Name: chromatin and rna splicing control
Uploaded: 2023-04-30T18:28:44.000Z
Duration: 2 min 41 s
Channel: JoVE

K12 Standards

Virginia  Standards of Learning

HIgh School

Biology

BIO.2

BIO.2.d

Chromatin Structure and RNA Splicing

In eukaryotes, the processing of pre-mRNA in the nucleus is tightly coupled to its transcription.&#160;
As soon as RNA polymerase starts transcribing, the newly synthesized pre-mRNA is immediately bound by various factors to be processed into mature and functional mRNA.&#160;
Therefore, the rate of gene transcription by the RNA polymerase directly affects the steps in pre-mRNA processing.&#160;
One of the major factors that regulate the rate of RNA polymerase activity is the gene&#39;s chromatin structure, which includes nucleosome positioning and histone modifications on the DNA template.&#160;
Nucleosomes are very strategically placed on certain regions of the DNA. They act as a barrier and temporarily pause the RNA polymerase activity on the DNA.&#160;
For example, in most genes, a nucleosome is positioned after the promoter element. It compels the RNA polymerase to pause at the transcriptional start site, giving enough time for the assembly of elongation factors and chromatin remodeling complex that helps to create nucleosome free region on the template DNA. In the meantime, the cell can recruit 5&#39; capping enzymes for the newly synthesized pre-mRNA.&#160;
Nucleosome positioning is also favored on the exons comp

chromatin structure and rna splicing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially the nucleosome positioning and histone modifications on the gene, can profoundly control the rate of RNA polymerase activity and pre-mRNA processing at the transcription site. Specific histone modifications on exon-specific nucleosomes help recruit splicing factors to the splice sites and play an active role in exon selection during splicing. For example, histone deacetylation leads to a tight chromatin structure. This slows down the RNA polymerase activity giving enough time to recruit splicing factors even at weak splice sites, leading to the inclusion of alternative exons in the mature mRNA. On the contrary, histone acetylation results in a more open chromatin structure that allows a faster RNA polymerase activity and recruitment of splicing factors only to the strong splice sites, resulting in the exclusion of alternative exons. Therefore, chromatin structure plays an important role in constitutive as well as alternative splicing of the pre-mRNA and regulates the gene expression patterns in the cell.
Another example of regulation of RNA splicing by the chromatin structure is the enriched trimethylation of H3 histone lysine 36 on the nucleosomes, which helps to recruit splicing factors to the splicing site. Mutations in the methylation process of H3 histone can disrupt the splicing process and result in intron retention in the mature mRNA.
Overall, the regulation of pre-mRNA processing, especially splicing, results in creating a diverse pool of mRNA transcripts and hence, enormous protein diversity from a finite set of genes.

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into ...

Education

JoVE Core

Cell Biology

Unit 1

Transcription: DNA to RNA

KEY TERMS AND CONCEPTS

chromatin and rna splicing control

Chromatin and RNA splicing work together to shape how genes are used in a cell. Chromatin is the DNA-protein material that packages genetic information, and RNA splicing is a step in which introns are removed from a pre-mRNA transcript. The video explains how chromatin structure can influence this RNA processing step.

A compact chromatin structure can make a gene less accessible, while a more open structure can make it easier for the cell to use that gene. This change in access can affect how pre-mRNA is processed after transcription. The transcript links chromatin state to splicing outcomes, showing that gene packaging is part of gene regulation.

The video also highlights that RNA splicing does not happen in isolation. It is connected to the broader process of turning DNA information into a mature RNA message. Understanding this relationship helps explain how cells control which RNA products are made from the same genetic sequence.

Chromatin and RNA Splicing Control

what is gene expression?

How Cells Control Gene Expression

Cells control gene expression to decide when a gene makes a protein. A gene is a stretch of DNA that holds the instructions for functional RNAs and proteins. Because DNA is built from nucleotides and proteins are built from amino acids, messenger RNA (mRNA) acts as the link between them. The first step is transcription. During transcription, mRNA copies the DNA blueprint. In eukaryotes, this happens in the nucleus through complementary base-pairing with the DNA template. The mRNA is then...

rna structure

RNA Shapes and Protein Synthesis

RNA shapes and protein synthesis are linked through the molecule’s single-stranded structure. RNA is made of ribonucleotides joined by phosphodiester bonds, and it can fold into secondary and tertiary shapes that help control transcription and translation. These shapes are important in both regulation and protein production. Messenger RNA, transfer RNA, and ribosomal RNA are the three main RNA types used in protein synthesis. They all share the same basic build: a single strand of nucleotides.

