Downstream promoter element

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Overview of the four core promoter elements B recognition element (BRE), TATA box, initiator motif (Inr), and downstream promoter element (DPE), showing their respective consensus sequences and their distance from the transcription start site. Core promoter elements.svg
Overview of the four core promoter elements B recognition element (BRE), TATA box , initiator motif (Inr), and downstream promoter element (DPE), showing their respective consensus sequences and their distance from the transcription start site.

In molecular biology, a downstream promoter element (DPE) is a core promoter element. Like all core promoters, the DPE plays an important role in the initiation of gene transcription by RNA polymerase II. The DPE was first described by T. W. Burke and James T. Kadonaga in Drosophila melanogaster at the University of California, San Diego in 1996. [2] It is also present in other species including humans, but not Saccharomyces cerevisiae . [3]

Contents

Together with the initiator motif (Inr), another core promoter element, the DPE is recognized by the transcription factor II D (TFIID) subunits TAF6 and TAF9. [2] [4] [5] It has been shown that DPE-dependent basal transcription depends highly on the Inr (and vice versa) and on correct spacing between the two elements. [2] [4] [6]

The DPE consensus sequence was originally thought to be RGWCGTG, [2] however more recent studies have suggested it to be the similar but more general sequence RGWYV(T). [lower-alpha 1] [1] [3] [7] It is located about 28–33 nucleotides downstream of the transcription start site. [3]

Occurrence

It has been shown that the DPE is about as widely used as the TATA box in D. melanogaster. [6] While a DPE was found in many promoters that do not contain a TATA box, there are also promoters that contain both a TATA box and a DPE. [6]

The promoters of nearly all Hox genes of D. melanogaster, with the exception of the evolutionarily most recent genes, Ubx and Abd-A , contain a DPE motif and lack a TATA box. [8] Drosophila promoters containing the DPE sequence include Abd-B , Antp P2 , bride of sevenless , brown , caudal , E74 , E75 , engrailed , Gsα , labial , nmMHC , ras2 , singed , stellate , and white . [2] In organisms other than D. melanogaster, the promoter of the human and mouse IRF1 gene has been found to contain a DPE consensus sequence at the appropriate distance from the transcription start site. This promoter, too, does not contain a TATA box.

DPE has also been reported to play role in primitive Eukaryote Entamoeba histolytica . [9]

Notes

  1. ↑ In nucleic acid notation for DNA, R (puRine) stands for A/G (adenine or guanine, which are both purines); W (Weak) stands for A/T (adenine or thymine, which both form only two hydrogen bonds); Y (pYrimidine) stands for C/T (cytosine or thymine, which are both pyrimidines); and V stands for A/C/G.

Related Research Articles

<span class="mw-page-title-main">Promoter (genetics)</span> Region of DNA encouraging transcription

In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can have a function in and of itself, such as tRNA or rRNA. Promoters are located near the transcription start sites of genes, upstream on the DNA . Promoters can be about 100–1000 base pairs long, the sequence of which is highly dependent on the gene and product of transcription, type or class of RNA polymerase recruited to the site, and species of organism.

In molecular biology, the TATA box is a sequence of DNA found in the core promoter region of genes in archaea and eukaryotes. The bacterial homolog of the TATA box is called the Pribnow box which has a shorter consensus sequence.

<span class="mw-page-title-main">Transcription preinitiation complex</span> Complex of proteins necessary for gene transcription in eukaryotes and archaea

The preinitiation complex is a complex of approximately 100 proteins that is necessary for the transcription of protein-coding genes in eukaryotes and archaea. The preinitiation complex positions RNA polymerase II at gene transcription start sites, denatures the DNA, and positions the DNA in the RNA polymerase II active site for transcription.

<span class="mw-page-title-main">General transcription factor</span> Class of protein transcription factors

General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA. GTFs, RNA polymerase, and the mediator constitute the basic transcriptional apparatus that first bind to the promoter, then start transcription. GTFs are also intimately involved in the process of gene regulation, and most are required for life.

<span class="mw-page-title-main">TATA-binding protein</span> Protein-coding gene in the species Homo sapiens

The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters.

Transcription factor II D (TFIID) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex. RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins. Before the start of transcription, the transcription Factor II D (TFIID) complex binds to the core promoter DNA of the gene through specific recognition of promoter sequence motifs, including the TATA box, Initiator, Downstream Promoter, Motif Ten, or Downstream Regulatory elements.

<span class="mw-page-title-main">Eukaryotic transcription</span> Transcription is heterocatalytic function of DNA

Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells. Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes comes in three variations, each translating a different type of gene. A eukaryotic cell has a nucleus that separates the processes of transcription and translation. Eukaryotic transcription occurs within the nucleus where DNA is packaged into nucleosomes and higher order chromatin structures. The complexity of the eukaryotic genome necessitates a great variety and complexity of gene expression control.

Transcription factor TFIIA is a nuclear protein involved in the RNA polymerase II-dependent transcription of DNA. TFIIA is one of several general (basal) transcription factors (GTFs) that are required for all transcription events that use RNA polymerase II. Other GTFs include TFIID, a complex composed of the TATA binding protein TBP and TBP-associated factors (TAFs), as well as the factors TFIIB, TFIIE, TFIIF, and TFIIH. Together, these factors are responsible for promoter recognition and the formation of a transcription preinitiation complex (PIC) capable of initiating RNA synthesis from a DNA template.

