Name: sirna in gene silencing
Uploaded: 2023-04-30T18:28:46.000Z
Duration: 2 min 30 s
Channel: JoVE

K12 Standards

Alabama Course of Study Science

9-12

Biology

from-molecules-to-organisms-structures-and-processes

From Molecules to Organisms: Structures and Processes

9-12.B.1.2

Small interfering RNAs (siRNA)

Small interfering RNAs, or siRNAs, are non-coding RNAs, about 22 nucleotides long, that regulate mRNA synthesis and stability.
siRNA can originate from within the cell by DNA transcription, can be processed from viral RNA, or can be added by scientists for experimental purposes.
siRNAs are processed from long double-stranded RNA. This RNA is cleaved into multiple short siRNAs with the help of an endonuclease, Dicer.&#160;
Each siRNA then binds to Argonaute, along with other proteins, leading to the formation of the RNA induced silencing complex, or RISC.
In RISC, the RNA guide strand is separated from its complementary strand and remains in the complex, so it can then pair with the target mRNA. Then, the target mRNA is cleaved with the help of Argonaute and subsequently degraded in the cytoplasm.&#160;
During their life cycle, RNA based viruses enter a host cell and produce double-stranded RNA. This RNA is recognized by Dicer and processed into siRNA. These siRNAs help fight viral infections by promoting the degradation of viral mRNA.&#160;
In the nucleus, centromere-associated DNA repeats encode transcripts that are processed by Dicer to produce specific types of siRNA.&#160; Unlike cytoplasmic siRNA

small interfering rnas (sirna)

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level&#160;in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the ATP-dependent riboendonuclease, Dicer, into 21-23 nucleotide long fragments with two nucleotide overhangs at both ends. This siRNA is then loaded onto another protein, Argonaute. Argonaute has four different domains &#8211; N-terminal, PAZ, Mid, and PIWI. Its PIWI domain has an RNase activity that enables Argonaute to cleave target mRNA. The Argonaute-siRNA complex then binds with a helicase and other proteins to form the RNA induced silencing complex (RISC). In RISC, the sense strand is separated from the antisense, or guide strand, which is thought to be catalyzed by the helicase. The sense strand is degraded in the cytoplasm, and the guide strand directs RISC towards a complementary target mRNA.
The fate of the target mRNA is determined by whether the guide mRNA shows optimal or suboptimal base-pairing with the target mRNA. If the guide strand shows optimal base-pairing with the target mRNA, then the target mRNA is cleaved by Argonaute. The RISC complex is then reused again to target another mRNA. In contrast, if the guide strand shows suboptimal base-pairing with the target mRNA strand, Argonaute will not cleave the mRNA. Instead, it will lead to translational arrest since the RISC complex will obstruct the ribosome binding and translocation. These mRNAs are then directed to the processing bodies (P-bodies) where they are gradually degraded. In the nucleus, siRNA can silence transposable DNA elements and thereby prevent their unwanted and dangerous random insertions in the genome.
siRNA Applications
As siRNA silences specific genes, it has important applications in both molecular biology research and therapeutic applications. In research, they can be used to study specific gene functions in vivo and in vitro by silencing that gene. They can also be used to silence genes from deadly viruses and can be employed as an effective anti-viral agent. siRNAs are being explored as a potential treatment for several diseases including neurological disorders such as Alzheimer&#8217;s and cancers by targeting respective disease-causing genes. The siRNAs can be used in personalized gene therapy as they are highly specific and can be easily designed for different target genes. Also, therapeutic siRNAs are programmed to target mRNA rather than DNA and therefore there is a significantly reduced risk of permanent DNA modification.&#160;

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional ...

Education

JoVE Core

Cell Biology

Unit 1

Control of Gene Expression

KEY TERMS AND CONCEPTS

sirna in gene silencing

Small interfering RNA, or siRNA, is a short RNA molecule that helps silence genes. It works after a gene has been copied into RNA, making it part of post-transcriptional gene silencing. Scientists study siRNA because it shows how cells can control which genetic messages are used.

siRNA acts by guiding the cell to destroy a matching RNA message. This lowers the amount of protein that can be made from that message. The process is specific, because the siRNA must match the target RNA sequence closely.

