Regulation of gene expression in eukaryotes

A set of fill-in-the-blank flashcards covering chromatin structure, histone modifications, chromatin states, DNA methylation, small RNA regulation, GAL system, splicing, and 3D genome organization.

__ is a complex of proteins (principally histones), RNA, and DNA that forms chromosomes within nuclei of eukaryotes.

Chromatin

Euchromatin is open, ATP-dependent, and relatively accessible to __.

enzymes

Heterochromatin is __ and inaccessible.

highly condensed

Repressive histone modifications include Lysine methylation at (H3K9, H3K27, H4K20); these are examples of __ modifications.

Lysine methylation

There are four major chromatin states: active euchromatin, inactive euchromatin, facultative heterochromatin, and __ heterochromatin.

constitutive

Changing chromatin state is a way of regulating gene expression – sometimes called __ control.

epigenetic

Histone tails can be chemically modified; these __ recruit transcription factors to nucleosomes.

modifications

Histone __ is usually associated with active transcription; methylation is variable.

acetylation

Parts of genome permanently in heterochromatin are gene poor with little transcription - constitutive __.

heterochromatin

Some heterochromatic regions can change to euchromatin: __ heterochromatin (e.g., Barr body/inactive X chromosome).

facultative

Changing chromatin state is a way of regulating gene expression – sometimes called __ control.

epigenetic

Gal4 recruits a __ modifier to the region when activated.

chromatin

The GAL system via Gal4 is a classical activator system, but it works by causing changes in __ structure.

chromatin

DNA methylation typically occurs on CG dinucleotides; presence of DNA methylation in the promoter usually correlates with __ expression.

repression

The enzyme that methylates DNA recognizes hemimethylated DNA and methylates the opposite C.

opposite

CG dinucleotides are methylated; DNA methylation is able to be __ following DNA replication.

inherited

Dicer complex cuts long double-stranded RNA into short (20-24 nucleotide) __.

dsRNA

RISC binds the small RNA, denatures it, and incorporates one strand; RISC complex finds complementary mRNA and __ it.

degrades

Small RNAs with perfect complementarity to their target mRNAs are called __; they act with RISC to cleave mRNA.

siRNAs

Small RNAs with partial complementarity to their target mRNA are called __; they act with RISC to inhibit translation.

miRNAs

Let-7 and miR-34 are small RNAs that inhibit expression of key pluripotency factors – they help keep differentiated cells from reverting back to __ cells.

stem

Small RNAs in research are powerful because their effects are __ (transient).

transient

Most eukaryotic genes have __ that require splicing by the spliceosome.

introns

Alternative splicing produces proteins with different __.

exons

BRCA1 breast cancer susceptibility gene in humans has huge number of alternative __ variants.

splice

In eukaryotes, transcription and translation are separated by the __; in bacteria they can occur simultaneously.

nucleus

Promoter is immediately upstream of gene; enhancers are more distant and can regulate expression via 3D interactions; chromatin needs unwinding from nucleosomes. These are called __ of transcription.

enhancers

Mediator protein complex interacts with transcription factors and __ to promote transcription.

RNA polymerase

Transcription factors bind to promoters and enhancers, usually helping RNA polymerase to bind the __.

promoter

Enhancers that repress transcription are called __.

silencers

Chromosomes organized into 3D territory loops are called __ (TADs).

topologically associated domains

Swapping Gal4 __ domain with DNA binding domains of different proteins allows transcriptional control of genes bound by the other proteins.

DNA binding

UASG stands for __.

Upstream Activating Sequence

In the absence of galactose, __ binds Gal4 and prevents activation.

GAL80

When galactose is present, it binds to __ and brings about a change so GAL80 binds GAL3 rather than GAL4.

Gal3

Gal4 can activate gene expression by binding to __ and recruiting the transcription machinery to initiate transcription.

Mediator

In the GAL system, transcriptional activation involves looping of DNA to bring all factors/sites into close proximity and stimulate transcription; this requires interaction with the __.

Mediator