types of rna

RNA Roles in Protein Synthesis

RNA plays key roles in protein synthesis, and its main forms work together to make proteins in the cell. Messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA) each have a specific job. RNA can also be grouped as protein-coding or non-coding RNA. mRNA is the protein-coding RNA. It carries codons, which are sets of three nucleotides that specify an amino acid. tRNA and rRNA are non-coding RNAs. tRNA acts as an adaptor that reads the mRNA sequence and brings amino acids into the...

transcription

RNA Synthesis and Gene Control

Transcription is the process that makes RNA from a DNA sequence. RNA polymerase carries out this synthesis. It is the first step in turning a gene into a protein, and several other proteins and control sequences help make messenger RNA, or mRNA, correctly. In eukaryotes, DNA is first copied into pre-mRNA. This RNA can then be processed into mature mRNA, which serves as the template for protein synthesis. In prokaryotes, translation into a polypeptide can start before transcription has finished.

bacterial rna polymerase

Bacterial RNA Polymerase and Sigma Factor

Bacterial RNA polymerase carries out transcription, the process of copying DNA into RNA. It is the enzyme that starts RNA synthesis in bacteria and helps control which genes are used. The core enzyme works with a sigma factor, which is a protein that helps the polymerase find the right place to begin. Together, they form the holoenzyme. The sigma factor is important for promoter recognition, so the enzyme can bind near the start of a gene. Once transcription begins, RNA polymerase separates...

eukaryotic rna polymerases

Three Eukaryotic RNA Polymerases

Eukaryotic RNA polymerases are the enzymes that make RNA from DNA in cells with a nucleus. In eukaryotes, this work is divided among three main RNA polymerases. Each enzyme has a specific role in transcription, the process of copying genetic information into RNA. RNA polymerase I makes most ribosomal RNA, or rRNA. RNA polymerase II produces messenger RNA, or mRNA, which carries the instructions for making proteins. RNA polymerase III makes transfer RNA, or tRNA, and also some small RNAs used...

general transcription factors

Tissue-Specific Transcription Factors in Gene Control

Tissue-specific transcription factors help control which genes turn on in different mammal cells. These proteins bind to promoter sequences and can direct a gene to be expressed in one tissue but not another. This selective control helps cells carry out very different jobs in the body. A clear example is the beta globin gene, which makes part of hemoglobin. The gene is present in all body cells, but it is expressed only in red blood cells. That happens because the transcription factors needed...

rna polymerase ii accessory proteins

RNA Polymerase II Helper Proteins

RNA polymerase II helper proteins support the transcription process in eukaryotic cells. They work with RNA polymerase II, the enzyme that makes RNA from a DNA template. These proteins help the enzyme start, move, and finish transcription in the right way. Some helper proteins act as accessory factors. They can assist RNA polymerase II at different stages of gene expression. Their roles are important because transcription must be controlled accurately for cells to make the correct RNA...

transcription elongation factors

RNA Polymerase Pausing and Elongation

RNA polymerase pausing and elongation factors help control how RNA is made from DNA. During transcription, RNA polymerase moves along the gene and builds an RNA strand. Elongation factors support this process by helping the enzyme continue after it pauses. These factors are part of the elongation stage of transcription. They are not the same as the proteins used to start transcription. Their role is to keep RNA polymerase moving so RNA can be copied efficiently. In high school biology, this...

pre-mrna processing: modification of pre-mrna ends

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

How Pre-mRNA Becomes Mature mRNA

Pre-mRNA becomes mature mRNA through a series of processing steps in eukaryotic cells. RNA polymerase first makes the transcript, and the RNA is modified before it leaves the nucleus. The unprocessed form is called precursor mRNA, or pre-mRNA, to separate it from mature mRNA. After about 20 to 40 ribonucleotides have been added, enzymes place a cap on the 5' end of the growing RNA. This cap replaces the 5' phosphate with modified guanosine, which carries a methyl group called 7-methyl...

pre-mrna processing: rna splicing

Pre-mRNA Splicing and Intron Removal

Pre-mRNA splicing removes introns from a pre-mRNA molecule and joins the remaining exons together. This step is part of pre-mRNA processing, which helps turn the first RNA copy into a mature message that can be used later in gene expression. Splicing is carried out by the spliceosome, a large RNA-protein complex. The spliceosome recognizes the intron boundaries and cuts out the intron. It then links the exons together in the correct order. A key feature of splicing is the lariat, a looped RNA...

