Lec 11 - Structure and function of the nucleus

What is the nucleus

A membrane-bound organelle that houses DNA and organizes gene expression separate from the cytoplasm.

What is the nucleolus

The largest electron-dense nuclear body where rRNA is transcribed and ribosome assembly begins.

What are nuclear bodies

Distinct, non-membrane sub-compartments in the nucleus with specialized functions (e.g., Cajal bodies, speckles, polycomb bodies).

Are nuclear bodies membrane-bound

No, they are not surrounded by membranes; they form microenvironments by other means.

What does the nuclear envelope consist of

Two membranes (inner and outer), nuclear pore complexes, and an underlying nuclear lamina.

What is the outer nuclear membrane (ONM) continuous with

The rough endoplasmic reticulum; the perinuclear space is continuous with the ER lumen.

What is the inner nuclear membrane (INM)

A membrane distinct from the ONM that contains proteins connecting to the nuclear lamina.

What are nuclear pore complexes (NPCs)

Protein assemblies that form channels between the cytoplasm and nucleoplasm to regulate transport.

How many repeating units does each NPC have

Eight repeating subunits (spokes) surrounding a central channel.

What are nucleoporins (NUPs)

The ~30 different proteins that build the NPC; FG-NUPs form the selective permeability barrier.

What are FG-NUPs

Nucleoporins with phenylalanine-glycine repeats that create the NPC’s diffusion barrier and enable selective transport.

What NPC structures project into the cytoplasm and nucleus

Cytoplasmic filaments and a nuclear basket extend from the NPC rings.

What signal allows proteins to enter the nucleus

A nuclear localization signal (NLS) recognized by importin transport receptors.

What processes occur in the nucleus vs cytoplasm

DNA replication, transcription, and RNA processing occur in the nucleus; translation occurs in the cytoplasm.

Why separate transcription and translation

It allows tight, selective control of gene expression by regulating nuclear transport and processing steps.

What is the nuclear lamina

A meshwork of intermediate filament proteins (lamins) that supports nuclear shape and organizes the envelope.

Which proteins connect the lamina to the INM

Emerin and Lamin B Receptor (LBR) bind lamins to anchor the lamina to the inner nuclear membrane.

What is the LINC complex

SUN–KASH transmembrane protein bridges that link nucleoskeleton (lamins) to the cytoskeleton across the envelope.

Why is the LINC connection important

It transmits mechanical forces that can influence nuclear shape and gene expression (mechanotransduction).

What are the lamin types

Lamin A, Lamin C (an alternatively spliced form of LMNA), and Lamin B (widely expressed).

How are lamins organized

Lamins form flexible, rope-like intermediate filaments in a meshwork under the INM without intrinsic polarity.

Do lamins have an NLS

Yes; lamins are translated in the cytoplasm and imported into the nucleus via their NLS.

What is the CaaX motif

A C-terminal sequence (Cys–aliphatic–aliphatic–X) that can be isoprenylated (e.g., farnesylated) to help membrane association.

Which PTMs regulate lamin A/B function and location

Isoprenylation, phosphorylation, and carboxyl methylation.

What is farnesylation

Addition of a 15-carbon isoprenoid to the CaaX motif by farnesyl transferase (FTase) to promote membrane association.

What happens to prelamin A after farnesylation

It is further processed (Rce1 cleavage, ICMT methylation) and then cleaved by Zmpste24, removing the farnesyl group to form mature lamin A.

Why temporarily farnesylate lamin A

To target lamin A to the INM for proper assembly, then remove the lipid for stable incorporation into the lamina.

What triggers nuclear envelope breakdown in mitosis

Phosphorylation of lamins causes lamina disassembly and envelope dissolution at mitotic entry.

What is euchromatin

Decondensed, transcriptionally active chromatin distributed throughout the nucleoplasm.

What is heterochromatin

Highly condensed, transcriptionally inactive chromatin often near nucleoli and the lamina.

What are LADs

Lamina-associated domains where heterochromatin contacts the nuclear lamina; genes in LADs are usually repressed.

What are NADs

Nucleolus-associated domains where heterochromatin associates with nucleolar periphery; genes in NADs are generally repressed.

Which chromosome is gene-rich vs gene-poor (example)

Chromosome 19 is gene-rich and chromosome 18 is gene-poor in typical chromosome territory maps.

What are the nucleolus subregions

Fibrillar center (FC), dense fibrillar component (DFC), and granular component (GC), each with distinct roles in rRNA synthesis and assembly.

What happens in the fibrillar center (FC)

It contains the rRNA gene loci (nucleolar organizing regions) and is associated with rRNA transcription initiation sites.

What happens in the DFC (dense fibrillar center)

Active transcription of rRNA genes by RNA polymerase I and early processing steps.

What happens in the GC (granular component)

Assembly of ribosomal subunits as rRNA combines with ribosomal proteins.

What is 45S pre-rRNA

The initial Pol I transcript that is processed into 18S, 5.8S, and 28S rRNAs in the nucleolus.

How many rRNA gene copies and NORs are typical

More than 200 rRNA gene copies across chromosomes 13, 14, 15, 21, and 22; 10 NORs per diploid cell.

What reforms nucleoli after mitosis

Newly transcribed 45S pre-rRNA nucleates new nucleoli at NORs.

What enzymes/processes guide pre-rRNA processing

snoRNAs and snoRNPs guide site-specific cleavages and methylations, including pseudouridine formation.

What is pseudouridine

A modified nucleotide (Ψ) formed from uridine during rRNA processing.

Which rRNA is made outside the nucleolus

5S rRNA is produced by RNA polymerase III outside the nucleolus.

