3: DNA, Chromosomes, and the Interphase Nucleus
- Page ID
- 173529
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)The structure and function of the interphase nucleus are fascinating and are a topic with a very long history. As one of the largest organelles in the eukaryotic cell, the nucleus was identified and characterized hundreds of years before we knew what DNA was. And yet the nucleus has also been a bit of a mystery. The DNA that is housed in the nucleus is so essential to function, it can be difficult to study. Perturbations of the nucleus can easily kill the cell, which does not help us learn about how it works. In recent years, advances in microscopy technology and bioinformatics have given us new options for studying the architecture of the nucleus and how the cell manages and controls all of that DNA.
We’ll start with a discussion of how the DNA of the genome is organized and contained within the nucleus during interphase. Then we’ll look at how the cell regulates gene expression through a combination of managing access to DNA by controlling chromatin structure, the use of transcription factors, and other mechanisms. Finally, we’ll end by looking at the structure of the rest of the nucleus (i.e., the membrane, pores, and other components that help create this protective compartment around the genome) as well as how the cell controls what enters/leaves the nucleus in order to protect the DNA.
- 3.1: Chromatin and Chromosomes
- This page discusses the organization of the eukaryotic genome, focusing on chromatin's structure, including euchromatin and heterochromatin. It explains how histone modifications and nucleosome formation contribute to chromatin remodeling and gene accessibility. The text also describes higher-order packing, the roles of structural maintenance complexes, and the division of the nucleus into active (A) and inactive (B) compartments.
- 3.2: Regulation of Gene Expression
- This page covers gene regulation in eukaryotic cells, highlighting the complexity of their genomes compared to prokaryotes. Key topics include DNA/histone modifications, transcription factors, mRNA splicing/processing, and chromatin remodeling. Histone variants, particularly H2A.Z, and their roles in transcription are examined. The significance of RNA processing, including splicing and its impact on protein diversity, is discussed alongside techniques like ChIP used for studying these processes.
- 3.3: The Interphase Nucleus—Structure, Function, and Protein Import
- This page discusses the interphase nucleus's role in eukaryotic cell function, highlighting its structure, including the nuclear envelope, nuclear lamina, and nucleolus, which is essential for ribosome synthesis. It details nuclear pore complexes that regulate protein and RNA trafficking, emphasizing the importance of targeting signals for correct localization.
- 3.4: End-of-Chapter Material
- This page emphasizes the nucleus as a central organelle for DNA regulation, highlighting its roles in compaction, transcription, and RNA synthesis. It discusses transcription factors, mRNA splicing, and the nuclear lamina's structural support. The chapter reviews experimental techniques like ChIP for studying chromatin, while addressing key questions about gene regulation and protein-DNA interactions, offering a thorough overview of nuclear functions.
Thumbnail: Pair of human chromosome 1 after G-banding. One is from mother, one is from father. (Public Domain; National Human Genome Research Institute via Wikipedia)