Chromatin and RNA splicing work together to shape how genes are used in a cell. Chromatin is the DNA-protein material that packages genetic information, and RNA splicing is a step in which introns are removed from a pre-mRNA transcript. The video explains how chromatin structure can influence this RNA processing step. A compact chromatin structure can make a gene less accessible, while a more open structure can make it easier for the cell to use that gene. This change in access can affect how...

alternative rna splicing

RNA Splicing in Gene Expression

RNA splicing in gene expression helps cells turn one gene into different RNA messages. During RNA processing, introns are removed and exons are joined together. This editing step changes which parts of the RNA stay in the final message. Alternative splicing gives cells a way to make more than one protein from the same gene. By including or skipping different exons, a cell can produce different RNA versions from one starting transcript. This process adds flexibility to gene expression without...

nuclear export of mrna

How mRNA Leaves the Nucleus

Messenger RNA, or mRNA, must move from the nucleus to the cytoplasm before it can be used to make protein. This step is called nuclear export of mRNA. It connects gene expression in the nucleus with protein production in the cytoplasm. During export, the cell selects mRNA molecules that are ready to leave the nucleus. These molecules pass through nuclear pores, which are openings in the nuclear envelope. The process helps keep mRNA transport organized and controlled. Once mRNA reaches the...

transfer rna synthesis

tRNA Genes and RNA Processing

Transfer RNA synthesis begins with transcription of tRNA genes into a primary RNA copy. That first copy is not yet ready to function in protein building. It must be processed before it can become mature transfer RNA. During processing, the cell trims the ends of the RNA and removes extra segments when needed. The transcript also shows that some transfer RNAs carry modified bases. These changes help create the final tRNA structure. Mature transfer RNA folds into a shape that can work in...

ribosomal rna synthesis

Ribosomal RNA and Ribosome Formation

Ribosomal RNA synthesis is part of how cells build ribosomes. Ribosomes are the structures that help make proteins. In this process, cells produce ribosomal RNA, or rRNA, which becomes a key part of the ribosome. The transcript focuses on the making of rRNA and its role in ribosome formation. Ribosomal RNA is not just a message like messenger RNA. It is a structural and functional part of the ribosome itself. Because of that, rRNA synthesis is closely tied to the assembly of ribosomes. This...

the nucleolus

Nucleolus and Ribosome Assembly

The nucleolus is a small structure inside the nucleus. It is the site where ribosome assembly begins. Ribosomes are the cell structures that help make proteins. The nucleolus forms around nucleolar organizer regions, or NORs. These regions contain the genes used to make ribosomal RNA, also called rRNA. Inside the nucleolus, rRNA is produced and combined with proteins to start building ribosomes. Because of this role, the nucleolus is closely tied to protein production in the cell. Its work...

additional subnuclear structures

Subnuclear Bodies and Their Roles

Subnuclear structures are specialized bodies inside the nucleus. They help organize nuclear activity and appear as distinct regions under the microscope. The nucleolus is one of the best-known subnuclear structures. It is the site where ribosomes begin to assemble. Cajal bodies are another nuclear structure. They are linked to the processing and assembly of RNA-related particles. These additional subnuclear structures show that the nucleus is not a uniform space. Instead, it contains...

key terms and concepts

Learn how chromatin structure affects RNA splicing and pre-mRNA processing, and why DNA packaging can influence which RNA message a cell makes.

Chromatin and RNA Splicing Control | 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.

Alabama Course of Study Science

9-12

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

From Molecules to Organisms: Structures and Processes

9-12.B.1.2

9-12.B.1.2.b

Florida Department of Education

High School

Life Science

SC.912.L.16

SC.912.L.16.6

south-carolina-college-and-career-ready-science-standards

South Carolina College and Career Ready Science Standards

B-LS1-1.

Functions of Life

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pH Homeostasis

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BIO.2.a

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Macromolecules

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Lipid-derived Compounds in the Human Body

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What are Proteins?

Protein Organization

Globular Proteins

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Fibrous Proteins

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Protein Denaturation

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Role of Proteins in the Human Body

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Nucleic Acids and Nucleotides

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Nucleic Acid Structure

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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, ...

The student will investigate and understand that chemical and biochemical processes are essential for life.Key ideas include  macromolecules have roles in maintaining life processes;

BIO.2.b

structural-organization-of-the-human-body-an-overview

Structural Organization of the Human Body: An Overview

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Introduction to Enzyme Kinetics

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Turnover Number and Catalytic Efficiency

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Ligand Binding and Linkage

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Ribozymes

The student will investigate and understand that chemical and biochemical processes are essential for life. Key ideas include  enzymes have a role in biochemical processes;

BIO.2.c

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, ...

The Nucleus

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The DNA Helix

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The Central Dogma

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Mutations

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DNA as a Genetic Template

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Chromosome Structure

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RNA Structure

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Types of RNA

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Transcription

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Bacterial RNA Polymerase

Eukaryotic RNA Polymerases

General Transcription Factors

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RNA Polymerase II Accessory Proteins

Transcription Elongation Factors

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

Alternative RNA Splicing

The student will investigate and understand that chemical and biochemical processes are essential for life. Key ideas include protein synthesis is the process of forming proteins which influences inheritance and evolution; and

Chromatin and RNA Splicing Control

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