This topic is important for understanding gene regulation in cells. It also helps explain how RNA can do more than carry information. In high school biology, siRNA is a key example of how cells can turn gene expression down without changing DNA.

siRNA in Gene Silencing

cell specific gene expression

Cell-Specific Gene Expression in Development

Cell-specific gene expression helps explain how different cells make different proteins, even when they contain the same DNA. This process is central to development and to the way specialized tissues form. Gene expression is controlled by regulatory signals that turn particular genes on or off in specific cells. As a result, one cell can follow a different molecular program from another cell in the same organism. These differences help create the variety of cell types needed for normal...

regulation of expression occurs at multiple steps

regulation-of-expression-occurs-at-multiple-steps

Gene Expression Control at Every Stage

Gene expression control happens at several stages. Cells can change when a gene is active and how much product it makes. This regulation helps the cell respond to changing needs. One major control point is transcription. In eukaryotes, transcription can be regulated before it starts. It can also be regulated while it is already underway. These steps help determine whether a gene is copied into RNA. Cells can also regulate expression after transcription. The RNA may be processed, moved, or...

cis-regulatory sequences

DNA Switches That Control Gene Expression

Cis-regulatory sequences are DNA switches that help control gene expression. They do not code for proteins. Instead, they can turn nearby genes on or off and help determine when a gene is active. These sequences include promoters and enhancers. They are often found near the genes they regulate, and their effect depends on where they are in the genome. Because they work through DNA itself, they help cells control which genes are used in different situations. Cis-regulatory sequences are an...

cooperative binding of transcription regulators

cooperative-binding-of-transcription-regulators

How Transcription Regulators Work Together

Transcription regulators can bind cooperatively to control gene expression. In cooperative binding, the binding of one regulator can make it easier for another regulator to bind nearby DNA. This shared effect helps cells fine-tune when genes are turned on or off. The topic also connects to how regulators interact with each other and with DNA. These interactions can strengthen binding at a target site. They can also change how strongly a gene is controlled in a specific cell or condition. <br...

prokaryotic transcriptional activators and repressors

prokaryotic-transcriptional-activators-and-repressors

How Prokaryotic Gene Regulators Work

Prokaryotic gene regulators control transcription by helping or blocking RNA polymerase. Activators and repressors are two main types of regulatory proteins that influence whether a gene is expressed. These proteins let bacteria adjust gene activity in response to changing conditions. Activators help transcription start. They bind to specific DNA sequences near a promoter, which is the region where RNA polymerase begins transcription. By making RNA polymerase bind more easily, activators...

the eukaryotic promoter region

Promoter Sequences in Eukaryotes

Eukaryotic promoter sequences control where transcription begins. A promoter is a DNA region that helps start gene expression. In eukaryotes, this region is usually found upstream of the gene it regulates. The promoter contains specific DNA sequences that can bind proteins needed for transcription. These sequences help position RNA polymerase at the correct start site. They also help determine whether a gene is turned on at the right time and in the right cell type. Eukaryotic promoters can...

co-activators and co-repressors

Gene Regulation by Co-activators and Co-repressors

Co-activators and co-repressors help control gene expression. They do not usually bind DNA themselves. Instead, they work with transcription factors to change how strongly a gene is turned on or off. Co-activators support transcription. They help transcription factors and RNA polymerase work together, which can increase gene expression. Co-repressors do the opposite. They help reduce transcription and lower gene expression. These proteins are important because cells need precise control over...

master transcription regulators

Master Transcription Regulators in Gene Control

Master transcription regulators help control when genes turn on and off. These proteins sit at the top of gene regulation networks and shape how cells respond to signals. In many cases, they act early in development and influence which cell types form. These regulators bind DNA and affect transcription, which is the first step in making RNA from a gene. By turning transcription on or off, they can change the levels of many downstream genes at once. That broad effect makes them important for...

regulated mrna transport

mRNA Localization During Cell Control

mRNA localization helps cells move messenger RNA to specific places before proteins are made. This process is regulated, so the cell can control when and where a protein is produced. Messenger RNA, or mRNA, carries genetic instructions from DNA to the protein-making machinery. By transporting mRNA to a defined location, a cell can keep protein production focused where it is needed most. Regulated mRNA transport is an important part of this control. It links the movement of RNA with later...

mrna stability and gene expression

mRNA Degradation and Protein Output

mRNA degradation helps control how much protein a cell makes. Messenger RNA, or mRNA, carries the genetic message from DNA to the ribosome, where proteins are built. When mRNA stays intact longer, it can be used more often. When it breaks down faster, protein production drops. Cells regulate mRNA stability with cis-acting elements. These are sequences within the mRNA itself that influence how long the message lasts. They can affect whether the mRNA is protected or targeted for decay. This...

micrornas

How miRNA Silences Genes

MicroRNA (miRNA) is a short regulatory RNA that helps control gene expression. It is transcribed from introns, which are non-coding parts of a gene, or from intergenic regions, which are stretches of DNA between genes. miRNA begins as a longer primary transcript and must go through several processing steps before it becomes active. The first transcript, called primary miRNA or pri-mRNA, folds back on itself to form a stem-loop structure. In the nucleus, the endonuclease Drosha shortens this...

