6.1 Nucleus and nuclear envelope

Nucleus and Nuclear Envelope

The nucleus is the largest organelle in eukaryotic cells and serves as the central hub for storing, reading, and copying genetic information. Its surrounding double membrane, the nuclear envelope, creates a controlled boundary that separates nuclear processes like transcription from cytoplasmic processes like translation. This physical separation is what allows eukaryotic cells to regulate gene expression in ways that prokaryotes cannot.

Structure and Function of the Nucleus

The nucleus contains nearly all of a cell's DNA, organized as chromatin, along with one or more nucleoli. A double-membrane nuclear envelope encloses everything inside:

• The outer nuclear membrane is continuous with the endoplasmic reticulum (ER), meaning ribosomes can sit on its cytoplasmic face just like on rough ER.
• The inner nuclear membrane is lined by the nuclear lamina, a meshwork of intermediate filament proteins called lamins. The lamina provides structural support, helps anchor chromatin, and plays a role in DNA replication and cell division.
• Nuclear pore complexes (NPCs) perforate the envelope at points where the inner and outer membranes fuse, creating channels that regulate molecular traffic in and out of the nucleus.

The nucleolus is a dense, non-membrane-bound structure visible within the nucleus. It's the site of ribosomal RNA (rRNA) synthesis and ribosome subunit assembly. Cells with high protein output (like secretory cells) often have prominent nucleoli because they need to produce ribosomes rapidly.

Chromatin refers to the DNA-protein complex inside the nucleus. DNA wraps around histone octamers to form nucleosomes, which further compact into higher-order structures. Two functional states matter most:

• Euchromatin: less condensed, more accessible to transcription machinery, and associated with actively expressed genes.
• Heterochromatin: tightly packed, less accessible, and associated with repressed genes. Some heterochromatin is constitutive (always condensed, like centromeric regions), while some is facultative (condensed only in certain cell types or conditions).

Role of the Nuclear Envelope

The nuclear envelope acts as a selective barrier that maintains distinct chemical environments in the nucleus and cytoplasm. This separation is critical: it keeps pre-mRNA processing (splicing, capping, polyadenylation) confined to the nucleus so that only mature mRNA reaches the ribosomes in the cytoplasm.

NPCs mediate all transport across the envelope through two modes:

1. Passive diffusion for small molecules (ions, metabolites, and proteins smaller than ~40 kDa). These pass freely through the pore channel.
2. Active, signal-dependent transport for larger molecules. Proteins destined for the nucleus carry a nuclear localization signal (NLS), while RNA and proteins leaving the nucleus carry a nuclear export signal (NES). Transport receptors recognize these signals and shuttle cargo through the pore.

The Ran GTPase gradient drives directionality. A concentration gradient of Ran-GTP (high in the nucleus) versus Ran-GDP (high in the cytoplasm) ensures that cargo moves the right way:

• Import: Importins bind NLS-tagged cargo in the cytoplasm and carry it through the NPC. Inside the nucleus, Ran-GTP binds the importin, causing it to release its cargo.
• Export: Exportins bind NES-tagged cargo and Ran-GTP in the nucleus, forming a trimeric complex that moves through the NPC. In the cytoplasm, RanGAP stimulates GTP hydrolysis, converting Ran-GTP to Ran-GDP, which disassembles the complex and releases the cargo.

Two key regulators maintain this gradient:

• RCC1 (a guanine nucleotide exchange factor) is chromatin-bound and generates Ran-GTP in the nucleus.
• RanGAP (a GTPase-activating protein) is cytoplasmic and stimulates hydrolysis of Ran-GTP to Ran-GDP.

Proteins in Nuclear Pore Complexes

NPCs are among the largest protein assemblies in the cell, built from ~30 different nucleoporins (Nups) in vertebrates. These fall into three functional categories:

• Structural Nups form the scaffold that maintains NPC architecture. The Nup107-160 complex and Nup93 complex are major examples. They organize the ring-like framework of the pore.
• FG-Nups contain disordered regions rich in phenylalanine-glycine (FG) repeats. These repeats extend into the central channel and form a selective permeability barrier, often described as a hydrogel or "molecular sieve." Transport receptors (importins and exportins) interact transiently with FG repeats to pass through, while other large molecules are excluded. Key examples include Nup98, Nup153, and Nup214.
• Transmembrane Nups anchor the entire NPC into the nuclear envelope at the point where the inner and outer membranes fuse. Examples include Pom121, Ndc1, and gp210.

Chromatin Organization and Gene Expression

Chromatin structure directly controls which genes are accessible for transcription. The basic unit is the nucleosome: ~147 base pairs of DNA wrapped around an octamer of histone proteins (two copies each of H2A, H2B, H3, and H4). Nucleosomes compact further into chromatin fibers, loops, and topologically associating domains (TADs).

Histone modifications are a major mechanism for marking chromatin as active or repressed. Specific chemical groups added to histone tails serve as signals:

• Euchromatin is enriched in marks like $H3K4me3$ (trimethylation of lysine 4 on histone H3) and $H3K36me3$, both associated with active transcription.
• Heterochromatin carries repressive marks like $H3K9me3$ and $H3K27me3$, which recruit silencing complexes and promote compaction.

Chromatin remodeling complexes use ATP hydrolysis to physically alter chromatin accessibility. They can reposition nucleosomes along DNA, evict them entirely, or exchange standard histones for variant forms. Four major families carry out this work: SWI/SNF, ISWI, CHD, and INO80. Each has distinct roles, but the net effect is the same: changing whether transcription factors can physically reach their target DNA sequences.

The functional consequence is straightforward:

• Open chromatin (euchromatin) allows transcription factors to bind promoters and enhancers, activating gene expression.
• Closed chromatin (heterochromatin) physically blocks transcription factor access, keeping genes silent.

Nuclear Bodies

The nucleus also contains several distinct, non-membrane-bound compartments called nuclear bodies. These concentrate specific proteins and RNAs to carry out specialized functions:

• Cajal bodies: sites of small nuclear ribonucleoprotein (snRNP) biogenesis and modification. snRNPs are essential components of the spliceosome.
• PML bodies: involved in diverse processes including transcriptional regulation, DNA damage response, and apoptosis. They're named for the promyelocytic leukemia protein that forms their scaffold.
• Nuclear speckles: enriched in pre-mRNA splicing factors. They serve as storage and assembly sites for splicing machinery, positioned near actively transcribed genes.