What makes up the 40S ribosomal subunit

18S rRNA plus 33 ribosomal proteins.

What makes up the 60S ribosomal subunit

5.8S and 28S rRNAs plus 46 ribosomal proteins, with 5S rRNA added from outside the nucleolus.

Where are ribosomal proteins made and how do they reach the nucleolus

Their mRNAs are transcribed by Pol II, translated in the cytoplasm, and the proteins are imported into the nucleus for assembly.

How are ribosomal subunits exported

40S and 60S subunits are exported separately through NPCs using exportin Crm1.

What do NPCs regulate to control gene expression

Import of transcription factors and export of mRNAs and ribosome components.

What are speckles

Nuclear storage sites for snRNPs and splicing factors that are recruited to active genes for pre-mRNA processing.

What are Cajal bodies

Sites for assembly/storage of snRNPs and other RNPs; also involved in telomerase assembly.

What are polycomb bodies

Centers of transcriptional repression marked by H3K27 methylation, often associated with heterochromatin.

What are PML bodies

Nuclear bodies involved in transcriptional regulation and DNA repair.

What are clastosomes

Nuclear bodies associated with proteasomal proteolysis.

• process where proteins are degraded by the proteasome, a large protein complex. It breaks down unneeded or damaged proteins into small peptides, helping regulate protein quality and quantity within the cell.

What is the histone locus body

A nuclear body for transcription and processing of histone pre-mRNAs.

How many nucleoli per nucleus are typical

Usually 1–4 per nucleus.

How many speckles per nucleus are typical

Approximately 20–50 per nucleus.

How many PML bodies per nucleus are typical

Approximately 10–30 per nucleus.

How many polycomb bodies per nucleus are typical

Approximately 10–20 per nucleus.

How many Cajal bodies per nucleus are typical

Often 0–10 per nucleus.

How many clastosomes per nucleus are typical

Often 0–3 per nucleus.

How many histone locus bodies per nucleus are typical

Typically 2–4 per nucleus.

What chromatin levels of packing are seen

From 2 nm DNA to 10 nm nucleosomes to 30 nm fibers, looped domains, higher-order condensed chromatin, and metaphase chromosomes.

Where does RNA processing occur

Primarily in the nucleus, including splicing of pre-mRNA into mature mRNA with a 5′ cap and poly(A) tail.

How do NPCs appear structurally

Regularly spaced circular structures embedded between INM and ONM forming a continuous transport channel.

What recognizes the NLS

Importins, which ferry cargo through the FG-NUP barrier of NPCs.

What is the perinuclear space

The lumen between INM and ONM, continuous with the ER lumen.

How do lamins support nuclear mechanics

Their meshwork resists deformation, allowing shape changes without damage.

What is the role of emerin and LBR

INM proteins that bind lamins to tether the lamina to the envelope.

What effect does mechanical stress have on nuclei via LINC

Force transmission can alter nuclear shape and impact gene expression programs.

What is isoprenylation beyond farnesylation

Addition of isoprenyl groups like geranyl (C10) or geranylgeranyl (C20) to a CaaX motif; lamin A primarily uses farnesylation.

What enzyme removes the farnesylated tail from prelamin A

Zmpste24 (also called FACE-1) cleaves to generate non-farnesylated mature lamin A.

What other enzyme processes the CaaX tail

Rce1 cleaves after isoprenylation, and ICMT methylates the C-terminus before Zmpste24 cleavage.

Why is NPC transport important for gene regulation

It controls nuclear access of transcription factors and exit of mRNAs, tuning gene expression responses.

What happens to the nuclear envelope at mitotic exit

It reassembles as lamins dephosphorylate and reform the lamina, restoring nuclear architecture.

Clinical: What mutation causes HGPS (Hutchinson-Gilford progeria syndrome)

• It's a rare genetic condition that causes rapid aging in children, leading to symptoms like growth delays, loss of body fat, and cardiovascular problems.

An LMNA mutation that removes ~50 amino acids including the Zmpste24 cleavage site, preventing removal of the farnesyl anchor.

Clinical: What is progerin

The aberrant farnesylated LMNA product in HGPS that cannot be properly processed and remains membrane-anchored.

Clinical: How does progerin affect nuclear structure

It disrupts lamina assembly, causing abnormally shaped “crinkled” nuclei and altered nuclear envelope integrity.

Clinical: How can HGPS impact cell function

It disturbs nuclear structure and transcription, and may also impair DNA repair.

Clinical: What are laminopathies

Diseases from mutations in lamins or lamina-associated proteins (e.g., LMNA or emerin).

Clinical: Name laminopathies linked to LMNA.

HGPS, autosomal dominant Emery–Dreifuss muscular dystrophy, Charcot–Marie–Tooth type 2B1, dilated cardiomyopathy, and Dunnigan-type familial partial lipodystrophy.

Clinical: Which Emery–Dreifuss MD is X-linked and what gene is affected

• Emery-Dreifuss muscular dystrophy (EDMD) is a rare inherited condition that affects both skeletal and heart muscles. It’s characterized by slowly progressive muscle weakness, early joint contractures in the elbows, ankles, and neck, and potentially life-threatening heart problems, especially conduction defects and arrhythmias.

The X-linked form involves emerin mutations; LMNA mutations cause an autosomal dominant form.

Clinical: Why is lamin A processing a therapeutic target

Blocking farnesylation or correcting processing could reduce toxic progerin anchoring and improve nuclear morphology in HGPS.

Clinical: How can mechanics influence pathology via LINC

Faulty nucleo-cytoskeletal coupling can misregulate mechanosensitive genes, contributing to diseases like cardiomyopathies.