Small interfering RNA, or siRNA, is a short RNA molecule that helps silence genes. It works after a gene has been copied into RNA, making it part of post-transcriptional gene silencing. Scientists study siRNA because it shows how cells can control which genetic messages are used. siRNA acts by guiding the cell to destroy a matching RNA message. This lowers the amount of protein that can be made from that message. The process is specific, because the siRNA must match the target RNA sequence...

lncrna - long non-coding rnas

Long Non-coding RNAs in Cell Control

Long non-coding RNAs, or lncRNAs, are RNA molecules that do not code for proteins. Instead, they can help control how genes are used in cells. This makes them important regulators of cell behavior. lncRNAs can work in several ways. Some influence chromatin modification, which changes how tightly DNA is packed and how easy it is for genes to be turned on or off. Others help guide the process of cell differentiation, when unspecialized cells develop into more specific cell types. Because of...

epigenetic regulation

DNA Methylation and X Inactivation

DNA methylation and X-chromosome inactivation help control which genes are turned on or off. These epigenetic changes alter the physical structure of DNA without changing the DNA sequence. They help each cell make only the proteins it needs. For example, bone growth proteins are not made in muscle cells. Epigenetic control is important for normal development. It also helps cells keep the right patterns of gene activity. When these controls fail, diseases can develop. Cancer is one example, but...

key terms and concepts

Learn how small interfering RNA helps silence genes after transcription by guiding cells to destroy matching RNA messages and reduce protein production.

siRNA in Gene Silencing | JoVE K12

cell biology

JoVE Core Cell Biology illustrates complex cellular processes in easy-to-understand yet comprehensive animated video lessons. This collection focuses on the essential components and functions of cells, including organelles and membranes, cellular transport, and cell energetics. It is complemented by scientist-in-action videos that demonstrate the application of cell biology in real-world research experiments.

9-12.B.1.2.b

What are Cells?

Cells are the smallest and basic units of life, whether it is a single cell that forms the entire organism, e.g., in a bacterium or trillions of them, ...

Cell Size

Cell sizes vary widely among and within organisms. Bacterial cells range between 1-10 micrometers (&#x3BC;m)and are considerably smaller than most ...

Eukaryotic Compartmentalization

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry ...

Prokaryotic Cells

Prokaryotes are small unicellular organisms that include the domains&#x2014;Archaea and Bacteria. Bacteria include many common organisms, such as ...

Cytoplasm

The cytoplasm consists of organelles and a framework of protein scaffolds called the cytoskeleton suspended in an aqueous solution, the cytosol. The ...

The Nucleus

The nucleus is a membrane-bound organelle that acts as a control center in a eukaryotic cell. It contains chromosomal DNA, which controls gene expression ...

Endoplasmic Reticulum

Endoplasmic ReticulumThe endoplasmic reticulum (ER) is an extensive network of membranous sacs and tubules in eukaryotic cells, continuous with the outer ...

Ribosomes

Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that ...

Golgi Apparatus

As they leave the Endoplasmic Reticulum (ER), properly folded and assembled proteins are selectively packaged into vesicles. These vesicles are ...

Lysosomes

Lysosomes are membrane-enclosed spherical sacs derived from the Golgi apparatus. The most important function of the lysosome is degrading macromolecules ...

Peroxisomes

Peroxisomes and mitochondria are two important oxygen-utilizing organelles in eukaryotic cells. Mitochondria carry out cellular respiration&#x2014;the ...

Introduction to the Cytoskeleton

Overview of the Cytoskeleton
The cytoskeleton is a network of protein filaments present within the cell, having three distinct filaments ...

Introduction to Actin

Actin is a highly conserved cytoskeletal protein found abundantly in eukaryotic cells. It constitutes 10% weight of the total cellular protein in muscle ...

overview-of-myosin-structure-and-function

Overview of Myosin Structure and Function

Myosins are a family of molecular motor proteins, first identified in the skeletal muscles, where they are responsible for muscle contraction. Along with ...

Microtubules

Microtubules are the thickest cytoskeletal filaments with a diameter of 25 nm. In prokaryotic organisms, microtubules are commonly found in locomotory ...

The Structure of Intermediate Filaments

The intermediate filaments are one of three widely studied cytoskeletal filaments. They are so named as their diameter (10 nm) is in between that of ...

