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Pribnow box
the bacterial homolog of the TATA box that has a shorter consensus sequence
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CTD
- carboxyl terminal domain
- The CTD sequence is subject to reversible phosphorylation at Ser2 and Ser5 (possibly also Ser7 and Thr4)
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TATA box
- classical core element in eukaryotes
- best characterized element that can function by itself (i.e. in absence of all elements)
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DPE
Downstream promoter element (eukaryotes)
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MTE
Motif ten element (eukaryotes)
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BRE
- TFIIB recognition element
- classical core promoter element in eukaryotes
- recognized by TFIIB... (most core promoter genes are recognized by TFIID)
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DCE
Downstream Core element (eukaryots)
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CAAT box
- proximal promoter elements (eukaryotes)
- target of binding for various transcription factors (eg CBF and Sp1)
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GC box
- proximal promoter elements (eukaryotes)
- target of binding for various transcription factors (eg CBF and Sp1)
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LCRs
locus control regions
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MARs
matrix attachment regions
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GTFs
- general transcription factors
- Six classical GTFs: TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH
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Gal4
- one of the yeast TFs required for growth on galactose
- in non-inducing conditions, Gal4 is bound to the upstream activating sequences for galactose (UAS_gal) but is prevented from activated by Gal80
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Ubx
- Ultrabithorx
- a gene that, when inactivated by mutation, causes drosophila flies to produce an extra pair of wings
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HAT
- histone acetyltransferase
- acetylate histone proteins, weakening the association of DNA with histones and making the dDNA more accessible to transcription
- transcription is induced
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HDAC
- Histone deacetylases
- deacetylate histone proteins
- strengthens the association of DNA with histones and make DNA less accessible to transcription
- transcription repressed
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CDK
- cyclin dependent kinases
- regulate cell-cycle checkpoints and transcriptional events
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HTH
- Helix-turn-helix motif
- DNA binding domain: present in both prokaryotes and eukaryotes
- recognition helix on the C-terminal (major groove)
- bracing helix on the N-terminal
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RXR
- cis-retinoic acid receptor
- forms from several different heteromeres
- DNA-binding domains?
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bHLH
- Basic helix-loop-helix motif
- consists of a HLH region and a basic region
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HLH
- helix-loop-helix
- part of the basic helix-loop-helix (bHLH) motif
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MyoD
- protein required for muscle development
- an example of a bHLH protein
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IDRs
- Intrinsically disordered regions
- found in many TFs, and allow for weak mutivalent interaction with other TFs and co factors
- lead to formation of nuclear condensates
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qPCR
- quantitative PCR
- method for measuring DNA by PCR
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LLPS
Liquid-liquid phase seperation
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ROS
- reactive oxygen species
- examples: superoxide radicals like O2D, hydrogen peroxide H2O2 and hydroxyl radicals OHD
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Ada
- example of O6-alkylguanine-DNA alkyltransferase (AGT)
- When the Ada protein is methylated, it becomes a transcription factor that induces expression of its own gene!
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AGT
- O6-alkylguanine-DNA alkyltransferase
- Accepts alkyl group transfers, inactivates this protein and stabilizes the guanine aa in direct damage reversal
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DDB
- DNA-damage binding complexes
- constantly scan the genome and recognize helix distortions
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TLS
- Translesion synthesis
- a collection of DNA plolymerases that take over from DNA Pol ε and η during repair of a lesion
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PLA
- Proximity Ligation Assay
- helps overcome the difficulties that arise when attempting to visualize and study single proteins/ protein-protein interactions, post-tranlational modificaitons
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NHEJ
non homologous end joining
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DSBR
- double-strand break repair
- (double holliday junction model)
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SDSA
synthesis dependent strand annealing
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α subunit
- made of two domains: α-NTD and α-CTD, connected by a flexible linker arm
- interacts wit the UP element
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CAP
- catabolic activator protein
- (aka cAMP receptor protein, CRP)
- binds to the DNA sequence immediately upstream of the lac operon promoter at the CAP site
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CTD
carboxyl terminal domain
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subunit II0
- Rpb1 with a highly phosphorylated form of CTD
- aka (RNAPII0)
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subunit IIa
- non-phosphorylated CTD
- aka (RNAPIIA)
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PHD
- Plant HomeoDomain
- recognizes tri-methyl-lysines
- Histone tail interactors
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Tudor domain
- Histone tail interactor
- recognizes tri-methyl-lysines
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HAT
histone acetyltransferase
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PRMT
protein arginine methyltransferase
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HMTase
histone methyltransferase
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MBT
Malignant Brain Tumor
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NuRD
- Nucleosome Remodeling and Deacetylase (NuRD) complex
- The NuRD complex triggers gene repression through changes in histone modifications, most notably H3 lysine deacetylation and other chromatin remodeling activities such as histone variant deposition
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DNMT
DNA methyltransferase
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HP1
heterochromatin protein 1
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