Genetics Lect 18 (copy)

Transcription Factors

• proteins that influence the ability of RNA polymerase to transcribe a given gene

• Two types: general & regulatory transcription factors

General transcription factors

Proteins required for the binding of RNA polymerase to the core promoter and progression to elongation, which are necessary for basal transcription

Regulatory transcription factors

• Proteins that regulate the rate of transcription of target genes by influencing the ability of RNA polymerase to initiate transcription

• do not bind directly to RNA polymerase

• Ex: control elements, regulatory elements, or regulatory sequences

Cis-regulatory elements

DNA sequences located near the core promoter that regulate adjacent or local genes on the same DNA molecule when bound by regulatory transcription factors

Activator

A regulatory protein that increases the rate of transcription by binding to an enhancer sequence

Enhancer

A cis-regulatory DNA sequence that binds an activator protein to stimulate transcription

Repressor

A regulatory protein that decreases or inhibits the rate of transcription by binding to a silencer sequence

Silencer

A cis-regulatory DNA sequence that binds a repressor protein to inhibit transcription

Combinatorial control

The regulation of a single eukaryotic gene by the coordinated action of multiple factors, including activators, repressors, effector molecules, protein-protein interactions, chromatin remodeling, and covalent modifications

Regulatory Proteins

alter nucleosomes near the promoter

DNA Methylation

• may inhibit transcription

  • prevent binding of an activator protein

  • recruiting proteins that compact the chromatin

Domain

A structurally and functionally distinct region of a transcription factor protein that carries out a specific function, such as DNA binding or effector molecule binding.

Motif

A domain, or portion of a domain, that shares a highly similar structure across many different proteins.

Up-regulation

An increase in transcription rate, typically by $10\text{- to }1{,}000\text{-fold}$, triggered by the binding of a transcription factor to an enhancer.

Down-regulation

A decrease in transcription rate caused by the binding of a transcription factor to a silencer

Are response elements bidirectional/orientation independent

function in the forward or reverse orientation

Regulation via TFIID

A general transcription factor that binds the core promoter either directly or through coactivators

Regulation via Mediator

• A multiprotein complex that regulates transcription elongation

• activators stimulate it to promote phosphorylation of the carboxyl-terminal domain of RNA polymerase, whereas repressors prevent phosphorylation

Regulation via chromatin structure

changes in chromatin structure

Steroid receptors

Regulatory transcription factors that directly bind to steroid hormones, causing conformational changes that affect gene transcription (produced by endocrine glands)

Glucocorticoids

Steroid hormones that influence nutrient metabolism by promoting glucose utilization, fat mobilization, and protein breakdown.

Gonadocorticoids

Steroid hormones, such as estrogen and testosterone, that influence the growth and function of the gonads.

Glucocorticoid Response Elements (GRE)

Enhancer sequences located near dozens of different genes that are recognized and bound by glucocorticoid receptor homodimers to activate transcription

Closed conformation

A tightly packed chromatin state in which DNA is inaccessible to transcription factors and transcription is difficult or impossible.

Open conformation

A loose, accessible chromatin state that allows transcription factors to bind DNA and permit transcription to occur.

ATP-dependent chromatin remodeling

Dynamic changes in chromatin structure—including nucleosome repositioning, eviction, or replacement—driven by the energy of ATP hydrolysis.

DNA translocase

The catalytic ATPase subunit present in all ATP-dependent chromatin-remodeling complexes

How does chromatin remodeling complexes change chromatin structure

• Change in the position of nucleosomes

• Eviction of histone octamers

• Change in the composition of nucleosomes

Histone variants

Histone proteins encoded by specialized genes with mutated amino acid sequences that replace standard histones to confer specific chromatin functions

What are the five repetitive histone genes

H1, H2A, H2B, H3, & H4

Histone code

The pattern of covalent modifications (acetylation, methylation, phosphorylation) on the amino-terminal tails of histones that provides binding sites for proteins that alter chromatin structure.

Histone acetyltransferase (HAT)

An enzyme that transfers acetyl groups ($\text{COCH}_3$) onto histone amino-terminal tails, loosening DNA binding and promoting transcription.

Histone deacetylase (HDAC)

An enzyme that removes acetyl groups from histone tails, restoring tight DNA-histone association and transcriptional repression.

Chromatin Immunoprecipitation Sequencing (ChIP-Seq)

A genome-wide technique that maps the exact positions of specific nucleosomes, histone variants, or modified histones by crosslinking proteins to DNA, enzymatically digesting linker DNA, immunoprecipitating with antibodies, and sequencing.

Micrococcal nuclease

An enzyme used during ChIP-Seq that cuts linker DNA between nucleosomes while leaving protein-crosslinked DNA intact.

Nucleosome-free region (NFR)

A segment of DNA lacking nucleosomes, commonly found at the core promoter/transcriptional start site and the transcriptional termination site of protein-encoding genes.

Preinitiation complex

A multiprotein assembly composed of RNA polymerase II and general transcription factors bound to the core promoter before the initiation of transcription.

Transcriptional Activation

involves changes in nucleosome position and composition and modifications to histones

Activators & Histones

recruit chromatin remodeling complexes and histone-modifying enzymes to the promoter region

Elongation & Histones

During elongation, histones ahead of the open complex are covalently modified by acetylation and evicted. Behind the open complex, histones are deacetylated and become tightly bound to the DNA.