Types of Intermediate Filaments

The intermediate filaments are an essential component of the cytoskeleton. Presently six types of intermediate filament have been identified. Type I and ...

Gap Junctions

Multicellular organisms employ a variety of ways for cells to communicate with each other. Gap junctions are specialized proteins that form pores between ...

The Extracellular Matrix

In order to maintain tissue organization, many animal cells are surrounded by structural molecules that make up the extracellular matrix (ECM). Together, ...

Tissues

Cells with similar structure and function are grouped into tissues. A group of tissues with a specialized function is called an organ. There are four main ...

Plant Cell Wall

The plant cell wall gives plant cells shape, support, and protection. As a cell matures, its cell wall specializes according to the cell type. For ...

Plasmodesmata

The organs in a multicellular organism&#x2019;s body are made up of tissues formed by cells. To work together cohesively, cells must communicate. One way ...

pH Regulation in Cells

pH plays a critical role in maintaining normal cellular activities. It helps maintain the structure and function of various proteins, dictates the charge ...

Chemistry of the Cell

Introduction to Cellular Respiration

Organisms harvest energy from food, but this energy cannot be directly used by cells. Cells convert the energy stored in nutrients into a more usable ...

ATP Energy Storage and Release

ATP and Macromolecule Synthesis

Biological macromolecules are organic compounds, predominantly composed of carbon atoms. The carbon atoms are covalently bonded with hydrogen, oxygen, ...

1. Engage in evidence-based argument to relate a cell's function to the structure, function, and diversity of its components. Examples: Muscle cells have a large number of mitochondria, which create energy for contraction in the form of ATP. Some plant cells have a large vacuole which is used for storage and transport of excess nutrients in changing environments.

9-12.B.1.1

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised&#160; of nucleotides and proteins are ...

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form ...

Types of RNA

Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse ...

Transcription

Transcription is the synthesis of RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. ...

Bacterial RNA Polymerase

Eukaryotic RNA Polymerases

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of ...

RNA Polymerase II Accessory Proteins

Transcription Elongation Factors

pre-mrna-processing-modification-of-pre-mrna-ends

Pre-mRNA Processing: Modification of pre-mRNA Ends

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or ...

Pre-mRNA Processing: RNA Splicing

Chromatin Structure and RNA Splicing

Alternative RNA Splicing

Nuclear Export of mRNA

Transfer RNA Synthesis

Ribosomal RNA Synthesis

The Nucleolus

Additional Subnuclear Structures

Translation

Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes ...

tRNA Activation

Initiation of Translation

Termination of Translation

Improving Translational Accuracy

Prokaryotic Transcriptional Activators and Repressors

Nonsense-mediated mRNA Decay

The Eukaryotic Promoter Region

Molecular Chaperones and Protein Folding

Co-activators and Co-repressors

The Proteasome

Master Transcription Regulators

Regulated Protein Degradation

Regulated mRNA Transport

Proteins: From Genes to Degradation

mRNA Stability and Gene Expression

Cell Specific Gene Expression

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between ...

Regulation of Expression Occurs at Multiple Steps

Cis-regulatory Sequences

lncRNA - Long Non-coding RNAs

Cooperative Binding of Transcription Regulators

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. ...

2. Obtain and evaluate information to explain the role of DNA and RNA in transcription and translation leading to protein synthesis and cellular function.

Nucleic Acids and Nucleotides

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell&#39;s genetic blueprint and have instructions for its ...

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group ...

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the ...

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the ...

The DNA Helix

Overview

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most ...

Base-pairing and DNA Repair

a. Use a model to describe the structure and sequence of DNA, including nucleotide structure, base pairing, and the structure of the helix.

9-12.B.1.2.a

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 ...

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational ...

Spreading of Chromatin Modifications

The histone&#160;proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are ...

Histone Variants at the Centromere

Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as &#8220;mutant&#8221; forms that ...

b. Obtain and evaluate information to explore additional functions and regulatory roles of RNA, DNA, and protein, including their roles in gene expression and cellular differentiation. Examples: RNA contributing to ribosome structure, histone modification altering chromatin structure, and transcription factors and non-coding DNA involved in nuclear regulatory functions Clarification: Discussion should include proteins that regulate and carry out essential functions of life including enzymes, structural proteins, hormones, and receptors.

Recombinant DNA

Bacterial Transformation

c. Obtain, evaluate, and communicate information regarding how DNA and genetic technology apply to daily life. Examples: CRISPR can be used to develop species-specific pest control tools. GMO technology is used to produce drought-resistant plants to increase food supplies. Genetic screening is used in neonatal healthcare.

9-12.B.1.2.c

siRNA in Gene Silencing

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