomal RNA (rRNA)—all of which contribute to protein synthesis. With few exceptions, all of the cells in the human body have the same genetic information in them, from neurons in the brain to muscle cells in the heart. So how do cells assume such diverse forms and functions? To a large extent, the answer lies in the regulation of transcription during development of the organism. Specifically, transcriptional regulation plays a central ro

 Core: Biology

Hemogenic Reprogramming of Human Fibroblasts by Enforced Expression of Transcription Factors

1Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 2Wallenberg Center for Molecular, Lund University, 3Center for Neuroscience and Cell Biology, University of Coimbra, 4Skolkovo Institute of Science and Technology, 5Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 6Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai

JoVE 60112

 Developmental Biology

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

1Institute for Diabetes and Obesity (IDO), German Center for Diabetes Research (DZD), Helmholtz Zentrum München, 2Institute for Informatics, Ludwig-Maximilians-Universität München, 3Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg

JoVE 56752

 Genetics

What is Gene Expression?

JoVE 10797

Gene expression is the process in which DNA directs the synthesis of functional products, such as proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino acids, a mediator is required to convert the information that is encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription takes place in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and transported into the cytoplasm where it serves as a template for protein synthesis during translation. In prokaryotes, which lack a nucleus, the processes of transcription and translation occur at the same location and almost simultaneously since the newly-formed mRNA is susceptible to rapid degradation. Every cell of an organism contains the same DNA, and consequently the same set of genes. However, not all genes in a cell are “turned on” or use to synthesize proteins. A gene is said to be “expressed” when the protein it encodes is produced by the cell. Gen

 Core: Biology

Intracellular Signaling Cascades

JoVE 10721

Intracellular signaling cascades amplify a signal originating extracellularly and directs it to its intended intracellular target resulting in transcription, translation, protein modifications, enzyme activation, cellular metabolism, mitosis, and/or apoptosis.

The most basic of signaling cascades involves the activation of second messengers and the release of kinases. Kinases activate or deactivate proteins and enzymes by adding a phosphate group to them. Phosphatases remove phosphate groups resulting in the deactivation or reactivation of proteins. The cyclic AMP (cAMP) pathway is named for its second messenger, cAMP. This pathway is most often initiated when a ligand binds to a G-coupled protein receptor. The G-protein decouples from the receptor and triggers adenylate cyclase to synthesize cAMP from ATP. For each ligand-receptor interaction, multiple cAMP molecules are generated—amplifying the signal. cAMP activates protein kinase A (PKA). PKA is a tetramer molecule with two regulatory subunits and two active subunits. When four cAMP molecules interact with a PKA molecule, it releases the two active subunits. These PKA subunits phosphorylate target proteins and enzymes. In the case of gene expression, PKA activates CREB, a transcription factor in the nucleus. The steps that precede the intracellular signaling cascade that is the lig

 Core: Biology

Bacterial Signaling

JoVE 10713

At times, a group of bacteria behaves like a community. To achieve this, they engage in quorum sensing, the perception of higher cell density that results in a shift in gene expression. Quorum sensing involves both extracellular and intracellular signaling. The signaling cascade starts with a molecule called an autoinducer (AI). Individual bacteria produce AIs that move out of the bacterial cell membrane into the extracellular space. AIs can move passively along a concentration gradient out of the cell, or be actively transported across the bacterial membrane. When cell density in the bacterial populations is low, the AIs diffuse away from the bacteria, keeping the environmental concentration of AIs low. As bacteria reproduce and continue to excrete AIs, the concentration of AIs increases, eventually reaching a threshold concentration. This threshold permits AIs to bind membrane receptors on the bacteria, triggering changes in gene expression across the whole bacterial community. Many bacteria are broadly classified as gram positive or gram negative. These terms refer to the color that the bacteria take on when treated with a series of staining solutions which were developed by Hans Christian Joachim Gram over a century ago. If bacteria pick up a purple color, they are gram-positive; if they look red, they are gram-negative. These stain colors are pic

 Core: Biology

Internal Receptors

JoVE 11011

Many cellular signals are hydrophilic and therefore cannot pass through the plasma membrane. However, small or hydrophobic signaling molecules can cross the hydrophobic core of the plasma membrane and bind to internal, or intracellular, receptors that reside within the cell. Many mammalian steroid hormones use this mechanism of cell signaling, as does nitric oxide (NO) gas.

Similar to membrane-bound receptors, binding of a ligand to a receptor located in the cytoplasm or nucleus of a cell causes a conformational change in the receptor. Like transcription factors, the active receptor can bind to receptor-specific DNA binding sites to increase or decrease the transcription of target genes. In the case of an intracellular receptor located in the cytoplasm, the receptor-ligand complex must first cross the nuclear membrane. Many steroid hormones, including estrogen and testosterone, use intracellular receptors to induce specific effects. As an example, estrogen can diffuse across the membrane; binding of estrogen to its receptor results in dimerization of the receptors and transport of the ligand-receptor complex to the nucleus. Once in the nucleus, the complex can bind to DNA sequences called Estrogen-Response Elements (EREs). Depending on the other transcription factors and co-activators, binding of activated estrogen receptors (ERs) to EREs may cause an incre

 Core: Biology

Intracellular Hormone Receptors

JoVE 10876

Lipid-soluble hormones diffuse across the plasma and nuclear membrane of target cells to bind to their specific intracellular receptors. These receptors act as transcription factors that regulate gene expression and protein synthesis in the target cell

Based on their mode of action, intracellular hormone receptors are classified as Type I or Type II receptors. Type I receptors, including steroid hormone receptors such as the androgen receptor, are present in the cytoplasm. Hormone binding transports the hormone-receptor complex to the nucleus, where it binds to regulatory DNA sequences called hormone response elements and activates gene transcription. Type II receptors, such as the thyroid hormone receptor, are bound to their DNA response elements within the nucleus even in the absence of hormone. In this state, the receptor acts as an active repressor of transcription. However, upon hormone binding, the receptor-hormone complex activates transcription of thyroid hormone-inducible genes.

 Core: Biology

Induced Pluripotent Stem Cells

JoVE 10812

Stem cells are undifferentiated cells that divide and produce different types of cells. Ordinarily, cells that have differentiated into a specific cell type are post-mitotic—that is, they no longer divide. However, scientists have found a way to reprogram these mature cells so that they “de-differentiate” and return to an unspecialized, proliferative state. These cells are also pluripotent like embryonic stem cells—able to produce all cell types—and are therefore called induced pluripotent stem cells (iPSCs). iPSCs are potentially valuable in medicine, because a patient who needs a particular cell type—for instance, someone with a damaged retina due to macular degeneration—could receive a transplant of the required cells, generated from another cell type in their own body. This is called autologous transplantation, and it reduces the risk of transplant rejection that can occur when tissues are transplanted between individuals. To create iPSCs, mature cells such as skin fibroblasts or blood cells from a person are grown in culture. Then, genes for multiple transcription factors are delivered into the cells using a viral vector, and the transcription factor proteins are expressed using the cell’s machinery. The transcription factors then turn on many other genes that are expressed by embryonic stem cells, re

 Core: Biology
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