<span class="mw-page-title-main">Initiator element</span>

The initiator element (Inr), sometimes referred to as initiator motif, is a core promoter that is similar in function to the Pribnow box or the TATA box. The Inr is the simplest functional promoter that is able to direct transcription initiation without a functional TATA box. It has the consensus sequence YYANWYY in humans. Similarly to the TATA box, the Inr element facilitates the binding of transcription Factor II D (TFIID). The Inr works by enhancing binding affinity and strengthening the promoter.

<span class="mw-page-title-main">TAF1</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 1, also known as transcription initiation factor TFIID 250 kDa subunit (TAFII-250) or TBP-associated factor 250 kDa (p250), is a protein that in humans is encoded by the TAF1 gene.

<span class="mw-page-title-main">TAF9</span> Protein-coding gene in the species Homo sapiens

TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa, also known as TAF9, is a protein that in humans is encoded by the TAF9 gene.

<span class="mw-page-title-main">TAF4</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 4 is a protein that in humans is encoded by the TAF4 gene.

<span class="mw-page-title-main">TAF2</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 2 is a protein that in humans is encoded by the TAF2 gene.

<span class="mw-page-title-main">TAF10</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 10 is a protein that in humans is encoded by the TAF10 gene.

<span class="mw-page-title-main">TAF11</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 11 also known as TAFII28, is a protein that in humans is encoded by the TAF11 gene.

<span class="mw-page-title-main">DR1 (gene)</span> Protein-coding gene in the species Homo sapiens

Protein Dr1 is a protein that in humans is encoded by the DR1 gene.

<span class="mw-page-title-main">TAF8</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 8 is a protein that in humans is encoded by the TAF8 gene.

RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins.

<span class="mw-page-title-main">B recognition element</span>

The B recognition element (BRE) is a DNA sequence found in the promoter region of most genes in eukaryotes and Archaea. The BRE is a cis-regulatory element that is found immediately near TATA box, and consists of 7 nucleotides. There are two sets of BREs: one (BREu) found immediately upstream of the TATA box, with the consensus SSRCGCC; the other (BREd) found around 7 nucleotides downstream, with the consensus RTDKKKK.

<span class="mw-page-title-main">TBP-associated factor</span> Protein domains

The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.

References

  1. 1 2 Butler, Jennifer E F; Kadonaga, James T (15 October 2002). "The RNA polymerase II core promoter: a key component in the regulation of gene expression". Genes & Development. 16 (20): 2583–2592. doi: 10.1101/gad.1026202 . PMID   12381658.
  2. 1 2 3 4 5 Burke, T W; Kadonaga, J T (15 March 1996). "Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters". Genes & Development. 10 (6): 711–724. doi: 10.1101/gad.10.6.711 . PMID   8598298.
  3. 1 2 3 Juven-Gershon, Tamar; Kadonaga, James T. (March 2010). "Regulation of gene expression via the core promoter and the basal transcriptional machinery". Developmental Biology. 339 (2): 225–229. doi:10.1016/j.ydbio.2009.08.009. PMC   2830304 . PMID   19682982.
  4. 1 2 Burke, Thomas W.; Kadonaga, James T. (15 November 1997). "The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila". Genes & Development. 11 (22): 3020–3031. doi:10.1101/gad.11.22.3020. PMC   316699 . PMID   9367984.
  5. ↑ Yang, Chuhu; Bolotin, Eugene; Jiang, Tao; Sladek, Frances M.; Martinez, Ernest (March 2007). "Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters". Gene. 389 (1): 52–65. doi:10.1016/j.gene.2006.09.029. PMC   1955227 . PMID   17123746.
  6. 1 2 3 Kutach, Alan K; Kadonaga, James T (1 July 2000). "The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters". Molecular and Cellular Biology. 20 (13): 4754–4764. doi:10.1128/MCB.20.13.4754-4764.2000. PMC   85905 . PMID   10848601.
  7. ↑ Kadonaga, James T (September 2002). "The DPE, a core promoter element for transcription by RNA polymerase II". Experimental & Molecular Medicine. 34 (4): 259–264. doi: 10.1038/emm.2002.36 . PMID   12515390.
  8. ↑ Juven-Gershon, Tamar; Hsu, Jer-Yuan; Kadonaga, James T. (15 October 2008). "Caudal, a key developmental regulator, is a DPE-specific transcriptional factor". Genes & Development. 22 (20): 2823–2830. doi:10.1101/gad.1698108. PMC   2569877 . PMID   18923080.
  9. ↑ Naiyer, Sarah; Kaur, Devinder; Ahamad, Jamaluddin; Singh, Shashi Shekhar; Singh, Yatendra Pratap; Thakur, Vivek; Bhattacharya, Alok; Bhattacharya, Sudha (2019-03-12). "Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica". BMC Genomics. 20 (1): 206. doi: 10.1186/s12864-019-5570-z . PMC   6416950 . PMID   30866809.
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